####################################################### ## 2018-01-23T15:40:11+00:00 ## Building khmer ####################################################### ####################################################### ## 2018-01-23T15:40:11+00:00 ## System state ####################################################### WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Listing... adduser/unstable,now 3.116 all [installed,automatic] apt/unstable,now 1.6~alpha7 amd64 [installed,automatic] apt-file/unstable,now 3.1.5 all [installed,automatic] apt-utils/unstable,now 1.6~alpha7 amd64 [installed] at/unstable,now 3.1.20-3.1 amd64 [installed,automatic] autoconf/unstable,now 2.69-11 all [installed,automatic] automake/unstable,now 1:1.15.1-3 all [installed,automatic] autopoint/unstable,now 0.19.8.1-4 all [installed,automatic] autotools-dev/unstable,now 20171216.1 all [installed,automatic] base-files/unstable,now 10.1 amd64 [installed,automatic] base-passwd/unstable,now 3.5.44 amd64 [installed,automatic] bash/unstable,now 4.4-5 amd64 [installed] binutils/unstable,now 2.29.1-13 amd64 [installed,automatic] binutils-common/unstable,now 2.29.1-13 amd64 [installed,automatic] binutils-x86-64-linux-gnu/unstable,now 2.29.1-13 amd64 [installed,automatic] bsdmainutils/unstable,now 11.1.2 amd64 [installed,automatic] bsdutils/unstable,now 1:2.30.2-0.3 amd64 [installed,automatic] build-essential/unstable,now 12.4 amd64 [installed] bzip2/unstable,now 1.0.6-8.1 amd64 [installed,automatic] ca-certificates/unstable,now 20170717 all [installed,automatic] coreutils/unstable,now 8.28-1 amd64 [installed,automatic] cpp/unstable,now 4:7.2.0-1d1 amd64 [installed,automatic] cpp-7/unstable,now 7.2.0-19 amd64 [installed,automatic] cron/unstable,now 3.0pl1-128.1 amd64 [installed,automatic] curl/unstable,now 7.57.0-1 amd64 [installed,automatic] dash/unstable,now 0.5.8-2.5 amd64 [installed,automatic] dctrl-tools/unstable,now 2.24-2+b1 amd64 [installed,automatic] debconf/unstable,now 1.5.65 all [installed,automatic] debhelper/unstable,now 11.1.3 all [installed] debian-archive-keyring/unstable,now 2017.7 all [installed,automatic] debian-keyring/unstable,now 2017.11.24 all [installed,automatic] debianutils/unstable,now 4.8.4 amd64 [installed,automatic] devscripts/unstable,now 2.17.12 amd64 [installed,automatic] dh-autoreconf/unstable,now 15 all [installed] 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[installed,automatic] libssl1.0.2/unstable,now 1.0.2n-1 amd64 [installed,automatic] libssl1.1/unstable,now 1.1.0g-2 amd64 [installed,automatic] libstdc++-7-dev/unstable,now 7.2.0-19 amd64 [installed,automatic] libstdc++6/unstable,now 7.2.0-19 amd64 [installed,automatic] libstrictures-perl/unstable,now 2.000003-1 all [installed,automatic] libstring-copyright-perl/unstable,now 0.003005-1 all [installed,automatic] libstring-escape-perl/unstable,now 2010.002-1 all [installed,automatic] libsub-exporter-perl/unstable,now 0.987-1 all [installed,automatic] libsub-exporter-progressive-perl/unstable,now 0.001013-1 all [installed,automatic] libsub-identify-perl/unstable,now 0.14-1 amd64 [installed,automatic] libsub-install-perl/unstable,now 0.928-1 all [installed,automatic] libsub-name-perl/unstable,now 0.21-1+b2 amd64 [installed,automatic] libsub-quote-perl/unstable,now 2.004000-1 all [installed,automatic] libsys-hostname-long-perl/unstable,now 1.5-1 all [installed,automatic] libsystemd0/unstable,now 236-3+b1 amd64 [installed,automatic] libtask-weaken-perl/unstable,now 1.05-1 all [installed,automatic] libtasn1-6/unstable,now 4.13-2 amd64 [installed,automatic] libtcl8.6/unstable,now 8.6.8+dfsg-2 amd64 [installed,automatic] libtext-glob-perl/unstable,now 0.10-1 all [installed,automatic] libtext-levenshtein-perl/unstable,now 0.13-1 all [installed,automatic] libtimedate-perl/unstable,now 2.3000-2 all [installed,automatic] libtinfo5/unstable,now 6.0+20171125-1 amd64 [installed,automatic] libtk8.6/unstable,now 8.6.8-2 amd64 [installed,automatic] libtool/unstable,now 2.4.6-2 all [installed,automatic] libtry-tiny-perl/unstable,now 0.30-1 all [installed,automatic] libtsan0/unstable,now 7.2.0-19 amd64 [installed,automatic] libubsan0/unstable,now 7.2.0-19 amd64 [installed,automatic] libudev1/unstable,now 236-3+b1 amd64 [installed,automatic] libunicode-utf8-perl/unstable,now 0.60-1+b4 amd64 [installed,automatic] libunistring2/unstable,now 0.9.8-1 amd64 [installed,automatic] liburi-perl/unstable,now 1.73-1 all [installed,automatic] libuuid1/unstable,now 2.30.2-0.3 amd64 [installed,automatic] libvariable-magic-perl/unstable,now 0.62-1 amd64 [installed,automatic] libwrap0/unstable,now 7.6.q-27 amd64 [installed,automatic] libwww-perl/unstable,now 6.31-1 all [installed,automatic] libwww-robotrules-perl/unstable,now 6.01-1 all [installed,automatic] libx11-6/unstable,now 2:1.6.4-3 amd64 [installed,automatic] libx11-data/unstable,now 2:1.6.4-3 all [installed,automatic] libxau6/unstable,now 1:1.0.8-1+b2 amd64 [installed,automatic] libxcb1/unstable,now 1.12-1 amd64 [installed,automatic] libxdmcp6/unstable,now 1:1.1.2-3 amd64 [installed,automatic] libxext6/unstable,now 2:1.3.3-1+b2 amd64 [installed,automatic] libxft2/unstable,now 2.3.2-1+b2 amd64 [installed,automatic] libxml-libxml-perl/unstable,now 2.0128+dfsg-5 amd64 [installed,automatic] libxml-namespacesupport-perl/unstable,now 1.12-1 all [installed,automatic] libxml-parser-perl/unstable,now 2.44-2+b3 amd64 [installed,automatic] libxml-sax-base-perl/unstable,now 1.09-1 all [installed,automatic] libxml-sax-expat-perl/unstable,now 0.40-2 all [installed,automatic] libxml-sax-perl/unstable,now 0.99+dfsg-2 all [installed,automatic] libxml-simple-perl/unstable,now 2.24-1 all [installed,automatic] libxml2/unstable,now 2.9.4+dfsg1-6.1 amd64 [installed,automatic] libxmlrpc-lite-perl/unstable,now 0.717-1 all [installed,automatic] libxmuu1/unstable,now 2:1.1.2-2 amd64 [installed,automatic] libxrender1/unstable,now 1:0.9.10-1 amd64 [installed,automatic] libxss1/unstable,now 1:1.2.2-1+b2 amd64 [installed,automatic] libyaml-0-2/unstable,now 0.1.7-2 amd64 [installed,automatic] libyaml-libyaml-perl/unstable,now 0.69+repack-1 amd64 [installed,automatic] licensecheck/unstable,now 3.0.31-2 all [installed,automatic] lintian/unstable,now 2.5.71 all [installed,automatic] linux-libc-dev/unstable,now 4.14.13-1 amd64 [installed,automatic] login/unstable,now 1:4.5-1 amd64 [installed,automatic] lsb-base/unstable,now 9.20170808 all [installed,automatic] lsb-release/unstable,now 9.20170808 all [installed,automatic] m4/unstable,now 1.4.18-1 amd64 [installed,automatic] mailutils/unstable,now 1:3.4-1 amd64 [installed,automatic] mailutils-common/unstable,now 1:3.4-1 all [installed,automatic] make/unstable,now 4.1-9.1 amd64 [installed,automatic] man-db/unstable,now 2.7.6.1-4 amd64 [installed,automatic] mawk/unstable,now 1.3.3-17+b3 amd64 [installed,automatic] mime-support/unstable,now 3.60 all [installed,automatic] mount/unstable,now 2.30.2-0.3 amd64 [installed,automatic] multiarch-support/unstable,now 2.26-4 amd64 [installed,auto-removable] mysql-common/unstable,now 5.8+1.0.4 all [installed,automatic] ncurses-base/unstable,now 6.0+20171125-1 all [installed,automatic] ncurses-bin/unstable,now 6.0+20171125-1 amd64 [installed,automatic] netbase/unstable,now 5.4 all [installed,automatic] openssh-client/unstable,now 1:7.6p1-3 amd64 [installed,automatic] openssl/unstable,now 1.1.0g-2 amd64 [installed,automatic] passwd/unstable,now 1:4.5-1 amd64 [installed,automatic] patch/unstable,now 2.7.5-1+b2 amd64 [installed,automatic] patchutils/unstable,now 0.3.4-2 amd64 [installed,automatic] perl/unstable,now 5.26.1-4 amd64 [installed,automatic] perl-base/unstable,now 5.26.1-4 amd64 [installed,automatic] perl-modules-5.26/unstable,now 5.26.1-4 all [installed,automatic] perl-openssl-defaults/unstable,now 3 amd64 [installed,automatic] pinentry-curses/unstable,now 1.0.0-3 amd64 [installed,automatic] po-debconf/unstable,now 1.0.20 all [installed,automatic] psmisc/unstable,now 23.1-1 amd64 [installed,automatic] publicsuffix/unstable,now 20171228.1526-2 all [installed,automatic] python-apt-common/unstable,now 1.4.0~beta3 all [installed,automatic] python3/unstable,now 3.6.4-1 amd64 [installed,automatic] python3-apt/unstable,now 1.4.0~beta3+b1 amd64 [installed,automatic] python3-certifi/unstable,now 2017.11.5-1 all [installed,automatic] python3-chardet/unstable,now 3.0.4-1 all [installed,automatic] python3-debian/unstable,now 0.1.31 all [installed,automatic] python3-distutils/unstable,now 3.6.4-2 all [installed,automatic] python3-gpg/unstable,now 1.10.0-1 amd64 [installed,automatic] python3-idna/unstable,now 2.6-1 all [installed,automatic] python3-lib2to3/unstable,now 3.6.4-2 all [installed,automatic] python3-magic/unstable,now 1:5.32-1 all [installed,automatic] python3-minimal/unstable,now 3.6.4-1 amd64 [installed,automatic] python3-pkg-resources/unstable,now 38.2.4-2 all [installed,automatic] python3-requests/unstable,now 2.18.4-1 all [installed,automatic] python3-six/unstable,now 1.11.0-1 all [installed,automatic] python3-unidiff/unstable,now 0.5.4-1 all [installed,automatic] python3-urllib3/unstable,now 1.22-1 all [installed,automatic] python3-xdg/unstable,now 0.25-4 all [installed,automatic] python3.6/unstable,now 3.6.4-3 amd64 [installed,automatic] python3.6-minimal/unstable,now 3.6.4-3 amd64 [installed,automatic] rake/unstable,now 12.3.0-1 all [installed] readline-common/unstable,now 7.0-3 all [installed,automatic] ri/now 1:2.3.3+faux all [installed,local] ruby/now 1:2.3.3+faux amd64 [installed,local] ruby-all-dev/now 1:2.3.3+faux amd64 [installed,local] ruby-dev/now 1:2.3.3+faux amd64 [installed,local] ruby-did-you-mean/unstable,now 1.0.0-2 all [installed,automatic] ruby-full/now 1:2.3.3+faux all [installed,local] ruby-minitest/unstable,now 5.10.3-1 all [installed,automatic] ruby-net-telnet/unstable,now 0.1.1-2 all [installed,automatic] ruby-power-assert/unstable,now 0.3.0-1 all [installed,automatic] ruby-setup/unstable,now 3.4.1-9 all [installed,automatic] ruby-tcltk/now 1:2.3.3+faux all [installed,local] ruby-test-unit/unstable,now 3.2.5-1 all [installed,automatic] ruby2.3/unstable,now 2.3.6-2 amd64 [installed,automatic] ruby2.3-dev/unstable,now 2.3.6-2 amd64 [installed,automatic] ruby2.3-doc/unstable,now 2.3.6-2 all [installed,automatic] ruby2.3-tcltk/unstable,now 2.3.6-2 amd64 [installed,automatic] ruby2.5/unstable,now 2.5.0-4 amd64 [installed,automatic] ruby2.5-dev/unstable,now 2.5.0-4 amd64 [installed,automatic] ruby2.5-doc/unstable,now 2.5.0-4 all [installed,automatic] rubygems-integration/unstable,now 1.11 all [installed,automatic] sed/unstable,now 4.4-1 amd64 [installed,automatic] sensible-utils/unstable,now 0.0.11 all [installed,automatic] shared-mime-info/unstable,now 1.9-2 amd64 [installed,automatic] strace/unstable,now 4.19-1 amd64 [installed,automatic] sysvinit-utils/unstable,now 2.88dsf-59.10 amd64 [installed,automatic] t1utils/unstable,now 1.41-2 amd64 [installed,automatic] tar/unstable,now 1.29b-2 amd64 [installed,automatic] tzdata/unstable,now 2018b-1 all [installed,automatic] ucf/unstable,now 3.0036 all [installed,automatic] unzip/unstable,now 6.0-21 amd64 [installed,automatic] util-linux/unstable,now 2.30.2-0.3 amd64 [installed,automatic] wdiff/unstable,now 1.2.2-2 amd64 [installed,automatic] x11-common/unstable,now 1:7.7+19 all [installed,automatic] xauth/unstable,now 1:1.0.10-1 amd64 [installed,automatic] xdg-user-dirs/unstable,now 0.16-1 amd64 [installed,automatic] xz-utils/unstable,now 5.2.2-1.3 amd64 [installed,automatic] zip/unstable,now 3.0-11+b1 amd64 [installed,automatic] zlib1g/unstable,now 1:1.2.8.dfsg-5 amd64 [installed,automatic] ####################################################### ## 2018-01-23T15:40:12+00:00 ## Download source ####################################################### Reading package lists... NOTICE: 'khmer' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/khmer.git Please use: git clone https://anonscm.debian.org/git/debian-med/khmer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 18.1 MB of source archives. Get:1 http://deb.debian.org/debian sid/main khmer 2.1.2+dfsg-2 (dsc) [2897 B] Get:2 http://deb.debian.org/debian sid/main khmer 2.1.2+dfsg-2 (tar) [18.1 MB] Get:3 http://deb.debian.org/debian sid/main khmer 2.1.2+dfsg-2 (diff) [13.5 kB] dpkg-source: info: extracting khmer in khmer-2.1.2+dfsg dpkg-source: info: unpacking khmer_2.1.2+dfsg.orig.tar.gz dpkg-source: info: unpacking khmer_2.1.2+dfsg-2.debian.tar.xz dpkg-source: info: applying update-manifest dpkg-source: info: applying setup-py-py3 dpkg-source: info: applying local-libs dpkg-source: info: applying older-setuptools dpkg-source: info: applying disable_google_analytics dpkg-source: info: applying get_version dpkg-source: info: applying install-prefix dpkg-source: info: applying cpython-bug-empty-exceptions dpkg-source: info: applying amend-skip dpkg-source: info: applying setup.py-py3 dpkg-source: info: applying python3 Fetched 18.1 MB in 2s (7545 kB/s) W: Download is performed unsandboxed as root as file 'khmer_2.1.2+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) ####################################################### ## 2018-01-23T15:40:17+00:00 ## Build dependencies ####################################################### Note, using directory '.' to get the build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: multiarch-support Use 'apt autoremove' to remove it. The following NEW packages will be installed: asciidoctor cython3 dh-exec docutils-common fonts-liberation libbz2-dev libexpat1-dev libjs-bootstrap libjs-sphinxdoc libjs-underscore libpython3-all-dev libpython3-dev libpython3.6 libpython3.6-dev python-babel-localedata python3-alabaster python3-all python3-all-dev python3-babel python3-bz2file python3-dev python3-docutils python3-guzzle-sphinx-theme python3-imagesize python3-jinja2 python3-markupsafe python3-py python3-pygments python3-pytest python3-pytest-runner python3-roman python3-screed python3-setuptools python3-sphinx python3-sphinxcontrib.autoprogram python3-tz python3.6-dev sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 16.0 MB of archives. After this operation, 73.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.29 [14.8 kB] Get:2 http://deb.debian.org/debian sid/main amd64 asciidoctor all 1.5.5-1 [183 kB] Get:3 http://deb.debian.org/debian sid/main amd64 cython3 amd64 0.26.1-0.4 [1955 kB] Get:4 http://deb.debian.org/debian sid/main amd64 dh-exec amd64 0.23+b1 [26.7 kB] Get:5 http://deb.debian.org/debian sid/main amd64 xml-core all 0.18 [23.4 kB] Get:6 http://deb.debian.org/debian sid/main amd64 docutils-common all 0.14+dfsg-2 [204 kB] Get:7 http://deb.debian.org/debian sid/main amd64 fonts-liberation all 1:1.07.4-5 [827 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libbz2-dev amd64 1.0.6-8.1 [29.4 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libexpat1-dev amd64 2.2.5-3 [140 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap all 3.3.7+dfsg-2 [274 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libjs-underscore all 1.8.3~dfsg-1 [63.8 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 1.6.6-1 [85.0 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libpython3.6 amd64 3.6.4-3 [1446 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3.6-dev amd64 3.6.4-3 [2484 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libpython3-dev amd64 3.6.4-1 [19.4 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpython3-all-dev amd64 3.6.4-1 [1044 B] Get:17 http://deb.debian.org/debian sid/main amd64 python-babel-localedata all 2.4.0+dfsg.1-2 [3415 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3-alabaster all 0.7.8-1 [18.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 python3-all amd64 3.6.4-1 [1020 B] Get:20 http://deb.debian.org/debian sid/main amd64 python3.6-dev amd64 3.6.4-3 [519 kB] Get:21 http://deb.debian.org/debian sid/main amd64 python3-dev amd64 3.6.4-1 [1228 B] Get:22 http://deb.debian.org/debian sid/main amd64 python3-all-dev amd64 3.6.4-1 [1044 B] Get:23 http://deb.debian.org/debian sid/main amd64 python3-tz all 2017.2-2 [27.3 kB] Get:24 http://deb.debian.org/debian sid/main amd64 python3-babel all 2.4.0+dfsg.1-2 [83.7 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3-bz2file all 0.98-1 [7714 B] Get:26 http://deb.debian.org/debian sid/main amd64 python3-roman all 2.0.0-3 [8768 B] Get:27 http://deb.debian.org/debian sid/main amd64 python3-docutils all 0.14+dfsg-2 [377 kB] Get:28 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.2.0+dfsg-1 [588 kB] Get:29 http://deb.debian.org/debian sid/main amd64 python3-markupsafe amd64 1.0-1+b1 [14.5 kB] Get:30 http://deb.debian.org/debian sid/main amd64 python3-jinja2 all 2.10-1 [106 kB] Get:31 http://deb.debian.org/debian sid/main amd64 python3-imagesize all 0.7.1-1 [3886 B] Get:32 http://deb.debian.org/debian sid/main amd64 sphinx-common all 1.6.6-1 [419 kB] Get:33 http://deb.debian.org/debian sid/main amd64 python3-sphinx all 1.6.6-1 [458 kB] Get:34 http://deb.debian.org/debian sid/main amd64 python3-guzzle-sphinx-theme all 0.7.11-2 [1345 kB] Get:35 http://deb.debian.org/debian sid/main amd64 python3-py all 1.4.34-3 [83.6 kB] Get:36 http://deb.debian.org/debian sid/main amd64 python3-pytest all 3.2.1-2 [200 kB] Get:37 http://deb.debian.org/debian sid/main amd64 python3-pytest-runner all 2.11.1-1 [8218 B] Get:38 http://deb.debian.org/debian sid/main amd64 python3-screed all 1.0-2 [71.8 kB] Get:39 http://deb.debian.org/debian sid/main amd64 python3-setuptools all 38.2.4-2 [229 kB] Get:40 http://deb.debian.org/debian sid/main amd64 python3-sphinxcontrib.autoprogram all 0.1.2-1 [6896 B] Get:41 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 16.0 MB in 3s (6205 kB/s) Selecting previously unselected package sgml-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 57695 files and directories currently installed.) Preparing to unpack .../00-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../01-asciidoctor_1.5.5-1_all.deb ... Unpacking asciidoctor (1.5.5-1) ... Selecting previously unselected package cython3. Preparing to unpack .../02-cython3_0.26.1-0.4_amd64.deb ... Unpacking cython3 (0.26.1-0.4) ... Selecting previously unselected package dh-exec. Preparing to unpack .../03-dh-exec_0.23+b1_amd64.deb ... Unpacking dh-exec (0.23+b1) ... Selecting previously unselected package xml-core. Preparing to unpack .../04-xml-core_0.18_all.deb ... Unpacking xml-core (0.18) ... Selecting previously unselected package docutils-common. Preparing to unpack .../05-docutils-common_0.14+dfsg-2_all.deb ... Unpacking docutils-common (0.14+dfsg-2) ... Selecting previously unselected package fonts-liberation. Preparing to unpack .../06-fonts-liberation_1%3a1.07.4-5_all.deb ... Unpacking fonts-liberation (1:1.07.4-5) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../07-libbz2-dev_1.0.6-8.1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.6-8.1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../08-libexpat1-dev_2.2.5-3_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.2.5-3) ... Selecting previously unselected package libjs-bootstrap. Preparing to unpack .../09-libjs-bootstrap_3.3.7+dfsg-2_all.deb ... Unpacking libjs-bootstrap (3.3.7+dfsg-2) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../10-libjs-underscore_1.8.3~dfsg-1_all.deb ... Unpacking libjs-underscore (1.8.3~dfsg-1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../11-libjs-sphinxdoc_1.6.6-1_all.deb ... Unpacking libjs-sphinxdoc (1.6.6-1) ... Selecting previously unselected package libpython3.6:amd64. Preparing to unpack .../12-libpython3.6_3.6.4-3_amd64.deb ... Unpacking libpython3.6:amd64 (3.6.4-3) ... Selecting previously unselected package libpython3.6-dev:amd64. Preparing to unpack .../13-libpython3.6-dev_3.6.4-3_amd64.deb ... Unpacking libpython3.6-dev:amd64 (3.6.4-3) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../14-libpython3-dev_3.6.4-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.6.4-1) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../15-libpython3-all-dev_3.6.4-1_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.6.4-1) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../16-python-babel-localedata_2.4.0+dfsg.1-2_all.deb ... Unpacking python-babel-localedata (2.4.0+dfsg.1-2) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../17-python3-alabaster_0.7.8-1_all.deb ... Unpacking python3-alabaster (0.7.8-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../18-python3-all_3.6.4-1_amd64.deb ... Unpacking python3-all (3.6.4-1) ... Selecting previously unselected package python3.6-dev. Preparing to unpack .../19-python3.6-dev_3.6.4-3_amd64.deb ... Unpacking python3.6-dev (3.6.4-3) ... Selecting previously unselected package python3-dev. Preparing to unpack .../20-python3-dev_3.6.4-1_amd64.deb ... Unpacking python3-dev (3.6.4-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../21-python3-all-dev_3.6.4-1_amd64.deb ... Unpacking python3-all-dev (3.6.4-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../22-python3-tz_2017.2-2_all.deb ... Unpacking python3-tz (2017.2-2) ... Selecting previously unselected package python3-babel. Preparing to unpack .../23-python3-babel_2.4.0+dfsg.1-2_all.deb ... Unpacking python3-babel (2.4.0+dfsg.1-2) ... Selecting previously unselected package python3-bz2file. Preparing to unpack .../24-python3-bz2file_0.98-1_all.deb ... Unpacking python3-bz2file (0.98-1) ... Selecting previously unselected package python3-roman. Preparing to unpack .../25-python3-roman_2.0.0-3_all.deb ... Unpacking python3-roman (2.0.0-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../26-python3-docutils_0.14+dfsg-2_all.deb ... Unpacking python3-docutils (0.14+dfsg-2) ... 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Unpacking python3-setuptools (38.2.4-2) ... Selecting previously unselected package python3-sphinxcontrib.autoprogram. Preparing to unpack .../39-python3-sphinxcontrib.autoprogram_0.1.2-1_all.deb ... Unpacking python3-sphinxcontrib.autoprogram (0.1.2-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../40-zlib1g-dev_1%3a1.2.8.dfsg-5_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up python3-roman (2.0.0-3) ... Setting up libbz2-dev:amd64 (1.0.6-8.1) ... Setting up python3-imagesize (0.7.1-1) ... Setting up libjs-underscore (1.8.3~dfsg-1) ... Setting up python3-py (1.4.34-3) ... Setting up asciidoctor (1.5.5-1) ... Setting up python3-alabaster (0.7.8-1) ... Setting up python3-pytest (3.2.1-2) ... Setting up libjs-sphinxdoc (1.6.6-1) ... Setting up sgml-base (1.29) ... Setting up fonts-liberation (1:1.07.4-5) ... Setting up python3-markupsafe (1.0-1+b1) ... Processing triggers for libc-bin (2.26-4) ... Setting up dh-exec (0.23+b1) ... Setting up python3-all (3.6.4-1) ... Setting up python3-jinja2 (2.10-1) ... Setting up python-babel-localedata (2.4.0+dfsg.1-2) ... Setting up sphinx-common (1.6.6-1) ... Setting up libexpat1-dev:amd64 (2.2.5-3) ... Processing triggers for man-db (2.7.6.1-4) ... Processing triggers for shared-mime-info (1.9-2) ... Setting up cython3 (0.26.1-0.4) ... Setting up libjs-bootstrap (3.3.7+dfsg-2) ... Setting up xml-core (0.18) ... Setting up python3-setuptools (38.2.4-2) ... Setting up python3-bz2file (0.98-1) ... Setting up python3-tz (2017.2-2) ... Setting up python3-pytest-runner (2.11.1-1) ... Setting up libpython3.6:amd64 (3.6.4-3) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up python3-screed (1.0-2) ... Setting up python3-pygments (2.2.0+dfsg-1) ... Setting up libpython3.6-dev:amd64 (3.6.4-3) ... Setting up python3-babel (2.4.0+dfsg.1-2) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3.6-dev (3.6.4-3) ... Setting up libpython3-dev:amd64 (3.6.4-1) ... Setting up python3-dev (3.6.4-1) ... Setting up libpython3-all-dev:amd64 (3.6.4-1) ... Setting up python3-all-dev (3.6.4-1) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-2) ... Processing triggers for sgml-base (1.29) ... Setting up python3-docutils (0.14+dfsg-2) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (1.6.6-1) ... Setting up python3-guzzle-sphinx-theme (0.7.11-2) ... Setting up python3-sphinxcontrib.autoprogram (0.1.2-1) ... Processing triggers for libc-bin (2.26-4) ... ####################################################### ## 2018-01-23T15:42:06+00:00 ## Build ####################################################### dpkg-buildpackage: info: source package khmer dpkg-buildpackage: info: source version 2.1.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-buildpackage: info: host architecture amd64 dpkg-source --before-build khmer-2.1.2+dfsg debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/khmer-2.1.2+dfsg' dh_auto_clean || /bin/true pybuild --clean --test-pytest -i python{version} -p 3.6 I: pybuild base:184: python3.6 setup.py clean running clean removing '/build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd src/oxli && /usr/bin/make clean make[2]: Entering directory '/build/khmer-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/khmer-2.1.2+dfsg/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/build/khmer-2.1.2+dfsg' dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/khmer-common.substvars debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars debian/files rm -fr -- debian/khmer-common/ debian/tmp/ debian/khmer/ debian/liboxli1/ debian/liboxli-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure --test-pytest -i python{version} -p 3.6 I: pybuild base:184: python3.6 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/khmer-2.1.2+dfsg' dh_auto_build pybuild --build --test-pytest -i python{version} -p 3.6 I: pybuild base:184: /usr/bin/python3 setup.py build running build running build_py creating /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/_version.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/kfile.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/khmer_args.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/khmer_logger.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/thread_utils.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/trimming.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer copying khmer/utils.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer creating /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/graph_features.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_banding.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_countgraph.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_counting_single.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_counttable.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_cython_assembly.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_cython_parsing.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_filter_abund.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_functions.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_graph.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_hashset.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_hll.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_labelhash.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_lump.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_nibblestorage.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_nodegraph.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_oxli_functions.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_read_aligner.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_read_handling.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_script_arguments.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_script_output.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_scripts.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_sequence_validation.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_streaming_io.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_subset_graph.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_tabletype.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_version.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/test_read_parsers.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests creating /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli copying oxli/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli copying oxli/build_graph.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli copying oxli/functions.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli copying oxli/partition.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli creating /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli running egg_info creating khmer.egg-info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt writing manifest file 'khmer.egg-info/SOURCES.txt' reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.cpp' under directory 'khmer/_oxli' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests creating /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli UPDATING /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_version.py set /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_version.py to '2.1.2' running build_ext building 'khmer._khmer' extension creating build creating build/temp.linux-amd64-3.6 creating build/temp.linux-amd64-3.6/src creating build/temp.linux-amd64-3.6/src/khmer creating build/temp.linux-amd64-3.6/src/oxli creating build/temp.linux-amd64-3.6/third-party creating build/temp.linux-amd64-3.6/third-party/smhasher x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_counttable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashset.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_khmer.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_utils.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/read_parsers.cc -o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from third-party/seqan/core/include/seqan/basic.h:62:0, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr instance; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > _gzStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > _bz2Stream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _mmapString; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr _plainStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _gzReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _bz2Reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _istreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _ifstreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (this != &other) ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ _horizontalScore = other._horizontalScore; ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (length(seqH) < length(seqV)) ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if ((actualCol == 0) || (actualRow == 0)) ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107:0, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr _writer; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107:0, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr _reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61:0, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (alignQualityStoreLengthPre == 0u) ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ sortAlignedReads(store.alignedReadStore, SortBeginPos()); ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/kmer_hash.cc -o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hashtable.cc -o build/temp.linux-amd64-3.6/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hashgraph.cc -o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/labelhash.cc -o build/temp.linux-amd64-3.6/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/subset.cc -o build/temp.linux-amd64-3.6/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] const unsigned int ksize = _ht->ksize(); ^~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/read_aligner.cc -o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hllcounter.cc -o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/traversal.cc -o build/temp.linux-amd64-3.6/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from src/oxli/traversal.cc:39:0: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:31: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] KmerFilterList filters; ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39:0: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:31: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] KmerFilterList filters; ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/kmer_filters.cc -o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/assembler.cc -o build/temp.linux-amd64-3.6/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] WordLength _ksize; ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] LinearAssembler::LinearAssembler(const Hashgraph * ht) : ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:18: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete this->linear_asm; ^~~~~~~~~~ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] WordLength _ksize; ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] Traverser traverser; ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] Traverser traverser; ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] LinearAssembler linear_asm; ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/alphabets.cc -o build/temp.linux-amd64-3.6/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/storage.cc -o build/temp.linux-amd64-3.6/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o build/temp.linux-amd64-3.6/src/oxli/hashtable.o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o build/temp.linux-amd64-3.6/src/oxli/labelhash.o build/temp.linux-amd64-3.6/src/oxli/subset.o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o build/temp.linux-amd64-3.6/src/oxli/traversal.o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o build/temp.linux-amd64-3.6/src/oxli/assembler.o build/temp.linux-amd64-3.6/src/oxli/alphabets.o build/temp.linux-amd64-3.6/src/oxli/storage.o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_khmer.cpython-36m-x86_64-linux-gnu.so -fopenmp cythoning khmer/_oxli/assembly.pyx to khmer/_oxli/assembly.cpp building 'khmer._oxli.assembly' extension creating build/temp.linux-amd64-3.6/khmer creating build/temp.linux-amd64-3.6/khmer/_oxli x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/assembly.cpp -o build/temp.linux-amd64-3.6/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/assembly.cpp:514: include/khmer/_cpy_utils.hh:17:0: warning: "PyInt_Check" redefined #define PyInt_Check(arg) PyLong_Check(arg) khmer/_oxli/assembly.cpp:300:0: note: this is the location of the previous definition #define PyInt_Check(op) PyLong_Check(op) In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/assembly.cpp:514: include/khmer/_cpy_utils.hh:18:0: warning: "PyInt_AsLong" redefined #define PyInt_AsLong(arg) PyLong_AsLong(arg) khmer/_oxli/assembly.cpp:307:0: note: this is the location of the previous definition #define PyInt_AsLong PyLong_AsLong In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/assembly.cpp:514: include/khmer/_cpy_utils.hh:19:0: warning: "PyInt_FromLong" redefined #define PyInt_FromLong(arg) PyLong_FromLong(arg) khmer/_oxli/assembly.cpp:304:0: note: this is the location of the previous definition #define PyInt_FromLong PyLong_FromLong x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.6/khmer/_oxli/assembly.o build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o build/temp.linux-amd64-3.6/src/oxli/hashtable.o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o build/temp.linux-amd64-3.6/src/oxli/labelhash.o build/temp.linux-amd64-3.6/src/oxli/subset.o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o build/temp.linux-amd64-3.6/src/oxli/traversal.o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o build/temp.linux-amd64-3.6/src/oxli/assembler.o build/temp.linux-amd64-3.6/src/oxli/alphabets.o build/temp.linux-amd64-3.6/src/oxli/storage.o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/assembly.cpython-36m-x86_64-linux-gnu.so -fopenmp cythoning khmer/_oxli/graphs.pyx to khmer/_oxli/graphs.cpp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/graphs.cpp -o build/temp.linux-amd64-3.6/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/graphs.cpp:514: include/khmer/_cpy_utils.hh:17:0: warning: "PyInt_Check" redefined #define PyInt_Check(arg) PyLong_Check(arg) khmer/_oxli/graphs.cpp:300:0: note: this is the location of the previous definition #define PyInt_Check(op) PyLong_Check(op) In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/graphs.cpp:514: include/khmer/_cpy_utils.hh:18:0: warning: "PyInt_AsLong" redefined #define PyInt_AsLong(arg) PyLong_AsLong(arg) khmer/_oxli/graphs.cpp:307:0: note: this is the location of the previous definition #define PyInt_AsLong PyLong_AsLong In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/graphs.cpp:514: include/khmer/_cpy_utils.hh:19:0: warning: "PyInt_FromLong" redefined #define PyInt_FromLong(arg) PyLong_FromLong(arg) khmer/_oxli/graphs.cpp:304:0: note: this is the location of the previous definition #define PyInt_FromLong PyLong_FromLong x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.6/khmer/_oxli/graphs.o build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o build/temp.linux-amd64-3.6/src/oxli/hashtable.o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o build/temp.linux-amd64-3.6/src/oxli/labelhash.o build/temp.linux-amd64-3.6/src/oxli/subset.o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o build/temp.linux-amd64-3.6/src/oxli/traversal.o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o build/temp.linux-amd64-3.6/src/oxli/assembler.o build/temp.linux-amd64-3.6/src/oxli/alphabets.o build/temp.linux-amd64-3.6/src/oxli/storage.o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/graphs.cpython-36m-x86_64-linux-gnu.so -fopenmp cythoning khmer/_oxli/hashing.pyx to khmer/_oxli/hashing.cpp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/hashing.cpp -o build/temp.linux-amd64-3.6/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.6/khmer/_oxli/hashing.o build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o build/temp.linux-amd64-3.6/src/oxli/hashtable.o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o build/temp.linux-amd64-3.6/src/oxli/labelhash.o build/temp.linux-amd64-3.6/src/oxli/subset.o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o build/temp.linux-amd64-3.6/src/oxli/traversal.o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o build/temp.linux-amd64-3.6/src/oxli/assembler.o build/temp.linux-amd64-3.6/src/oxli/alphabets.o build/temp.linux-amd64-3.6/src/oxli/storage.o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/hashing.cpython-36m-x86_64-linux-gnu.so -fopenmp cythoning khmer/_oxli/parsing.pyx to khmer/_oxli/parsing.cpp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/parsing.cpp -o build/temp.linux-amd64-3.6/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::__cxx11::string&, std::__cxx11::string&, bool)’: khmer/_oxli/parsing.cpp:5348:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.6/khmer/_oxli/parsing.o build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o build/temp.linux-amd64-3.6/src/oxli/hashtable.o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o build/temp.linux-amd64-3.6/src/oxli/labelhash.o build/temp.linux-amd64-3.6/src/oxli/subset.o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o build/temp.linux-amd64-3.6/src/oxli/traversal.o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o build/temp.linux-amd64-3.6/src/oxli/assembler.o build/temp.linux-amd64-3.6/src/oxli/alphabets.o build/temp.linux-amd64-3.6/src/oxli/storage.o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/parsing.cpython-36m-x86_64-linux-gnu.so -fopenmp cythoning khmer/_oxli/utils.pyx to khmer/_oxli/utils.cpp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/utils.cpp -o build/temp.linux-amd64-3.6/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.6/khmer/_oxli/utils.o build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o build/temp.linux-amd64-3.6/src/oxli/hashtable.o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o build/temp.linux-amd64-3.6/src/oxli/labelhash.o build/temp.linux-amd64-3.6/src/oxli/subset.o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o build/temp.linux-amd64-3.6/src/oxli/traversal.o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o build/temp.linux-amd64-3.6/src/oxli/assembler.o build/temp.linux-amd64-3.6/src/oxli/alphabets.o build/temp.linux-amd64-3.6/src/oxli/storage.o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/utils.cpython-36m-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.6 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.6 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.6 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.6 copying and adjusting scripts/count-median.py -> build/scripts-3.6 copying and adjusting scripts/do-partition.py -> build/scripts-3.6 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.6 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.6 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.6 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.6 copying and adjusting scripts/filter-abund.py -> build/scripts-3.6 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.6 copying and adjusting scripts/find-knots.py -> build/scripts-3.6 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.6 copying and adjusting scripts/load-graph.py -> build/scripts-3.6 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.6 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.6 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.6 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.6 copying and adjusting scripts/partition-graph.py -> build/scripts-3.6 copying and adjusting scripts/readstats.py -> build/scripts-3.6 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.6 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.6 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.6 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.6 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.6 changing mode of build/scripts-3.6/abundance-dist-single.py from 644 to 755 changing mode of build/scripts-3.6/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.6/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.6/count-median.py from 644 to 755 changing mode of build/scripts-3.6/do-partition.py from 644 to 755 changing mode of build/scripts-3.6/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.6/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.6/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.6/filter-abund-single.py from 644 to 755 changing mode of build/scripts-3.6/filter-abund.py from 644 to 755 changing mode of build/scripts-3.6/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.6/find-knots.py from 644 to 755 changing mode of build/scripts-3.6/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.6/load-graph.py from 644 to 755 changing mode of build/scripts-3.6/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.6/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.6/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.6/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.6/partition-graph.py from 644 to 755 changing mode of build/scripts-3.6/readstats.py from 644 to 755 changing mode of build/scripts-3.6/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.6/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.6/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.6/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.6/extract-paired-reads.py from 644 to 755 warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. ln -sf "`pwd`"/.pybuild/pythonX.Y_*/build/khmer/*.so khmer && \ ./setup.py develop --user && ./setup.py build_sphinx running develop running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext building 'khmer._khmer' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/src creating build/temp.linux-x86_64-3.6/src/khmer creating build/temp.linux-x86_64-3.6/src/oxli creating build/temp.linux-x86_64-3.6/third-party creating build/temp.linux-x86_64-3.6/third-party/smhasher x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.6/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.6/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from third-party/seqan/core/include/seqan/basic.h:62:0, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr instance; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > _gzStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > _bz2Stream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _mmapString; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr _plainStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _gzReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _bz2Reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _istreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _ifstreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function 'seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)': third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this != &other) ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' _horizontalScore = other._horizontalScore; ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)': third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (length(seqH) < length(seqV)) ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)': third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if ((actualCol == 0) || (actualRow == 0)) ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107:0, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr _writer; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107:0, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr _reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61:0, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)': third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (alignQualityStoreLengthPre == 0u) ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' sortAlignedReads(store.alignedReadStore, SortBeginPos()); ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.6/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.6/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.6/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.6/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.6/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ src/oxli/subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)': src/oxli/subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] const unsigned int ksize = _ht->ksize(); ^~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.6/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.6/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.6/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from src/oxli/traversal.cc:39:0: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] KmerFilterList filters; ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39:0: src/oxli/traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': src/oxli/traversal.cc:203:31: required from here include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] KmerFilterList filters; ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.6/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.6/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] WordLength _ksize; ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] LinearAssembler::LinearAssembler(const Hashgraph * ht) : ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': src/oxli/assembler.cc:189:18: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete this->linear_asm; ^~~~~~~~~~ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] WordLength _ksize; ^~~~~~ include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] Traverser traverser; ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] Traverser traverser; ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] LinearAssembler linear_asm; ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.6/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.6/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.6/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/khmer x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.6/src/oxli/read_parsers.o build/temp.linux-x86_64-3.6/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.6/src/oxli/hashtable.o build/temp.linux-x86_64-3.6/src/oxli/hashgraph.o build/temp.linux-x86_64-3.6/src/oxli/labelhash.o build/temp.linux-x86_64-3.6/src/oxli/subset.o build/temp.linux-x86_64-3.6/src/oxli/read_aligner.o build/temp.linux-x86_64-3.6/src/oxli/hllcounter.o build/temp.linux-x86_64-3.6/src/oxli/traversal.o build/temp.linux-x86_64-3.6/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.6/src/oxli/assembler.o build/temp.linux-x86_64-3.6/src/oxli/alphabets.o build/temp.linux-x86_64-3.6/src/oxli/storage.o build/temp.linux-x86_64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.6/khmer/_khmer.cpython-36m-x86_64-linux-gnu.so -fopenmp skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) building 'khmer._oxli.assembly' extension creating build/temp.linux-x86_64-3.6/khmer creating build/temp.linux-x86_64-3.6/khmer/_oxli x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-3.6/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/assembly.cpp:514: include/khmer/_cpy_utils.hh:17:0: warning: "PyInt_Check" redefined #define PyInt_Check(arg) PyLong_Check(arg) khmer/_oxli/assembly.cpp:300:0: note: this is the location of the previous definition #define PyInt_Check(op) PyLong_Check(op) In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/assembly.cpp:514: include/khmer/_cpy_utils.hh:18:0: warning: "PyInt_AsLong" redefined #define PyInt_AsLong(arg) PyLong_AsLong(arg) khmer/_oxli/assembly.cpp:307:0: note: this is the location of the previous definition #define PyInt_AsLong PyLong_AsLong In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/assembly.cpp:514: include/khmer/_cpy_utils.hh:19:0: warning: "PyInt_FromLong" redefined #define PyInt_FromLong(arg) PyLong_FromLong(arg) khmer/_oxli/assembly.cpp:304:0: note: this is the location of the previous definition #define PyInt_FromLong PyLong_FromLong creating build/lib.linux-x86_64-3.6/khmer/_oxli x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.6/src/oxli/read_parsers.o build/temp.linux-x86_64-3.6/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.6/src/oxli/hashtable.o build/temp.linux-x86_64-3.6/src/oxli/hashgraph.o build/temp.linux-x86_64-3.6/src/oxli/labelhash.o build/temp.linux-x86_64-3.6/src/oxli/subset.o build/temp.linux-x86_64-3.6/src/oxli/read_aligner.o build/temp.linux-x86_64-3.6/src/oxli/hllcounter.o build/temp.linux-x86_64-3.6/src/oxli/traversal.o build/temp.linux-x86_64-3.6/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.6/src/oxli/assembler.o build/temp.linux-x86_64-3.6/src/oxli/alphabets.o build/temp.linux-x86_64-3.6/src/oxli/storage.o build/temp.linux-x86_64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.6/khmer/_oxli/assembly.cpython-36m-x86_64-linux-gnu.so -fopenmp skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-3.6/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/graphs.cpp:514: include/khmer/_cpy_utils.hh:17:0: warning: "PyInt_Check" redefined #define PyInt_Check(arg) PyLong_Check(arg) khmer/_oxli/graphs.cpp:300:0: note: this is the location of the previous definition #define PyInt_Check(op) PyLong_Check(op) In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/graphs.cpp:514: include/khmer/_cpy_utils.hh:18:0: warning: "PyInt_AsLong" redefined #define PyInt_AsLong(arg) PyLong_AsLong(arg) khmer/_oxli/graphs.cpp:307:0: note: this is the location of the previous definition #define PyInt_AsLong PyLong_AsLong In file included from include/khmer/_cpy_khmer.hh:49:0, from khmer/_oxli/graphs.cpp:514: include/khmer/_cpy_utils.hh:19:0: warning: "PyInt_FromLong" redefined #define PyInt_FromLong(arg) PyLong_FromLong(arg) khmer/_oxli/graphs.cpp:304:0: note: this is the location of the previous definition #define PyInt_FromLong PyLong_FromLong x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.6/src/oxli/read_parsers.o build/temp.linux-x86_64-3.6/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.6/src/oxli/hashtable.o build/temp.linux-x86_64-3.6/src/oxli/hashgraph.o build/temp.linux-x86_64-3.6/src/oxli/labelhash.o build/temp.linux-x86_64-3.6/src/oxli/subset.o build/temp.linux-x86_64-3.6/src/oxli/read_aligner.o build/temp.linux-x86_64-3.6/src/oxli/hllcounter.o build/temp.linux-x86_64-3.6/src/oxli/traversal.o build/temp.linux-x86_64-3.6/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.6/src/oxli/assembler.o build/temp.linux-x86_64-3.6/src/oxli/alphabets.o build/temp.linux-x86_64-3.6/src/oxli/storage.o build/temp.linux-x86_64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.6/khmer/_oxli/graphs.cpython-36m-x86_64-linux-gnu.so -fopenmp skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-3.6/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.6/src/oxli/read_parsers.o build/temp.linux-x86_64-3.6/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.6/src/oxli/hashtable.o build/temp.linux-x86_64-3.6/src/oxli/hashgraph.o build/temp.linux-x86_64-3.6/src/oxli/labelhash.o build/temp.linux-x86_64-3.6/src/oxli/subset.o build/temp.linux-x86_64-3.6/src/oxli/read_aligner.o build/temp.linux-x86_64-3.6/src/oxli/hllcounter.o build/temp.linux-x86_64-3.6/src/oxli/traversal.o build/temp.linux-x86_64-3.6/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.6/src/oxli/assembler.o build/temp.linux-x86_64-3.6/src/oxli/alphabets.o build/temp.linux-x86_64-3.6/src/oxli/storage.o build/temp.linux-x86_64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.6/khmer/_oxli/hashing.cpython-36m-x86_64-linux-gnu.so -fopenmp skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-3.6/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ khmer/_oxli/parsing.cpp: In function 'bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::__cxx11::string&, std::__cxx11::string&, bool)': khmer/_oxli/parsing.cpp:5348:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.6/src/oxli/read_parsers.o build/temp.linux-x86_64-3.6/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.6/src/oxli/hashtable.o build/temp.linux-x86_64-3.6/src/oxli/hashgraph.o build/temp.linux-x86_64-3.6/src/oxli/labelhash.o build/temp.linux-x86_64-3.6/src/oxli/subset.o build/temp.linux-x86_64-3.6/src/oxli/read_aligner.o build/temp.linux-x86_64-3.6/src/oxli/hllcounter.o build/temp.linux-x86_64-3.6/src/oxli/traversal.o build/temp.linux-x86_64-3.6/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.6/src/oxli/assembler.o build/temp.linux-x86_64-3.6/src/oxli/alphabets.o build/temp.linux-x86_64-3.6/src/oxli/storage.o build/temp.linux-x86_64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.6/khmer/_oxli/parsing.cpython-36m-x86_64-linux-gnu.so -fopenmp skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-3.6/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/khmer/_oxli/utils.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.6/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.6/src/oxli/read_parsers.o build/temp.linux-x86_64-3.6/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.6/src/oxli/hashtable.o build/temp.linux-x86_64-3.6/src/oxli/hashgraph.o build/temp.linux-x86_64-3.6/src/oxli/labelhash.o build/temp.linux-x86_64-3.6/src/oxli/subset.o build/temp.linux-x86_64-3.6/src/oxli/read_aligner.o build/temp.linux-x86_64-3.6/src/oxli/hllcounter.o build/temp.linux-x86_64-3.6/src/oxli/traversal.o build/temp.linux-x86_64-3.6/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.6/src/oxli/assembler.o build/temp.linux-x86_64-3.6/src/oxli/alphabets.o build/temp.linux-x86_64-3.6/src/oxli/storage.o build/temp.linux-x86_64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.6/khmer/_oxli/utils.cpython-36m-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-3.6/khmer/_khmer.cpython-36m-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-3.6/khmer/_oxli/assembly.cpython-36m-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.6/khmer/_oxli/graphs.cpython-36m-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.6/khmer/_oxli/hashing.cpython-36m-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.6/khmer/_oxli/parsing.cpython-36m-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.6/khmer/_oxli/utils.cpython-36m-x86_64-linux-gnu.so -> khmer/_oxli Creating /build/khmer-2.1.2+dfsg/fakehome/.local/lib/python3.6/site-packages/khmer.egg-link (link to .) Adding khmer 2.1.2 to easy-install.pth file Installing abundance-dist-single.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing abundance-dist.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing annotate-partitions.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing count-median.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing do-partition.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-long-sequences.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-partitions.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing fastq-to-fasta.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund-single.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-stoptags.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing find-knots.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing interleave-reads.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-graph.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-into-counting.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing make-initial-stoptags.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing merge-partitions.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing normalize-by-median.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing partition-graph.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing readstats.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing sample-reads-randomly.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing split-paired-reads.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing trim-low-abund.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing unique-kmers.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-paired-reads.py script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Installed /build/khmer-2.1.2+dfsg Processing dependencies for khmer==2.1.2 Searching for screed==1.0 Best match: screed 1.0 Adding screed 1.0 to easy-install.pth file Installing screed script to /build/khmer-2.1.2+dfsg/fakehome/.local/bin Using /usr/lib/python3/dist-packages Searching for bz2file==0.98 Best match: bz2file 0.98 Adding bz2file 0.98 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for Cython==0.26.1 Best match: Cython 0.26.1 Adding Cython 0.26.1 to easy-install.pth file Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==2.1.2 running build_sphinx creating /build/khmer-2.1.2+dfsg/build/sphinx creating /build/khmer-2.1.2+dfsg/build/sphinx/doctrees creating /build/khmer-2.1.2+dfsg/build/sphinx/html Running Sphinx v1.6.6 loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [html]: targets for 41 source files that are out of date updating environment: 41 added, 0 changed, 0 removed reading sources... 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[100%] user/artifact-removal.png copying static files... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 2 warnings. asciidoctor --backend manpage -a reproducible debian/khmer.1.adoc cd src/oxli && /usr/bin/make clean all make[2]: Entering directory '/build/khmer-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashtable.o hashtable.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashgraph.o hashgraph.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hllcounter.o hllcounter.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_hash.o kmer_hash.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o labelhash.o labelhash.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o traversal.o traversal.cc In file included from traversal.cc:39:0: traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:203:31: required from here ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] KmerFilterList filters; ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ In file included from traversal.cc:39:0: traversal.cc: In instantiation of 'oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]': traversal.cc:203:31: required from here ../../include/oxli/traversal.hh:79:23: warning: 'oxli::NodeGatherer::graph' will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: 'oxli::KmerFilterList oxli::NodeGatherer::filters' [-Wreorder] KmerFilterList filters; ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_aligner.o read_aligner.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_parsers.o read_parsers.cc In file included from ../../third-party/seqan/core/include/seqan/basic.h:62:0, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr instance; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > _gzStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > _bz2Stream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _mmapString; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr _plainStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _gzReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _bz2Reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _istreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64:0, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _ifstreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:116:0, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function 'seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)': ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this != &other) ^~ ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' _horizontalScore = other._horizontalScore; ^~~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:166:0, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function 'int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)': ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (length(seqH) < length(seqV)) ^~ ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; ^~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:174:0, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function 'seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)': ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if ((actualCol == 0) || (actualRow == 0)) ^~ ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); ^~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107:0, from ../../third-party/seqan/core/include/seqan/store.h:41, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr _writer; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107:0, from ../../third-party/seqan/core/include/seqan/store.h:41, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr _reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:61:0, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/store/store_all.h: In function 'void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)': ../../third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (alignQualityStoreLengthPre == 0u) ^~ ../../third-party/seqan/core/include/seqan/store/store_all.h:1737:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' sortAlignedReads(store.alignedReadStore, SortBeginPos()); ^~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o subset.o subset.cc subset.cc: In member function 'size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)': subset.cc:136:24: warning: unused variable 'ksize' [-Wunused-variable] const unsigned int ksize = _ht->ksize(); ^~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_filters.o kmer_filters.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o assembler.o assembler.cc In file included from assembler.cc:38:0: ../../include/oxli/assembler.hh: In constructor 'oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)': ../../include/oxli/assembler.hh:80:23: warning: 'oxli::LinearAssembler::graph' will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ ../../include/oxli/assembler.hh:79:16: warning: 'oxli::WordLength oxli::LinearAssembler::_ksize' [-Wreorder] WordLength _ksize; ^~~~~~ assembler.cc:52:1: warning: when initialized here [-Wreorder] LinearAssembler::LinearAssembler(const Hashgraph * ht) : ^~~~~~~~~~~~~~~ assembler.cc: In destructor 'oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()': assembler.cc:189:18: warning: deleting object of polymorphic class type 'oxli::LinearAssembler' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete this->linear_asm; ^~~~~~~~~~ In file included from assembler.cc:38:0: ../../include/oxli/assembler.hh: In constructor 'oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)': ../../include/oxli/assembler.hh:158:16: warning: 'oxli::JunctionCountAssembler::_ksize' will be initialized after [-Wreorder] WordLength _ksize; ^~~~~~ ../../include/oxli/assembler.hh:153:15: warning: 'oxli::Traverser oxli::JunctionCountAssembler::traverser' [-Wreorder] Traverser traverser; ^~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ In file included from assembler.cc:38:0: ../../include/oxli/assembler.hh:153:15: warning: 'oxli::JunctionCountAssembler::traverser' will be initialized after [-Wreorder] Traverser traverser; ^~~~~~~~~ ../../include/oxli/assembler.hh:151:21: warning: 'oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm' [-Wreorder] LinearAssembler linear_asm; ^~~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o alphabets.o alphabets.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -c -o murmur3.o ../../third-party/smhasher/MurmurHash3.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o storage.o storage.cc g++ -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -Wl,-soname=liboxli.so.1 -shared -o liboxli.so.1 hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ln -sf liboxli.so.1 liboxli.so ar rcs liboxli.a hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ranlib liboxli.a sed -e 's,@prefix@,/usr/local,' -e 's,@VERSION@,,' oxli.pc.in >oxli.pc make[2]: Leaving directory '/build/khmer-2.1.2+dfsg/src/oxli' make[1]: Leaving directory '/build/khmer-2.1.2+dfsg' rm -f debian/khmer-common.debhelper.log debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/khmer-2.1.2+dfsg' dh_auto_install install -d debian/khmer-common debian/khmer debian/liboxli1 debian/liboxli-dev pybuild --install --test-pytest -i python{version} -p 3.6 --dest-dir /build/khmer-2.1.2\+dfsg/debian/tmp I: pybuild base:184: /usr/bin/python3 setup.py install --root /build/khmer-2.1.2+dfsg/debian/khmer '--install-scripts=/usr/lib/khmer/bin' running install running build running build_py running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_oxli/assembly.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli UPDATING /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_version.py set /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_version.py to '2.1.2' running build_ext building 'khmer._khmer' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_counttable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashset.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_khmer.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/khmer/_cpy_utils.cc -o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/read_parsers.cc -o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from third-party/seqan/core/include/seqan/basic.h:62:0, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr instance; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > _gzStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > _bz2Stream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _mmapString; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr _plainStream; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _gzReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr, SinglePass<> > > _bz2Reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _istreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64:0, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr > > _ifstreamReader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (this != &other) ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ _horizontalScore = other._horizontalScore; ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (length(seqH) < length(seqV)) ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174:0, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if ((actualCol == 0) || (actualRow == 0)) ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107:0, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr _writer; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107:0, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr _reader; ^~~~~~~~ In file included from /usr/include/c++/7/bits/locale_conv.h:41:0, from /usr/include/c++/7/locale:43, from /usr/include/c++/7/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61:0, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (alignQualityStoreLengthPre == 0u) ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ sortAlignedReads(store.alignedReadStore, SortBeginPos()); ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/kmer_hash.cc -o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hashtable.cc -o build/temp.linux-amd64-3.6/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hashgraph.cc -o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/labelhash.cc -o build/temp.linux-amd64-3.6/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/subset.cc -o build/temp.linux-amd64-3.6/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] const unsigned int ksize = _ht->ksize(); ^~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/read_aligner.cc -o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/hllcounter.cc -o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/traversal.cc -o build/temp.linux-amd64-3.6/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from src/oxli/traversal.cc:39:0: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:31: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] KmerFilterList filters; ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39:0: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:31: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] KmerFilterList filters; ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] NodeGatherer::NodeGatherer(const Hashgraph * ht, ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/kmer_filters.cc -o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/assembler.cc -o build/temp.linux-amd64-3.6/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] const Hashgraph * graph; ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] WordLength _ksize; ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] LinearAssembler::LinearAssembler(const Hashgraph * ht) : ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:18: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete this->linear_asm; ^~~~~~~~~~ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] WordLength _ksize; ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] Traverser traverser; ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38:0: include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] Traverser traverser; ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] LinearAssembler linear_asm; ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/alphabets.cc -o build/temp.linux-amd64-3.6/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c src/oxli/storage.cc -o build/temp.linux-amd64-3.6/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.6m -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.6/src/khmer/_cpy_countgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_counttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_graphlabels.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashset.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hashtable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_hllcounter.o build/temp.linux-amd64-3.6/src/khmer/_cpy_khmer.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodegraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_nodetable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readaligner.o build/temp.linux-amd64-3.6/src/khmer/_cpy_readparsers.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcountgraph.o build/temp.linux-amd64-3.6/src/khmer/_cpy_smallcounttable.o build/temp.linux-amd64-3.6/src/khmer/_cpy_subsetpartition.o build/temp.linux-amd64-3.6/src/khmer/_cpy_utils.o build/temp.linux-amd64-3.6/src/oxli/read_parsers.o build/temp.linux-amd64-3.6/src/oxli/kmer_hash.o build/temp.linux-amd64-3.6/src/oxli/hashtable.o build/temp.linux-amd64-3.6/src/oxli/hashgraph.o build/temp.linux-amd64-3.6/src/oxli/labelhash.o build/temp.linux-amd64-3.6/src/oxli/subset.o build/temp.linux-amd64-3.6/src/oxli/read_aligner.o build/temp.linux-amd64-3.6/src/oxli/hllcounter.o build/temp.linux-amd64-3.6/src/oxli/traversal.o build/temp.linux-amd64-3.6/src/oxli/kmer_filters.o build/temp.linux-amd64-3.6/src/oxli/assembler.o build/temp.linux-amd64-3.6/src/oxli/alphabets.o build/temp.linux-amd64-3.6/src/oxli/storage.o build/temp.linux-amd64-3.6/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_khmer.cpython-36m-x86_64-linux-gnu.so -fopenmp skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) running build_scripts running install_lib creating /build/khmer-2.1.2+dfsg/debian/khmer/usr creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6 creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/kfile.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/khmer_args.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/khmer_logger.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/thread_utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/trimming.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/graph_features.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_banding.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_countgraph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_counting_single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_counttable.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_cython_assembly.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_cython_parsing.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_filter_abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_hashset.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_hll.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_labelhash.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_lump.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_nibblestorage.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_nodegraph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_oxli_functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_read_aligner.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_read_handling.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_script_arguments.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_script_output.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_scripts.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_sequence_validation.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_streaming_io.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_subset_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_tabletype.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_version.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test_read_parsers.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/.gitignore -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/README.rst -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/all-A.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/bogus.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/empty-file -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/single-read.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/single-read.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-large.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-short.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/truncated.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test-data creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/assembly.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/assembly.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/graphs.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/graphs.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/hashing.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/hashing.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/parsing.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/parsing.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/traversal.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/utils.pxd -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/utils.pyx -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/assembly.cpython-36m-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/graphs.cpython-36m-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/hashing.cpython-36m-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/parsing.cpython-36m-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/utils.cpython-36m-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/assembly.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/graphs.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/hashing.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/parsing.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_oxli/utils.cpp -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_version.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/_khmer.cpython-36m-x86_64-linux-gnu.so -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli/__init__.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli/build_graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli/functions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli copying /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/oxli/partition.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/__init__.py to __init__.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/kfile.py to kfile.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/khmer_args.py to khmer_args.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/thread_utils.py to thread_utils.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/trimming.py to trimming.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/utils.py to utils.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/__init__.py to __init__.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_version.py to test_version.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer/_version.py to _version.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli/__init__.py to __init__.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli/build_graph.py to build_graph.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli/functions.py to functions.cpython-36.pyc byte-compiling /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/oxli/partition.py to partition.cpython-36.pyc running install_egg_info Copying khmer.egg-info to /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.6/dist-packages/khmer-2.1.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer creating /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/abundance-dist-single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/abundance-dist.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/annotate-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/count-median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/do-partition.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/extract-long-sequences.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/extract-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/fastq-to-fasta.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/filter-abund-single.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/filter-abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/filter-stoptags.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/find-knots.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/interleave-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/load-graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/load-into-counting.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/make-initial-stoptags.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/merge-partitions.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/normalize-by-median.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/partition-graph.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/readstats.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/sample-reads-randomly.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/split-paired-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/trim-low-abund.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/unique-kmers.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.6/extract-paired-reads.py -> /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$PATH ; \ cd {build_dir}; export PYTHONPATH=$(pwd); {interpreter} -m pytest \ -m 'not known_failing and not jenkins and not huge'" dh_auto_test pybuild --test --test-pytest -i python{version} -p 3.6 I: pybuild base:184: cd /build/khmer-2.1.2+dfsg; export PATH=/build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ; cd /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build; export PYTHONPATH=/build/khmer-2.1.2+dfsg; python3.6 -m pytest -m 'not known_failing and not jenkins and not huge' ============================= test session starts ============================== platform linux -- Python 3.6.4, pytest-3.2.1, py-1.4.34, pluggy-0.4.0 -- /usr/bin/python3.6 cachedir: ../../../.cache rootdir: /build/khmer-2.1.2+dfsg, inifile: pytest.ini collecting ... collected 1365 items khmer/tests/test_banding.py::test_banding_in_memory[21-5000000.0-1-2] PASSED khmer/tests/test_banding.py::test_banding_in_memory[21-5000000.0-1-4] PASSED khmer/tests/test_banding.py::test_banding_in_memory[21-5000000.0-1-8] PASSED khmer/tests/test_banding.py::test_banding_in_memory[21-5000000.0-1-16] PASSED khmer/tests/test_banding.py::test_banding_to_disk[21-5000000.0-3] PASSED khmer/tests/test_banding.py::test_banding_to_disk[21-5000000.0-11] PASSED khmer/tests/test_banding.py::test_banding_to_disk[21-5000000.0-23] PASSED khmer/tests/test_banding.py::test_banding_to_disk[21-5000000.0-29] PASSED khmer/tests/test_banding.py::test_banding_bad_params[Nodetable] PASSED khmer/tests/test_banding.py::test_banding_bad_params[Counttable] PASSED khmer/tests/test_banding.py::test_banding[Nodetable-8-3] PASSED khmer/tests/test_banding.py::test_banding[Counttable-8-3] PASSED khmer/tests/test_countgraph.py::test_count_1 PASSED khmer/tests/test_countgraph.py::test_count_2 PASSED khmer/tests/test_countgraph.py::test_revhash_1 PASSED khmer/tests/test_countgraph.py::Test_Countgraph::test_failed_get PASSED khmer/tests/test_countgraph.py::Test_Countgraph::test_collision_1 PASSED khmer/tests/test_countgraph.py::Test_Countgraph::test_collision_2 PASSED khmer/tests/test_countgraph.py::Test_Countgraph::test_collision_3 PASSED khmer/tests/test_countgraph.py::test_get_raw_tables PASSED khmer/tests/test_countgraph.py::test_get_raw_tables_smallcountgraph PASSED khmer/tests/test_countgraph.py::test_get_raw_tables_view PASSED khmer/tests/test_countgraph.py::test_get_raw_tables_view_smallcountgraph PASSED khmer/tests/test_countgraph.py::test_3_tables PASSED khmer/tests/test_countgraph.py::test_simple_median PASSED khmer/tests/test_countgraph.py::test_median_too_short PASSED khmer/tests/test_countgraph.py::test_median_at_least PASSED khmer/tests/test_countgraph.py::test_median_at_least_single_gt PASSED khmer/tests/test_countgraph.py::test_median_at_least_single_lt PASSED khmer/tests/test_countgraph.py::test_median_at_least_odd_gt PASSED khmer/tests/test_countgraph.py::test_median_at_least_odd_lt PASSED khmer/tests/test_countgraph.py::test_median_at_least_even_gt PASSED khmer/tests/test_countgraph.py::test_median_at_least_even_lt PASSED khmer/tests/test_countgraph.py::test_median_at_least_comp PASSED khmer/tests/test_countgraph.py::test_median_at_least_exception PASSED khmer/tests/test_countgraph.py::test_get_kmer_counts_too_short PASSED khmer/tests/test_countgraph.py::test_get_kmer_hashes_too_short PASSED khmer/tests/test_countgraph.py::test_get_kmers_too_short PASSED khmer/tests/test_countgraph.py::test_get_kmer_counts PASSED khmer/tests/test_countgraph.py::test_get_kmer_hashes PASSED khmer/tests/test_countgraph.py::test_get_kmer_hashes_as_hashset PASSED khmer/tests/test_countgraph.py::test_get_kmers PASSED khmer/tests/test_countgraph.py::test_save_load_occupied[temp.ct] PASSED khmer/tests/test_countgraph.py::test_save_load_occupied[temp.ct.gz] PASSED khmer/tests/test_countgraph.py::test_save_load_occupied_small[temp.ct] PASSED khmer/tests/test_countgraph.py::test_save_load_occupied_small[temp.ct.gz] PASSED khmer/tests/test_countgraph.py::test_save_load PASSED khmer/tests/test_countgraph.py::test_load_truncated PASSED khmer/tests/test_countgraph.py::test_load_gz PASSED khmer/tests/test_countgraph.py::test_save_load_gz PASSED khmer/tests/test_countgraph.py::test_load_empty_files[] PASSED khmer/tests/test_countgraph.py::test_load_empty_files[.gz] PASSED khmer/tests/test_countgraph.py::test_trim_full PASSED khmer/tests/test_countgraph.py::test_trim_short PASSED khmer/tests/test_countgraph.py::test_find_spectral_error_positions_1 PASSED khmer/tests/test_countgraph.py::test_find_spectral_error_positions_2 PASSED khmer/tests/test_countgraph.py::test_find_spectral_error_positions_6 PASSED khmer/tests/test_countgraph.py::test_find_spectral_error_positions_4 PASSED khmer/tests/test_countgraph.py::test_find_spectral_error_positions_5 PASSED khmer/tests/test_countgraph.py::test_find_spectral_error_locs7 PASSED khmer/tests/test_countgraph.py::test_find_spectral_error_positions_err PASSED khmer/tests/test_countgraph.py::test_maxcount PASSED khmer/tests/test_countgraph.py::test_maxcount_with_bigcount PASSED khmer/tests/test_countgraph.py::test_maxcount_with_bigcount_save PASSED khmer/tests/test_countgraph.py::test_bigcount_save PASSED khmer/tests/test_countgraph.py::test_nobigcount_save PASSED khmer/tests/test_countgraph.py::test_bigcount_abund_dist PASSED khmer/tests/test_countgraph.py::test_bigcount_abund_dist_2 PASSED khmer/tests/test_countgraph.py::test_bigcount_overflow PASSED khmer/tests/test_countgraph.py::test_get_ksize PASSED khmer/tests/test_countgraph.py::test_get_hashsizes PASSED khmer/tests/test_countgraph.py::test_load_notexist_should_fail PASSED khmer/tests/test_countgraph.py::test_load_truncated_should_fail PASSED khmer/tests/test_countgraph.py::test_load_gz_notexist_should_fail PASSED khmer/tests/test_countgraph.py::test_load_gz_truncated_should_fail PASSED khmer/tests/test_countgraph.py::test_counting_file_version_check PASSED khmer/tests/test_countgraph.py::test_counting_gz_file_version_check PASSED khmer/tests/test_countgraph.py::test_counting_file_type_check PASSED khmer/tests/test_countgraph.py::test_counting_gz_file_type_check PASSED khmer/tests/test_countgraph.py::test_counting_bad_primes_list PASSED khmer/tests/test_countgraph.py::test_bad_use_bigcount PASSED khmer/tests/test_countgraph.py::test_consume_absentfasta PASSED khmer/tests/test_countgraph.py::test_consume_absentfasta_with_reads_parser PASSED khmer/tests/test_countgraph.py::test_badconsume PASSED khmer/tests/test_countgraph.py::test_get_badmin_count PASSED khmer/tests/test_countgraph.py::test_get_badmax_count PASSED khmer/tests/test_countgraph.py::test_get_badmedian_count PASSED khmer/tests/test_countgraph.py::test_badget PASSED khmer/tests/test_countgraph.py::test_badget_2 PASSED khmer/tests/test_countgraph.py::test_badtrim PASSED khmer/tests/test_countgraph.py::test_badload PASSED khmer/tests/test_countgraph.py::test_badsave PASSED khmer/tests/test_countgraph.py::test_badksize PASSED khmer/tests/test_countgraph.py::test_badhashsizes PASSED khmer/tests/test_countgraph.py::test_badconsume_and_tag PASSED khmer/tests/test_countgraph.py::test_consume_seqfile_and_tag PASSED khmer/tests/test_countgraph.py::test_consume_and_retrieve_tags_1 PASSED khmer/tests/test_countgraph.py::test_consume_and_retrieve_tags_empty PASSED khmer/tests/test_countgraph.py::test_find_all_tags_list_error PASSED khmer/tests/test_countgraph.py::test_abund_dist_gz_bigcount PASSED khmer/tests/test_countgraph.py::test_abund_dist_gz_bigcount_compressed_first PASSED khmer/tests/test_countgraph.py::test_counting_load_bigcount PASSED khmer/tests/test_countgraph.py::test_bad_create PASSED khmer/tests/test_counting_single.py::test_collision PASSED khmer/tests/test_counting_single.py::test_badcount PASSED khmer/tests/test_counting_single.py::test_complete_no_collision PASSED khmer/tests/test_counting_single.py::test_complete_2_collision PASSED khmer/tests/test_counting_single.py::test_complete_4_collision PASSED khmer/tests/test_counting_single.py::test_maxcount PASSED khmer/tests/test_counting_single.py::test_maxcount_with_bigcount PASSED khmer/tests/test_counting_single.py::test_consume_uniqify_first PASSED khmer/tests/test_counting_single.py::test_maxcount_consume PASSED khmer/tests/test_counting_single.py::test_maxcount_consume_with_bigcount PASSED khmer/tests/test_counting_single.py::test_get_mincount PASSED khmer/tests/test_counting_single.py::test_get_maxcount PASSED khmer/tests/test_counting_single.py::test_get_maxcount_rc PASSED khmer/tests/test_counting_single.py::test_get_mincount_rc PASSED khmer/tests/test_counting_single.py::test_badget PASSED khmer/tests/test_counting_single.py::test_64bitshift PASSED khmer/tests/test_counting_single.py::test_64bitshift_2 PASSED khmer/tests/test_counting_single.py::test_very_short_read PASSED khmer/tests/test_counting_single.py::Test_ConsumeString::test_n_occupied PASSED khmer/tests/test_counting_single.py::Test_ConsumeString::test_simple PASSED khmer/tests/test_counting_single.py::Test_ConsumeString::test_simple_2 PASSED khmer/tests/test_counting_single.py::Test_ConsumeString::test_simple_rc PASSED khmer/tests/test_counting_single.py::Test_ConsumeString::test_min_count PASSED khmer/tests/test_counting_single.py::Test_ConsumeString::test_max_count PASSED khmer/tests/test_counting_single.py::Test_AbundanceDistribution::test_count_A PASSED khmer/tests/test_counttable.py::test_get_kmer_hashes PASSED khmer/tests/test_counttable.py::test_kmer_revcom_hash[GATTACAGATTACAGATTACA] PASSED khmer/tests/test_counttable.py::test_kmer_revcom_hash[ATGATGATGATGATGATGATG] PASSED khmer/tests/test_counttable.py::test_kmer_revcom_hash[AGGACAAGTATATGGAGGACA] PASSED khmer/tests/test_counttable.py::test_reverse_hash[21-Nodetable] PASSED khmer/tests/test_counttable.py::test_reverse_hash[21-Counttable] PASSED khmer/tests/test_counttable.py::test_reverse_hash[21-SmallCounttable] PASSED khmer/tests/test_counttable.py::test_reverse_hash[49-Nodetable] PASSED khmer/tests/test_counttable.py::test_reverse_hash[49-Counttable] PASSED khmer/tests/test_counttable.py::test_reverse_hash[49-SmallCounttable] PASSED khmer/tests/test_cpython_hierarchy.py::test_countgraph_vs_table PASSED khmer/tests/test_cpython_hierarchy.py::test_nodegraph_vs_table PASSED khmer/tests/test_cpython_hierarchy.py::test_counttable_no_unhash PASSED khmer/tests/test_cpython_hierarchy.py::test_smallcountgraph_vs_table PASSED khmer/tests/test_cython_assembly.py::test_mutate_sequence <- .pybuild/pythonX.Y_3.6/build/khmer/tests/graph_features.py PASSED khmer/tests/test_cython_assembly.py::test_mutate_position <- .pybuild/pythonX.Y_3.6/build/khmer/tests/graph_features.py PASSED khmer/tests/test_cython_assembly.py::test_reads <- .pybuild/pythonX.Y_3.6/build/khmer/tests/graph_features.py PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_start_positions[(Type=Nodegraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_start_positions[(Type=Nodegraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_start_positions[(Type=Nodegraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_start_positions[(Type=Countgraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_start_positions[(Type=Countgraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_start_positions[(Type=Countgraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_left_to_beginning[(Type=Nodegraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_left_to_beginning[(Type=Nodegraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_left_to_beginning[(Type=Nodegraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_left_to_beginning[(Type=Countgraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_left_to_beginning[(Type=Countgraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_left_to_beginning[(Type=Countgraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_right_to_end[(Type=Nodegraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_right_to_end[(Type=Nodegraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_right_to_end[(Type=Nodegraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_right_to_end[(Type=Countgraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_right_to_end[(Type=Countgraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_all_right_to_end[(Type=Countgraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_circular[(Type=Nodegraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_circular[(Type=Nodegraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_circular[(Type=Nodegraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_circular[(Type=Countgraph)-(L=500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_circular[(Type=Countgraph)-(L=1000)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestNonBranching::test_circular[(Type=Countgraph)-(L=1500)-LinearAssembler] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_branch_point[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_beginning_to_branch_revcomp[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_left_of_branch_to_beginning_revcomp[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_right_of_branch_outwards_to_ends[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_RightBranching::test_end_to_beginning[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_point[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_to_branch[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_branch_to_end[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_from_branch_to_ends_with_stopbf_revcomp[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_end_thru_tip_with_stopbf[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLinearAssembler_LeftBranching::test_single_node_flanked_by_hdns[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=Start)-(L=500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=Start)-(L=500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=Start)-(L=1000)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=Start)-(L=1000)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=Start)-(L=1500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=Start)-(L=1500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=End)-(L=500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=End)-(L=500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=End)-(L=1000)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=End)-(L=1000)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=End)-(L=1500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_double_fork[(Where=End)-(L=1500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=Start)-(L=500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=Start)-(L=500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=Start)-(L=1000)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=Start)-(L=1000)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=Start)-(L=1500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=Start)-(L=1500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=End)-(L=500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=End)-(L=500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=End)-(L=1000)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=End)-(L=1000)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=End)-(L=1500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_right_triple_fork[(Where=End)-(L=1500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=Start)-(L=500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=Start)-(L=500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=Start)-(L=1000)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=Start)-(L=1000)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=Start)-(L=1500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=Start)-(L=1500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=End)-(L=500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=End)-(L=500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=End)-(L=1000)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=End)-(L=1000)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=End)-(L=1500)-(Type=Nodegraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_left_double_fork[(Where=End)-(L=1500)-(Type=Countgraph)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_single[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_both[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_snp_bubble_stopbf[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[2-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[2-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[2-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[2-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[2-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[2-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[3-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[3-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[3-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[3-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[3-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[3-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[4-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[4-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[4-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[4-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[4-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[4-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[5-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[5-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[5-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[5-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[5-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[5-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[6-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[6-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[6-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[6-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[6-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[6-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[7-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[7-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[7-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[7-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[7-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[7-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[8-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[8-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[8-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[8-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[8-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestLabeledAssembler::test_assemble_tandem_repeats[8-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=Start)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Nodegraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Nodegraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Nodegraph)-(L=1500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Countgraph)-(L=500)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Countgraph)-(L=1000)] PASSED khmer/tests/test_cython_assembly.py::TestJunctionCountAssembler::test_beginning_to_end_across_tip[(Where=End)-(Type=Countgraph)-(L=1500)] PASSED khmer/tests/test_cython_parsing.py::test_FastxParser PASSED khmer/tests/test_cython_parsing.py::test_SanitizedFastxParser_convert_Ns PASSED khmer/tests/test_cython_parsing.py::test_SanitizedFastxParser_no_convert_Ns PASSED khmer/tests/test_cython_parsing.py::test_SanitizedFastxParser_invalid PASSED khmer/tests/test_cython_parsing.py::test_SanitizedFastxParser_lowercase PASSED khmer/tests/test_cython_parsing.py::test_alphabet_wrapper PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testDefault[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testDefault[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testMinLength[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testMinLength[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testMinLength_2[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testMinLength_2[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testForceSingle[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testForceSingle[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testForceSingleAndMinLength[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testForceSingleAndMinLength[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_HalfPass[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_HalfPass[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_SwappedHalfPass[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_SwappedHalfPass[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_NeitherPass[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_NeitherPass[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_SwappedNeitherPass[FastxParser] PASSED khmer/tests/test_cython_parsing.py::Test_BrokenPairedReader::testRequirePairedAndMinLength_SwappedNeitherPass[SanitizedFastxParser] PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_1 PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_2 PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_3_fq PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_3_broken_fq_1 PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_3_broken_fq_2 PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_3_fa PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_4 PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_4b PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_5 PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_6 PASSED khmer/tests/test_cython_parsing.py::test_check_is_pair_7 PASSED khmer/tests/test_cython_parsing.py::test_check_is_right PASSED khmer/tests/test_cython_parsing.py::test_check_is_left PASSED khmer/tests/test_cython_parsing.py::Test_Sequence::test_init_name_and_sequence PASSED khmer/tests/test_cython_parsing.py::Test_Sequence::test_init_name_only PASSED khmer/tests/test_cython_parsing.py::Test_Sequence::test_init_sequence_only PASSED khmer/tests/test_cython_parsing.py::Test_Sequence::test_init_with_cleaned_seq PASSED khmer/tests/test_filter_abund.py::test_filter_abund_1 PASSED khmer/tests/test_filter_abund.py::test_filter_abund_2 PASSED khmer/tests/test_filter_abund.py::test_filter_abund_2_stdin PASSED khmer/tests/test_filter_abund.py::test_filter_abund_2_stdin_gzip_out PASSED khmer/tests/test_filter_abund.py::test_filter_abund_3_fq_retained PASSED khmer/tests/test_filter_abund.py::test_filter_abund_4_fq_casava_18 PASSED khmer/tests/test_filter_abund.py::test_filter_abund_1_singlefile PASSED khmer/tests/test_filter_abund.py::test_filter_abund_2_singlefile PASSED khmer/tests/test_filter_abund.py::test_filter_abund_2_singlefile_fq_casava_18 PASSED khmer/tests/test_filter_abund.py::test_filter_abund_4_retain_low_abund PASSED khmer/tests/test_filter_abund.py::test_filter_abund_single_4_retain_low_abund PASSED khmer/tests/test_filter_abund.py::test_filter_abund_5_trim_high_abund PASSED khmer/tests/test_filter_abund.py::test_filter_abund_single_trim_high_abund PASSED khmer/tests/test_filter_abund.py::test_filter_abund_6_trim_high_abund_Z PASSED khmer/tests/test_filter_abund.py::test_filter_abund_7_retain_Ns PASSED khmer/tests/test_filter_abund.py::test_filter_abund_single_8_retain_Ns PASSED khmer/tests/test_filter_abund.py::test_outfile PASSED khmer/tests/test_filter_abund.py::test_filter_abund_1_quiet PASSED khmer/tests/test_filter_abund.py::test_filter_abund_1_singlefile_quiet PASSED khmer/tests/test_functions.py::test_forward_hash PASSED khmer/tests/test_functions.py::test_get_file_writer_fail PASSED khmer/tests/test_functions.py::test_forward_hash_no_rc PASSED khmer/tests/test_functions.py::test_reverse_hash PASSED khmer/tests/test_functions.py::test_reverse_complement PASSED khmer/tests/test_functions.py::test_reverse_complement_exception PASSED khmer/tests/test_functions.py::test_reverse_hash_longs PASSED khmer/tests/test_functions.py::test_reverse_hash_raises PASSED khmer/tests/test_functions.py::test_hash_murmur3 PASSED khmer/tests/test_functions.py::test_hash_no_rc_murmur3 PASSED khmer/tests/test_functions.py::test_get_primes PASSED khmer/tests/test_functions.py::test_get_primes_fal PASSED khmer/tests/test_functions.py::test_extract_countgraph_info_badfile PASSED khmer/tests/test_functions.py::test_extract_countgraph_info PASSED khmer/tests/test_functions.py::test_extract_nodegraph_info_badfile PASSED khmer/tests/test_functions.py::test_extract_nodegraph_info PASSED khmer/tests/test_functions.py::test_check_file_status_kfile PASSED khmer/tests/test_functions.py::test_check_file_status_kfile_force PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_counts PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_next_a PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_next_c PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_next_g PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_next_t PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_prev_a PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_prev_c PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_prev_g PASSED khmer/tests/test_graph.py::Test_ExactGraphFu::test_graph_links_prev_t PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_next_a PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_next_c PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_next_g PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_next_t PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_prev_a PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_prev_c PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_prev_g PASSED khmer/tests/test_graph.py::Test_InexactGraphFu::test_graph_links_prev_t PASSED khmer/tests/test_graph.py::Test_Partitioning::test_output_unassigned PASSED khmer/tests/test_graph.py::Test_Partitioning::test_not_output_unassigned PASSED khmer/tests/test_graph.py::Test_Partitioning::test_output_fq PASSED khmer/tests/test_graph.py::Test_Partitioning::test_disconnected_20_a PASSED khmer/tests/test_graph.py::Test_Partitioning::test_connected_20_a PASSED khmer/tests/test_graph.py::Test_Partitioning::test_disconnected_20_b PASSED khmer/tests/test_graph.py::Test_Partitioning::test_connected_20_b PASSED khmer/tests/test_graph.py::Test_Partitioning::test_disconnected_31_c PASSED khmer/tests/test_graph.py::Test_Partitioning::test_connected_31_c PASSED khmer/tests/test_graph.py::Test_PythonAPI::test_find_all_tags_kmersize PASSED khmer/tests/test_graph.py::Test_PythonAPI::test_ordered_connect PASSED khmer/tests/test_hashset.py::test_bad_construct PASSED khmer/tests/test_hashset.py::test_iter_double PASSED khmer/tests/test_hashset.py::test_iter_single PASSED khmer/tests/test_hashset.py::test_add PASSED khmer/tests/test_hashset.py::test_update PASSED khmer/tests/test_hashset.py::test_update_bad PASSED khmer/tests/test_hashset.py::test_remove PASSED khmer/tests/test_hashset.py::test_remove_2 PASSED khmer/tests/test_hashset.py::test_contains_1 PASSED khmer/tests/test_hashset.py::test_concat_1 PASSED khmer/tests/test_hashset.py::test_concat_2 PASSED khmer/tests/test_hashset.py::test_concat_1_fail PASSED khmer/tests/test_hashset.py::test_concat_2_fail PASSED khmer/tests/test_hll.py::test_hll_add_python PASSED khmer/tests/test_hll.py::test_hll_consume_string PASSED khmer/tests/test_hll.py::test_hll_empty_fasta PASSED khmer/tests/test_hll.py::test_hll_consume_seqfile PASSED khmer/tests/test_hll.py::test_hll_consume_seqfile_ep PASSED khmer/tests/test_hll.py::test_hll_consume_seqfile_estimate_bias PASSED khmer/tests/test_hll.py::test_hll_len PASSED khmer/tests/test_hll.py::test_hll_empty PASSED khmer/tests/test_hll.py::test_hll_readonly_alpha PASSED khmer/tests/test_hll.py::test_hll_cover_calc_alpha PASSED khmer/tests/test_hll.py::test_hll_invalid_base PASSED khmer/tests/test_hll.py::test_hll_invalid_error_rate PASSED khmer/tests/test_hll.py::test_hll_invalid_error_rate_max PASSED khmer/tests/test_hll.py::test_hll_error_rate_max PASSED khmer/tests/test_hll.py::test_hll_invalid_error_rate_min PASSED khmer/tests/test_hll.py::test_hll_error_rate_min PASSED khmer/tests/test_hll.py::test_hll_change_error_rate PASSED khmer/tests/test_hll.py::test_hll_change_ksize PASSED khmer/tests/test_hll.py::test_hll_get_counters PASSED khmer/tests/test_hll.py::test_hll_merge_1 PASSED khmer/tests/test_hll.py::test_hll_merge_2 PASSED khmer/tests/test_hll.py::test_hll_merge_3 PASSED khmer/tests/test_labelhash.py::test_error_create PASSED khmer/tests/test_labelhash.py::test_n_labels PASSED khmer/tests/test_labelhash.py::test_get_all_labels PASSED khmer/tests/test_labelhash.py::test_get_labels_save_load PASSED khmer/tests/test_labelhash.py::test_get_labels_save_load_wrong_ksize PASSED khmer/tests/test_labelhash.py::test_save_load_corrupted PASSED khmer/tests/test_labelhash.py::test_save_fail_readonly FAILED khmer/tests/test_labelhash.py::test_get_tag_labels PASSED khmer/tests/test_labelhash.py::test_consume_seqfile_and_tag_with_labels PASSED khmer/tests/test_labelhash.py::test_consume_partitioned_fasta_and_tag_with_labels PASSED khmer/tests/test_labelhash.py::test_consume_sequence_and_tag_with_labels PASSED khmer/tests/test_labelhash.py::test_sweep_tag_neighborhood PASSED khmer/tests/test_labelhash.py::test_sweep_label_neighborhood PASSED khmer/tests/test_labelhash.py::test_label_tag_correctness PASSED khmer/tests/test_labelhash.py::test_counting_label_tag_correctness PASSED khmer/tests/test_labelhash.py::test_label_tag_correctness_save_load PASSED khmer/tests/test_labelhash.py::test_load_wrong_filetype PASSED khmer/tests/test_labelhash.py::test_load_wrong_fileversion PASSED khmer/tests/test_lump.py::test_fakelump_together PASSED khmer/tests/test_lump.py::test_fakelump_stop PASSED khmer/tests/test_lump.py::test_fakelump_stop2 PASSED khmer/tests/test_lump.py::test_fakelump_repartitioning PASSED khmer/tests/test_lump.py::test_fakelump_load_stop_tags_trunc PASSED khmer/tests/test_lump.py::test_fakelump_load_stop_tags_notexist PASSED khmer/tests/test_nibblestorage.py::test_single_add PASSED khmer/tests/test_nibblestorage.py::test_split_byte_murmur PASSED khmer/tests/test_nibblestorage.py::test_overflow PASSED khmer/tests/test_nibblestorage.py::test_random_kmers PASSED khmer/tests/test_nibblestorage.py::test_read_write PASSED khmer/tests/test_nodegraph.py::test_bad_create PASSED khmer/tests/test_nodegraph.py::test__get_set_tag_density PASSED khmer/tests/test_nodegraph.py::test_update_from PASSED khmer/tests/test_nodegraph.py::test_update_from_2 PASSED khmer/tests/test_nodegraph.py::test_update_from_diff_ksize_2 PASSED khmer/tests/test_nodegraph.py::test_update_from_diff_tablesize PASSED khmer/tests/test_nodegraph.py::test_update_from_diff_num_tables PASSED khmer/tests/test_nodegraph.py::test_n_occupied_1 PASSED khmer/tests/test_nodegraph.py::test_bloom_python_1 PASSED khmer/tests/test_nodegraph.py::test_bloom_c_1 PASSED khmer/tests/test_nodegraph.py::test_n_occupied_2 PASSED khmer/tests/test_nodegraph.py::test_n_occupied_2_add_is_count PASSED khmer/tests/test_nodegraph.py::test_bloom_c_2 PASSED khmer/tests/test_nodegraph.py::test_combine_pe PASSED khmer/tests/test_nodegraph.py::test_load_partitioned PASSED khmer/tests/test_nodegraph.py::test_consume_partitioned_fail PASSED khmer/tests/test_nodegraph.py::test_count_within_radius_simple PASSED khmer/tests/test_nodegraph.py::test_count_within_radius_big PASSED khmer/tests/test_nodegraph.py::test_count_kmer_degree PASSED khmer/tests/test_nodegraph.py::test_kmer_neighbors PASSED khmer/tests/test_nodegraph.py::test_kmer_neighbors_wrong_ksize PASSED khmer/tests/test_nodegraph.py::test_save_load_tagset PASSED khmer/tests/test_nodegraph.py::test_save_load_tagset_noclear PASSED khmer/tests/test_nodegraph.py::test_stop_traverse PASSED khmer/tests/test_nodegraph.py::test_get_ksize PASSED khmer/tests/test_nodegraph.py::test_get_hashsizes PASSED khmer/tests/test_nodegraph.py::test_extract_unique_paths_0 PASSED khmer/tests/test_nodegraph.py::test_extract_unique_paths_1 PASSED khmer/tests/test_nodegraph.py::test_extract_unique_paths_2 PASSED khmer/tests/test_nodegraph.py::test_extract_unique_paths_3 PASSED khmer/tests/test_nodegraph.py::test_extract_unique_paths_4 PASSED khmer/tests/test_nodegraph.py::test_get_raw_tables PASSED khmer/tests/test_nodegraph.py::test_simple_median PASSED khmer/tests/test_nodegraph.py::test_badget PASSED khmer/tests/test_nodegraph.py::test_load_notexist_should_fail PASSED khmer/tests/test_nodegraph.py::test_load_truncated_should_fail PASSED khmer/tests/test_nodegraph.py::test_save_load_tagset_notexist PASSED khmer/tests/test_nodegraph.py::test_save_load_tagset_trunc PASSED khmer/tests/test_nodegraph.py::test_hashbits_file_version_check PASSED khmer/tests/test_nodegraph.py::test_nodegraph_file_type_check PASSED khmer/tests/test_nodegraph.py::test_stoptags_file_version_check PASSED khmer/tests/test_nodegraph.py::test_stoptags_ksize_check PASSED khmer/tests/test_nodegraph.py::test_stop_tags_filetype_check PASSED khmer/tests/test_nodegraph.py::test_tagset_file_version_check PASSED khmer/tests/test_nodegraph.py::test_stop_tags_truncate_check PASSED khmer/tests/test_nodegraph.py::test_tagset_ksize_check PASSED khmer/tests/test_nodegraph.py::test_tagset_filetype_check PASSED khmer/tests/test_nodegraph.py::test_bad_primes_list PASSED khmer/tests/test_nodegraph.py::test_consume_absentfasta_with_reads_parser PASSED khmer/tests/test_nodegraph.py::test_bad_primes PASSED khmer/tests/test_nodegraph.py::test_consume_seqfile_and_tag_with_badreads_parser PASSED khmer/tests/test_nodegraph.py::test_n_occupied_save_load PASSED khmer/tests/test_nodegraph.py::test_n_occupied_vs_countgraph PASSED khmer/tests/test_nodegraph.py::test_n_occupied_vs_countgraph_another_size PASSED khmer/tests/test_nodegraph.py::test_traverse_linear_path PASSED khmer/tests/test_nodegraph.py::test_find_high_degree_nodes PASSED khmer/tests/test_nodegraph.py::test_find_high_degree_nodes_2 PASSED khmer/tests/test_nodegraph.py::test_traverse_linear_path_2 PASSED khmer/tests/test_nodegraph.py::test_traverse_linear_path_3_stopgraph PASSED khmer/tests/test_nodegraph.py::test_assemble_linear_path_bad_seed PASSED khmer/tests/test_nodegraph.py::test_create_matching_nodegraph[4-100000.0] PASSED khmer/tests/test_nodegraph.py::test_create_matching_nodegraph[6-100000.0] PASSED khmer/tests/test_nodegraph.py::test_create_matching_nodegraph[8-100000.0] PASSED khmer/tests/test_nodegraph.py::test_create_matching_nodegraph[5-1000000.0] PASSED khmer/tests/test_nodegraph.py::test_create_matching_nodegraph[7-1000000.0] PASSED khmer/tests/test_nodegraph.py::test_create_matching_nodegraph[9-1000000.0] PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_indent PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_loadgraph_with_args PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_empty_file PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_quiet PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_unpaired_final_read PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_sanity_check_0 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_sanity_check_1 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_sanity_check_2 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_sanity_check_3 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_unforced_badfile PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_contradictory_args PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_stdout_3 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_report_fp PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_report_fp_hifreq PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_unpaired_and_paired PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_count_kmers_PE PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_double_file_name PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_stdin_no_out PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_overwrite PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_version PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_2 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_paired PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_paired_fq PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_impaired PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_force PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_no_bigcount PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_empty PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_emptycountgraph PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_fpr PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_streaming_0 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_streaming_1 PASSED khmer/tests/test_normalize_by_median.py::test_diginorm_basic_functionality_1 PASSED khmer/tests/test_normalize_by_median.py::test_diginorm_basic_functionality_2 PASSED khmer/tests/test_normalize_by_median.py::test_diginorm_basic_functionality_3 PASSED khmer/tests/test_normalize_by_median.py::test_diginorm_basic_functionality_4 PASSED khmer/tests/test_normalize_by_median.py::test_diginorm_basic_functionality_5 PASSED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_outfile_closed_err PASSED khmer/tests/test_oxli_functions.py::test_estimate_functions_1 PASSED khmer/tests/test_oxli_functions.py::test_estimate_functions_namedtup PASSED khmer/tests/test_oxli_functions.py::test_optimal_size_function PASSED khmer/tests/test_oxli_functions.py::test_output_gen PASSED khmer/tests/test_read_aligner.py::test_graph_attribute PASSED khmer/tests/test_read_aligner.py::test_align_nothing PASSED khmer/tests/test_read_aligner.py::test_alignnocov PASSED khmer/tests/test_read_aligner.py::test_align_middle PASSED khmer/tests/test_read_aligner.py::test_align_middle_trunc PASSED khmer/tests/test_read_aligner.py::test_align_middle_trunc_2 PASSED khmer/tests/test_read_aligner.py::test_align_fwd_nothing PASSED khmer/tests/test_read_aligner.py::test_align_fwd_nocov PASSED khmer/tests/test_read_aligner.py::test_align_fwd_middle PASSED khmer/tests/test_read_aligner.py::test_align_fwd_middle_trunc PASSED khmer/tests/test_read_aligner.py::test_align_fwd_middle_trunc_2 PASSED khmer/tests/test_read_aligner.py::test_align_fwd_covs_1 PASSED khmer/tests/test_read_aligner.py::test_align_fwd_covs_2 PASSED khmer/tests/test_read_aligner.py::test_align_fwd_covs_3 PASSED khmer/tests/test_read_aligner.py::test_align_fwd_covs_4 PASSED khmer/tests/test_read_aligner.py::test_align_fwd_covs_5 PASSED khmer/tests/test_read_aligner.py::test_simple_readalign PASSED khmer/tests/test_read_aligner.py::test_readalign PASSED khmer/tests/test_read_aligner.py::test_readaligner_load PASSED khmer/tests/test_read_handling.py::test_interleave_read_stdout PASSED khmer/tests/test_read_handling.py::test_interleave_read_seq1_fq PASSED khmer/tests/test_read_handling.py::test_interleave_read_badleft_badright PASSED khmer/tests/test_read_handling.py::test_interleave_reads_1_fq PASSED khmer/tests/test_read_handling.py::test_interleave_reads_no_reformat PASSED khmer/tests/test_read_handling.py::test_interleave_reads_broken_fq PASSED khmer/tests/test_read_handling.py::test_interleave_reads_broken_fq_2 PASSED khmer/tests/test_read_handling.py::test_interleave_reads_broken_fq_3 PASSED khmer/tests/test_read_handling.py::test_interleave_reads_broken_fq_5 PASSED khmer/tests/test_read_handling.py::test_interleave_reads_2_fa PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_1_fa PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_2_fq PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_2_mixed_fq_require_pair PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_2_stdin_no_out PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_2_mixed_fq PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_2_mixed_fq_orphans_to_file PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_2_mixed_fq_gzfile PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_2_mixed_fq_broken_pairing_format PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_3_output_dir PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_3_output_files PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_3_output_files_left PASSED khmer/tests/test_read_handling.py::test_split_paired_reads_3_output_files_right PASSED khmer/tests/test_read_handling.py::test_extract_paired_reads_unpaired PASSED khmer/tests/test_read_handling.py::test_extract_paired_reads_1_fa PASSED khmer/tests/test_read_handling.py::test_extract_paired_reads_2_fq PASSED khmer/tests/test_read_handling.py::test_extract_paired_reads_3_output_dir PASSED khmer/tests/test_read_handling.py::test_extract_paired_reads_4_output_files PASSED khmer/tests/test_read_handling.py::test_extract_paired_reads_5_stdin_error PASSED khmer/tests/test_read_handling.py::test_read_bundler PASSED khmer/tests/test_read_handling.py::test_read_bundler_single_read PASSED khmer/tests/test_read_handling.py::test_read_bundler_empty_file PASSED khmer/tests/test_read_handling.py::test_read_bundler_empty_list PASSED khmer/tests/test_read_parsers.py::test_read_type_basic PASSED khmer/tests/test_read_parsers.py::test_read_quality_none PASSED khmer/tests/test_read_parsers.py::test_read_type_attributes PASSED khmer/tests/test_read_parsers.py::test_read_type_cleaned_seq PASSED khmer/tests/test_read_parsers.py::test_read_properties PASSED khmer/tests/test_read_parsers.py::test_read_properties_fa PASSED khmer/tests/test_read_parsers.py::test_with_default_arguments PASSED khmer/tests/test_read_parsers.py::test_num_reads PASSED khmer/tests/test_read_parsers.py::test_num_reads_threads PASSED khmer/tests/test_read_parsers.py::test_num_reads_truncated PASSED khmer/tests/test_read_parsers.py::test_gzip_decompression PASSED khmer/tests/test_read_parsers.py::test_gzip_decompression_truncated PASSED khmer/tests/test_read_parsers.py::test_gzip_decompression_truncated_pairiter PASSED khmer/tests/test_read_parsers.py::test_bzip2_decompression PASSED khmer/tests/test_read_parsers.py::test_bzip2_decompression_truncated PASSED khmer/tests/test_read_parsers.py::test_bzip2_decompression_truncated_pairiter PASSED khmer/tests/test_read_parsers.py::test_badbzip2 PASSED khmer/tests/test_read_parsers.py::test_with_multiple_threads PASSED khmer/tests/test_read_parsers.py::test_with_multiple_threads_big PASSED khmer/tests/test_read_parsers.py::test_old_illumina_pair_mating PASSED khmer/tests/test_read_parsers.py::test_casava_1_8_pair_mating PASSED khmer/tests/test_read_parsers.py::test_read_truncated PASSED khmer/tests/test_read_parsers.py::test_iterator_identities PASSED khmer/tests/test_read_parsers.py::test_read_pair_iterator_in_error_mode_xfail PASSED khmer/tests/test_read_parsers.py::test_read_pair_iterator_in_error_mode_xfail_osxsafe PASSED khmer/tests/test_read_parsers.py::test_constructor PASSED khmer/tests/test_read_parsers.py::test_iternext PASSED khmer/tests/test_read_parsers.py::test_clean_seq PASSED khmer/tests/test_read_parsers.py::test_error_badly_formatted_file PASSED khmer/tests/test_read_parsers.py::test_error_file_does_not_exist PASSED khmer/tests/test_sandbox_scripts.py::test_import_succeeds[filename0] SKIPPED khmer/tests/test_sandbox_scripts.py::test_sweep_reads SKIPPED khmer/tests/test_sandbox_scripts.py::test_sweep_reads_fq SKIPPED khmer/tests/test_sandbox_scripts.py::test_sweep_reads_2 SKIPPED khmer/tests/test_sandbox_scripts.py::test_sweep_reads_3 SKIPPED khmer/tests/test_sandbox_scripts.py::test_collect_reads SKIPPED khmer/tests/test_sandbox_scripts.py::test_saturate_by_median SKIPPED khmer/tests/test_sandbox_scripts.py::test_count_kmers_1 SKIPPED khmer/tests/test_sandbox_scripts.py::test_count_kmers_2_single SKIPPED khmer/tests/test_sandbox_scripts.py::test_multirename_fasta SKIPPED khmer/tests/test_sandbox_scripts.py::test_extract_compact_dbg_1 SKIPPED khmer/tests/test_script_arguments.py::test_check_space PASSED khmer/tests/test_script_arguments.py::test_check_tablespace[countgraph-1] PASSED khmer/tests/test_script_arguments.py::test_check_tablespace[smallcountgraph-2] PASSED khmer/tests/test_script_arguments.py::test_check_tablespace[nodegraph-8] PASSED khmer/tests/test_script_arguments.py::test_check_tablespace_nodegraph[countgraph-3.0 million buckets] PASSED khmer/tests/test_script_arguments.py::test_check_tablespace_nodegraph[smallcountgraph-6.0 million buckets] PASSED khmer/tests/test_script_arguments.py::test_check_tablespace_nodegraph[nodegraph-24.0 million buckets] PASSED khmer/tests/test_script_arguments.py::test_normal_help PASSED khmer/tests/test_script_arguments.py::test_expert_help PASSED khmer/tests/test_script_arguments.py::test_check_space_force PASSED khmer/tests/test_script_arguments.py::test_check_tablespace_force PASSED khmer/tests/test_script_arguments.py::test_invalid_file_warn PASSED khmer/tests/test_script_arguments.py::test_check_valid_stdin_nowarn PASSED khmer/tests/test_script_arguments.py::test_create_countgraph_1 PASSED khmer/tests/test_script_arguments.py::test_create_countgraph_2 PASSED khmer/tests/test_script_arguments.py::test_create_countgraph_3 PASSED khmer/tests/test_script_arguments.py::test_create_countgraph_4 PASSED khmer/tests/test_script_arguments.py::test_create_countgraph_5 PASSED khmer/tests/test_script_arguments.py::test_create_countgraph_4_multiplier PASSED khmer/tests/test_script_arguments.py::test_create_nodegraph_1 PASSED khmer/tests/test_script_arguments.py::test_create_nodegraph_2 PASSED khmer/tests/test_script_arguments.py::test_create_nodegraph_3 PASSED khmer/tests/test_script_arguments.py::test_create_nodegraph_4 PASSED khmer/tests/test_script_arguments.py::test_create_nodegraph_5 PASSED khmer/tests/test_script_arguments.py::test_create_nodegraph_4_multiplier PASSED khmer/tests/test_script_arguments.py::test_report_on_config_bad_graphtype PASSED khmer/tests/test_script_arguments.py::test_fail_calculate_foograph_size PASSED khmer/tests/test_script_arguments.py::test_memory_setting PASSED khmer/tests/test_script_output.py::test_normalize_by_median_k21_C20_M1e7 PASSED khmer/tests/test_script_output.py::test_normalize_by_median_k21_C15_M1e7 PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_C0_M1e7_diginorm PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_C0_M1e7_diginorm_dn15 PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_C2_M1e7_diginorm_dn15 PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_M1e7_C2 PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_M1e7_C3 PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_M1e7_C4 PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_M1e7_C4_variable PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_M1e7_C4_variable_Z25 PASSED khmer/tests/test_script_output.py::test_trim_low_abund_k21_M1e7_C4_variable_Z15 PASSED khmer/tests/test_scripts.py::test_check_space PASSED khmer/tests/test_scripts.py::test_load_into_counting PASSED khmer/tests/test_scripts.py::test_load_into_counting_smallcount PASSED khmer/tests/test_scripts.py::test_load_into_counting_quiet PASSED khmer/tests/test_scripts.py::test_load_into_counting_autoargs_0 PASSED khmer/tests/test_scripts.py::test_load_into_counting_autoargs_1 PASSED khmer/tests/test_scripts.py::test_load_into_count_graphsize_warning PASSED khmer/tests/test_scripts.py::test_load_into_counting_max_memory_usage_parameter PASSED khmer/tests/test_scripts.py::test_load_into_counting_abundance_dist_nobig PASSED khmer/tests/test_scripts.py::test_load_into_counting_abundance_dist_squashing PASSED khmer/tests/test_scripts.py::test_load_into_counting_nonwritable FAILED khmer/tests/test_scripts.py::test_load_into_counting_fail PASSED khmer/tests/test_scripts.py::test_load_into_counting_multifile PASSED khmer/tests/test_scripts.py::test_load_into_counting_tsv PASSED khmer/tests/test_scripts.py::test_load_into_counting_json PASSED khmer/tests/test_scripts.py::test_load_into_counting_bad_summary_fmt PASSED khmer/tests/test_scripts.py::test_load_into_counting_info_version PASSED khmer/tests/test_scripts.py::test_filter_stoptags PASSED khmer/tests/test_scripts.py::test_filter_stoptags_fq PASSED khmer/tests/test_scripts.py::test_count_median PASSED khmer/tests/test_scripts.py::test_count_median_fq_csv PASSED khmer/tests/test_scripts.py::test_count_median_fq_csv_stdout PASSED khmer/tests/test_scripts.py::test_load_graph PASSED khmer/tests/test_scripts.py::test_load_graph_no_tags PASSED khmer/tests/test_scripts.py::test_load_graph_fail PASSED khmer/tests/test_scripts.py::test_load_graph_write_fp PASSED khmer/tests/test_scripts.py::test_load_graph_multithread PASSED khmer/tests/test_scripts.py::test_load_graph_max_memory_usage_parameter PASSED khmer/tests/test_scripts.py::test_partition_graph_1 PASSED khmer/tests/test_scripts.py::test_partition_graph_nojoin_k21 PASSED khmer/tests/test_scripts.py::test_partition_load_empty_pmap PASSED khmer/tests/test_scripts.py::test_partition_graph_nojoin_stoptags PASSED khmer/tests/test_scripts.py::test_partition_graph_big_traverse PASSED khmer/tests/test_scripts.py::test_partition_graph_no_big_traverse PASSED khmer/tests/test_scripts.py::test_partition_find_knots_execute PASSED khmer/tests/test_scripts.py::test_partition_find_knots_existing_stoptags PASSED khmer/tests/test_scripts.py::test_partition_graph_too_many_threads PASSED khmer/tests/test_scripts.py::test_annotate_partitions PASSED khmer/tests/test_scripts.py::test_annotate_partitions_2 PASSED khmer/tests/test_scripts.py::test_extract_partitions PASSED khmer/tests/test_scripts.py::test_extract_paired_inconsistent_formats PASSED khmer/tests/test_scripts.py::test_extract_partitions_header_whitespace PASSED khmer/tests/test_scripts.py::test_extract_partitions_fq PASSED khmer/tests/test_scripts.py::test_extract_partitions_output_unassigned PASSED khmer/tests/test_scripts.py::test_extract_partitions_no_output_groups PASSED khmer/tests/test_scripts.py::test_extract_partitions_pid_0 PASSED khmer/tests/test_scripts.py::test_extract_partitions_multi_groups PASSED khmer/tests/test_scripts.py::test_extract_partitions_no_groups PASSED khmer/tests/test_scripts.py::test_abundance_dist PASSED khmer/tests/test_scripts.py::test_abundance_dist_quiet PASSED khmer/tests/test_scripts.py::test_abundance_dist_stdout PASSED khmer/tests/test_scripts.py::test_abundance_dist_nobigcount PASSED khmer/tests/test_scripts.py::test_abundance_dist_threaded PASSED khmer/tests/test_scripts.py::test_abundance_dist_single_csv PASSED khmer/tests/test_scripts.py::test_abundance_dist_single_nobigcount PASSED khmer/tests/test_scripts.py::test_abundance_dist_single_smallcount PASSED khmer/tests/test_scripts.py::test_abundance_dist_single_nosquash PASSED khmer/tests/test_scripts.py::test_abundance_dist_single_quiet PASSED khmer/tests/test_scripts.py::test_abundance_dist_single_savegraph PASSED khmer/tests/test_scripts.py::test_do_partition PASSED khmer/tests/test_scripts.py::test_do_partition_no_big_traverse PASSED khmer/tests/test_scripts.py::test_do_partition_2 PASSED khmer/tests/test_scripts.py::test_do_partition_2_fq PASSED khmer/tests/test_scripts.py::test_make_initial_stoptags PASSED khmer/tests/test_scripts.py::test_make_initial_stoptags_load_stoptags PASSED khmer/tests/test_scripts.py::test_sample_reads_randomly PASSED khmer/tests/test_scripts.py::test_sample_reads_randomly_force_single PASSED khmer/tests/test_scripts.py::test_sample_reads_randomly_force_single_outfile PASSED khmer/tests/test_scripts.py::test_sample_reads_randomly_fq PASSED khmer/tests/test_scripts.py::test_sample_reads_randomly_stdin_no_out PASSED khmer/tests/test_scripts.py::test_fastq_to_fasta PASSED khmer/tests/test_scripts.py::test_fastq_to_fasta_streaming_compressed_gzip PASSED khmer/tests/test_scripts.py::test_fastq_to_fasta_streaming_compressed_bzip PASSED khmer/tests/test_scripts.py::test_extract_long_sequences_fa PASSED khmer/tests/test_scripts.py::test_extract_long_sequences_fq PASSED khmer/tests/test_scripts.py::test_sample_reads_randomly_S PASSED khmer/tests/test_scripts.py::test_screed_streaming_ufa PASSED khmer/tests/test_scripts.py::test_screed_streaming_ufq PASSED khmer/tests/test_scripts.py::test_screed_streaming_bzipfq PASSED khmer/tests/test_scripts.py::test_screed_streaming_bzipfa PASSED khmer/tests/test_scripts.py::test_read_parser_streaming_ufa PASSED khmer/tests/test_scripts.py::test_read_parser_streaming_ufq PASSED khmer/tests/test_scripts.py::test_read_parser_streaming_gzfq PASSED khmer/tests/test_scripts.py::test_read_parser_streaming_gzfa PASSED khmer/tests/test_scripts.py::test_readstats PASSED khmer/tests/test_scripts.py::test_readstats_csv PASSED khmer/tests/test_scripts.py::test_readstats_output PASSED khmer/tests/test_scripts.py::test_readstats_empty PASSED khmer/tests/test_scripts.py::test_trim_low_abund_1 PASSED khmer/tests/test_scripts.py::test_trim_low_abund_1_duplicate_filename_err PASSED khmer/tests/test_scripts.py::test_trim_low_abund_1_stdin_err PASSED khmer/tests/test_scripts.py::test_trim_low_abund_2 PASSED khmer/tests/test_scripts.py::test_trim_low_abund_2_o_gzip PASSED khmer/tests/test_scripts.py::test_trim_low_abund_3_fq_retained PASSED khmer/tests/test_scripts.py::test_trim_low_abund_4_retain_low_abund PASSED khmer/tests/test_scripts.py::test_trim_low_abund_5_trim_high_abund PASSED khmer/tests/test_scripts.py::test_trim_low_abund_6_trim_high_abund_Z PASSED khmer/tests/test_scripts.py::test_trim_low_abund_keep_paired PASSED khmer/tests/test_scripts.py::test_trim_low_abund_keep_paired_casava18 PASSED khmer/tests/test_scripts.py::test_trim_low_abund_highfpr PASSED khmer/tests/test_scripts.py::test_trim_low_abund_trimtest PASSED khmer/tests/test_scripts.py::test_trim_low_abund_trimtest_after_load PASSED khmer/tests/test_scripts.py::test_trim_low_abund_trimtest_savegraph PASSED khmer/tests/test_scripts.py::test_trim_low_abund_no_summary_info_by_default PASSED khmer/tests/test_scripts.py::test_trim_low_abund_summary_info_json PASSED khmer/tests/test_scripts.py::test_trim_low_abund_summary_info_tsv PASSED khmer/tests/test_scripts.py::test_trim_low_abund_stdout PASSED khmer/tests/test_scripts.py::test_trim_low_abund_output_named PASSED khmer/tests/test_scripts.py::test_trim_low_abund_diginorm_coverage_err PASSED khmer/tests/test_scripts.py::test_trim_low_abund_diginorm_single_pass PASSED khmer/tests/test_scripts.py::test_trim_low_abund_varcov_err PASSED khmer/tests/test_scripts.py::test_trim_low_abund_single_pass PASSED khmer/tests/test_scripts.py::test_trim_low_abund_quiet PASSED khmer/tests/test_scripts.py::test_trim_low_abund_reporting PASSED khmer/tests/test_scripts.py::test_roundtrip_casava_format_1 PASSED khmer/tests/test_scripts.py::test_roundtrip_casava_format_2 PASSED khmer/tests/test_scripts.py::test_existence_failure PASSED khmer/tests/test_scripts.py::test_roundtrip_commented_format PASSED khmer/tests/test_scripts.py::test_unique_kmers_defaults PASSED khmer/tests/test_scripts.py::test_unique_kmers_report_fp PASSED khmer/tests/test_scripts.py::test_unique_kmers_diagnostics PASSED khmer/tests/test_scripts.py::test_unique_kmers_multiple_inputs PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[abundance-dist-single.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[abundance-dist.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[annotate-partitions.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[count-median.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[do-partition.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[extract-long-sequences.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[extract-partitions.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[fastq-to-fasta.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[filter-abund-single.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[filter-abund.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[filter-stoptags.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[find-knots.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[interleave-reads.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[load-graph.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[load-into-counting.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[make-initial-stoptags.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[merge-partitions.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[normalize-by-median.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[partition-graph.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[readstats.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[sample-reads-randomly.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[split-paired-reads.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[trim-low-abund.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[unique-kmers.py] PASSED khmer/tests/test_scripts.py::test_version_and_basic_citation[extract-paired-reads.py] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_seqfile[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_seqfile[Counttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_seqfile[SmallCountgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_seqfile[SmallCounttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read[Counttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read[SmallCountgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read[SmallCounttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read_cleaned_seq[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read_cleaned_seq[Counttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read_cleaned_seq[SmallCountgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_consume_read_by_read_cleaned_seq[SmallCounttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_abundance_distribution[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_abundance_distribution[Counttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_abundance_distribution[SmallCountgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_abundance_distribution[SmallCounttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_lowercase[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_lowercase[Counttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_lowercase[SmallCountgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_lowercase[SmallCounttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_lowercase[Nodegraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_lowercase[Nodetable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_N[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_N[Counttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_N[SmallCountgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_N[SmallCounttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_bad_dna[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_bad_dna[Counttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_bad_dna[SmallCountgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_functions_bad_dna[SmallCounttable] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_output_partitions[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_output_partitions[Nodegraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_on_stoptags[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_read_cleaning_trim_on_stoptags[Nodegraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_seqfile_and_tag[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_seqfile_and_tag[Nodegraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_partitioned_seqfile[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_partitioned_seqfile[Nodegraph] PASSED khmer/tests/test_sequence_validation.py::test_output_partitioned_file[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_output_partitioned_file[Nodegraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_seqfile_and_tag_with_labels[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_seqfile_and_tag_with_labels[Nodegraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_partitioned_seqfile_and_label[Countgraph] PASSED khmer/tests/test_sequence_validation.py::test_consume_partitioned_seqfile_and_label[Nodegraph] PASSED khmer/tests/test_streaming_io.py::test_interleave_split_1 PASSED khmer/tests/test_streaming_io.py::test_interleave_split_2_fail PASSED khmer/tests/test_streaming_io.py::test_interleave_split_3_out1 PASSED khmer/tests/test_streaming_io.py::test_interleave_split_3_out2 PASSED khmer/tests/test_streaming_io.py::test_interleave_split_3_out0 PASSED khmer/tests/test_streaming_io.py::test_extract_paired_pe PASSED khmer/tests/test_streaming_io.py::test_extract_paired_se PASSED khmer/tests/test_streaming_io.py::test_extract_paired_stdin_equivalence PASSED khmer/tests/test_streaming_io.py::test_extract_paired_se_fail PASSED khmer/tests/test_streaming_io.py::test_norm_by_median_1 PASSED khmer/tests/test_streaming_io.py::test_norm_by_median_2_fail PASSED khmer/tests/test_streaming_io.py::test_sample_reads_randomly_1 PASSED khmer/tests/test_streaming_io.py::test_sample_reads_randomly_2_fail PASSED khmer/tests/test_streaming_io.py::test_extract_long_sequences_1 PASSED khmer/tests/test_streaming_io.py::test_fastq_to_fasta_1 PASSED khmer/tests/test_streaming_io.py::test_load_into_counting_1 PASSED khmer/tests/test_streaming_io.py::test_load_graph_1 PASSED khmer/tests/test_streaming_io.py::test_filter_abund_1 PASSED khmer/tests/test_streaming_io.py::test_filter_abund_2_fail PASSED khmer/tests/test_streaming_io.py::test_abundance_dist_1 PASSED khmer/tests/test_streaming_io.py::test_trim_low_abund_1 PASSED khmer/tests/test_streaming_io.py::test_trim_low_abund_smallcount PASSED khmer/tests/test_streaming_io.py::test_trim_low_abund_1_gzip_o PASSED khmer/tests/test_streaming_io.py::test_trim_low_abund_2_fail PASSED khmer/tests/test_streaming_io.py::test_count_median_1 PASSED khmer/tests/test_streaming_io.py::test_readstats_1 PASSED khmer/tests/test_streaming_io.py::test_unique_kmers_stream_out_fasta PASSED khmer/tests/test_streaming_io.py::test_unique_kmers_stream_out_fastq_with_N PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_3_merge_013 PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_3_merge_023 PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_5_merge_046 PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_random_20_a_succ PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_random_20_a_succ_II PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_random_20_a_succ_III PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_random_20_a_succ_IV PASSED khmer/tests/test_subset_graph.py::Test_RandomData::test_random_20_a_succ_IV_save PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_load_merge PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_load_merge_truncate PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_load_merge_2 PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_load_merge_nexist PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_merge_from_disk PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_merge_from_disk_2 PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_merge_from_disk_file_not_exist PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_merge_from_disk_file_bad_type PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_merge_from_disk_file_version PASSED khmer/tests/test_subset_graph.py::Test_SaveLoadPmap::test_save_merge_from_disk_ksize PASSED khmer/tests/test_subset_graph.py::test_save_load_merge_on_graph PASSED khmer/tests/test_subset_graph.py::test_save_load_on_graph_truncate PASSED khmer/tests/test_subset_graph.py::test_output_partitions PASSED khmer/tests/test_subset_graph.py::test_tiny_real_partitions PASSED khmer/tests/test_subset_graph.py::test_small_real_partitions PASSED khmer/tests/test_subset_graph.py::test_partition_on_abundance_1 PASSED khmer/tests/test_subset_graph.py::test_partition_on_abundance_2 PASSED khmer/tests/test_subset_graph.py::test_partition_on_abundance_3 PASSED khmer/tests/test_subset_graph.py::test_partition_overlap_2 PASSED khmer/tests/test_tabletype.py::test_presence[Countgraph] PASSED khmer/tests/test_tabletype.py::test_presence[Counttable] PASSED khmer/tests/test_tabletype.py::test_presence[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_presence[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_presence[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_presence[Nodetable] PASSED khmer/tests/test_tabletype.py::test_bad_create[Countgraph] PASSED khmer/tests/test_tabletype.py::test_bad_create[Counttable] PASSED khmer/tests/test_tabletype.py::test_bad_create[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_bad_create[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_bad_create[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_bad_create[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_ksize[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_ksize[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_ksize[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_ksize[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_ksize[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_ksize[Nodetable] PASSED khmer/tests/test_tabletype.py::test_hash[Countgraph] PASSED khmer/tests/test_tabletype.py::test_hash[Counttable] PASSED khmer/tests/test_tabletype.py::test_hash[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_hash[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_hash[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_hash[Nodetable] PASSED khmer/tests/test_tabletype.py::test_hash_bad_dna[Countgraph] PASSED khmer/tests/test_tabletype.py::test_hash_bad_dna[Counttable] PASSED khmer/tests/test_tabletype.py::test_hash_bad_dna[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_hash_bad_dna[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_hash_bad_dna[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_hash_bad_dna[Nodetable] PASSED khmer/tests/test_tabletype.py::test_hash_bad_length[Countgraph] PASSED khmer/tests/test_tabletype.py::test_hash_bad_length[Counttable] PASSED khmer/tests/test_tabletype.py::test_hash_bad_length[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_hash_bad_length[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_hash_bad_length[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_hash_bad_length[Nodetable] PASSED khmer/tests/test_tabletype.py::test_reverse_hash[Countgraph] PASSED khmer/tests/test_tabletype.py::test_reverse_hash[Counttable] SKIPPED khmer/tests/test_tabletype.py::test_reverse_hash[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_reverse_hash[SmallCounttable] SKIPPED khmer/tests/test_tabletype.py::test_reverse_hash[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_reverse_hash[Nodetable] SKIPPED khmer/tests/test_tabletype.py::test_hashsizes[Countgraph] PASSED khmer/tests/test_tabletype.py::test_hashsizes[Counttable] PASSED khmer/tests/test_tabletype.py::test_hashsizes[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_hashsizes[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_hashsizes[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_hashsizes[Nodetable] PASSED khmer/tests/test_tabletype.py::test_add_hashval[Countgraph] PASSED khmer/tests/test_tabletype.py::test_add_hashval[Counttable] PASSED khmer/tests/test_tabletype.py::test_add_hashval[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_add_hashval[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_add_hashval[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_add_hashval[Nodetable] PASSED khmer/tests/test_tabletype.py::test_add_dna_kmer[Countgraph] PASSED khmer/tests/test_tabletype.py::test_add_dna_kmer[Counttable] PASSED khmer/tests/test_tabletype.py::test_add_dna_kmer[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_add_dna_kmer[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_add_dna_kmer[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_add_dna_kmer[Nodetable] PASSED khmer/tests/test_tabletype.py::test_add_bad_dna_kmer[Countgraph] PASSED khmer/tests/test_tabletype.py::test_add_bad_dna_kmer[Counttable] PASSED khmer/tests/test_tabletype.py::test_add_bad_dna_kmer[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_add_bad_dna_kmer[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_add_bad_dna_kmer[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_add_bad_dna_kmer[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_hashval[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_hashval[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_hashval[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_hashval[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_hashval[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_hashval[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_hashval_rc[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_hashval_rc[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_hashval_rc[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_hashval_rc[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_hashval_rc[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_hashval_rc[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_dna_kmer[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_dna_kmer[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_dna_kmer[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_dna_kmer[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_dna_kmer[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_dna_kmer[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_bad_dna_kmer[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_bad_dna_kmer[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_bad_dna_kmer[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_bad_dna_kmer[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_bad_dna_kmer[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_bad_dna_kmer[Nodetable] PASSED khmer/tests/test_tabletype.py::test_consume_and_count[Countgraph] PASSED khmer/tests/test_tabletype.py::test_consume_and_count[Counttable] PASSED khmer/tests/test_tabletype.py::test_consume_and_count[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_consume_and_count[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_consume_and_count[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_consume_and_count[Nodetable] PASSED khmer/tests/test_tabletype.py::test_consume_and_count_bad_dna[Countgraph] PASSED khmer/tests/test_tabletype.py::test_consume_and_count_bad_dna[Counttable] PASSED khmer/tests/test_tabletype.py::test_consume_and_count_bad_dna[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_consume_and_count_bad_dna[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_consume_and_count_bad_dna[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_consume_and_count_bad_dna[Nodetable] PASSED khmer/tests/test_tabletype.py::test_consume_short[Countgraph] PASSED khmer/tests/test_tabletype.py::test_consume_short[Counttable] PASSED khmer/tests/test_tabletype.py::test_consume_short[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_consume_short[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_consume_short[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_consume_short[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_kmer_counts[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_kmer_counts[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_kmer_counts[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_kmer_counts[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_kmer_counts[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_kmer_counts[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_kmer_hashes[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_kmer_hashes[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_kmer_hashes[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_kmer_hashes[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_kmer_hashes[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_kmer_hashes[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_min_count[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_min_count[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_min_count[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_min_count[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_min_count[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_min_count[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_kmers[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_kmers[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_kmers[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_kmers[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_kmers[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_kmers[Nodetable] PASSED khmer/tests/test_tabletype.py::test_trim_on_abundance[Countgraph] PASSED khmer/tests/test_tabletype.py::test_trim_on_abundance[Counttable] PASSED khmer/tests/test_tabletype.py::test_trim_on_abundance[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_trim_on_abundance[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_trim_on_abundance[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_trim_on_abundance[Nodetable] PASSED khmer/tests/test_tabletype.py::test_trim_below_abundance[Countgraph] PASSED khmer/tests/test_tabletype.py::test_trim_below_abundance[Counttable] PASSED khmer/tests/test_tabletype.py::test_trim_below_abundance[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_trim_below_abundance[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_trim_below_abundance[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_trim_below_abundance[Nodetable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions[Countgraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions[Counttable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions[Nodetable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_6[Countgraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_6[Counttable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_6[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_6[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_6[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_6[Nodetable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_5[Countgraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_5[Counttable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_5[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_5[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_5[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_find_spectral_error_positions_5[Nodetable] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile_reads_parser[Countgraph] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile_reads_parser[Counttable] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile_reads_parser[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile_reads_parser[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile_reads_parser[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile_reads_parser[Nodetable] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile[Countgraph] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile[Counttable] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_consume_seqfile[Nodetable] PASSED khmer/tests/test_tabletype.py::test_save_load[Countgraph] PASSED khmer/tests/test_tabletype.py::test_save_load[Counttable] PASSED khmer/tests/test_tabletype.py::test_save_load[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_save_load[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_save_load[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_save_load[Nodetable] PASSED khmer/tests/test_tabletype.py::test_get_bigcount[Countgraph] PASSED khmer/tests/test_tabletype.py::test_get_bigcount[Counttable] PASSED khmer/tests/test_tabletype.py::test_get_bigcount[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_get_bigcount[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_get_bigcount[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_get_bigcount[Nodetable] PASSED khmer/tests/test_tabletype.py::test_set_bigcount[Countgraph] PASSED khmer/tests/test_tabletype.py::test_set_bigcount[Counttable] PASSED khmer/tests/test_tabletype.py::test_set_bigcount[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_set_bigcount[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_set_bigcount[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_set_bigcount[Nodetable] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A[Countgraph] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A[Counttable] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A[Nodetable] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A_readparser[Countgraph] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A_readparser[Counttable] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A_readparser[SmallCountgraph] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A_readparser[SmallCounttable] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A_readparser[Nodegraph] PASSED khmer/tests/test_tabletype.py::test_abund_dist_A_readparser[Nodetable] PASSED khmer/tests/test_threaded_sequence_processor.py::test_basic PASSED khmer/tests/test_threaded_sequence_processor.py::test_basic_fastq_like PASSED khmer/tests/test_threaded_sequence_processor.py::test_odd PASSED khmer/tests/test_threaded_sequence_processor.py::test_basic_2thread PASSED khmer/tests/test_threaded_sequence_processor.py::test_paired_2thread PASSED khmer/tests/test_threaded_sequence_processor.py::test_paired_2thread_more_seq PASSED khmer/tests/test_version.py::test_python_and_c_match_base PASSED =================================== FAILURES =================================== ___________________________ test_save_fail_readonly ____________________________ @pytest.mark.noroot def test_save_fail_readonly(): lb_pre = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb_pre.consume_seqfile_and_tag_with_labels(filename) # save labels to a file savepath = utils.get_temp_filename('saved.labels') fp = open(savepath, 'w') fp.close() os.chmod(savepath, 0x444) try: lb_pre.save_labels_and_tags(savepath) > assert 0, "this should fail: read-only file" E AssertionError: this should fail: read-only file E assert 0 khmer/tests/test_labelhash.py:188: AssertionError _____________________ test_load_into_counting_nonwritable ______________________ @pytest.mark.noroot def test_load_into_counting_nonwritable(): script = 'load-into-counting.py' args = ['-x', '1e3', '-N', '2', '-k', '20'] outfile = utils.get_temp_filename('test-nonwritable') with open(outfile, 'w') as fout: fout.write("This file is non-writable (after this)") os.chmod(outfile, stat.S_IWOTH | stat.S_IRUSR) infile = utils.get_test_data('test-abund-read-2.fa') args.extend([outfile, infile]) (status, out, err) = utils.runscript(script, args, fail_ok=True) > assert 'does not have write permission; exiting' in err, err E AssertionError: E || This is the script load-into-counting.py in khmer. E || You are running khmer version 2.1.2 E || You are also using screed version 1.0 E || E || If you use this script in a publication, please cite EACH of the following: E || E || * MR Crusoe et al., 2015. http://dx.doi.org/10.12688/f1000research.6924.1 E || * Q Zhang et al., http://dx.doi.org/10.1371/journal.pone.0101271 E || * A. Döring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11 E || E || Please see http://khmer.readthedocs.io/en/latest/citations.html for details. E E E PARAMETERS: E - kmer size = 20 (-k) E - n tables = 2 (-N) E - max tablesize = 1e+03 (-x) E Estimated memory usage is 0.0 Gb (2e+03 bytes = 2 bytes x 1e+03 entries / 1 entries per byte) E -------- E Saving k-mer countgraph to /tmp/khmertest_hc8mzwt7/test-nonwritable E Loading kmers from sequences in ['/build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.fa'] E making countgraph E consuming input /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.fa E Total number of unique k-mers: 94 E saving /tmp/khmertest_hc8mzwt7/test-nonwritable E fp rate estimated to be 0.008 E DONE. E wrote to: /tmp/khmertest_hc8mzwt7/test-nonwritable.info E E assert 'does not have write permission; exiting' in '\n|| This is the script load-into-counting.py in khmer.\n|| You are running khmer version 2.1.2\n|| You are also usin...zwt7/test-nonwritable\nfp rate estimated to be 0.008\nDONE.\nwrote to: /tmp/khmertest_hc8mzwt7/test-nonwritable.info\n' khmer/tests/test_scripts.py:246: AssertionError ----------------------------- Captured stdout call ----------------------------- running: load-into-counting.py in: /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build arguments ['load-into-counting.py', '-x', '1e3', '-N', '2', '-k', '20', '/tmp/khmertest_hc8mzwt7/test-nonwritable', '/build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build/khmer/tests/test-data/test-abund-read-2.fa'] =============================== warnings summary =============================== .pybuild/pythonX.Y_3.6/build/khmer/tests/test_read_aligner.py::test_readalign_new yield tests are deprecated, and scheduled to be removed in pytest 4.0 -- Docs: http://doc.pytest.org/en/latest/warnings.html ============================= 24 tests deselected ============================== 2 failed, 1325 passed, 14 skipped, 24 deselected, 1 warnings in 43.73 seconds = E: pybuild pybuild:283: test: plugin custom failed with: exit code=1: cd /build/khmer-2.1.2+dfsg; export PATH=/build/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ; cd /build/khmer-2.1.2+dfsg/.pybuild/pythonX.Y_3.6/build; export PYTHONPATH=/build/khmer-2.1.2+dfsg; python3.6 -m pytest -m 'not known_failing and not jenkins and not huge' dh_auto_test: pybuild --test --test-pytest -i python{version} -p 3.6 returned exit code 13 make[1]: *** [override_dh_auto_test] Error 25 debian/rules:26: recipe for target 'override_dh_auto_test' failed make[1]: Leaving directory '/build/khmer-2.1.2+dfsg' debian/rules:16: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2