I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 19 10:59:36 +14 2022 I: pbuilder-time-stamp: 1660856376 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [tnseq-transit_3.2.1-1.dsc] I: copying [./tnseq-transit_3.2.1.orig.tar.gz] I: copying [./tnseq-transit_3.2.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Vd0kaICr/trustedkeys.kbx': General error gpgv: Signature made Fri Dec 25 08:30:31 2020 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tnseq-transit_3.2.1-1.dsc dpkg-source: info: extracting tnseq-transit in tnseq-transit-3.2.1 dpkg-source: info: unpacking tnseq-transit_3.2.1.orig.tar.gz dpkg-source: info: unpacking tnseq-transit_3.2.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_requiring_non_existing_input_data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/35737/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/35737/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/35737/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=12dfdbb231fc42e08167d3bdf37d9e95 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=35737 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.pA0Bync9yC/pbuilderrc_aAEu --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.pA0Bync9yC/b2 --logfile b2/build.log --extrapackages usrmerge tnseq-transit_3.2.1-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Jun 22 2021 bash -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash -rwxr-xr-x 1 root root 124904 Sep 23 2020 date -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd -rwxr-xr-x 1 root root 100752 Sep 23 2020 df -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir -rwxr-xr-x 1 root root 83644 Feb 8 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln -rwxr-xr-x 1 root root 55572 Feb 8 2020 login -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 8 2021 more -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 19 10:59 sh -> bash lrwxrwxrwx 1 root root 4 Aug 18 05:48 sh.distrib -> dash -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty -rwsr-xr-x 1 root root 79396 Feb 8 2021 su -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch -rwxr-xr-x 1 root root 34664 Sep 23 2020 true -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/35737/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-dev, python3-setuptools, python3-numpy, python3-scipy, python3-pil, python3-matplotlib, python3-statsmodels, python3-pubsub, bwa dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-pil; however: Package python3-pil is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-statsmodels; however: Package python3-statsmodels is not installed. pbuilder-satisfydepends-dummy depends on python3-pubsub; however: Package python3-pubsub is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} bwa{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libpipeline1{a} libpng16-16{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-patsy{a} python3-pil{a} python3-pkg-resources{a} python3-pubsub{a} python3-pyparsing{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-statsmodels{a} python3-statsmodels-lib{a} python3-tz{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} ttf-bitstream-vera{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-bottleneck python3-bs4 python3-colorama python3-cvxopt python3-html5lib python3-jinja2 python3-joblib python3-lxml python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables python3-tk python3-xlwt wget 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 74.0 MB of archives. After unpacking 301 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 mailcap all 3.69 [31.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 bwa i386 0.7.17-6+b1 [241 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 fonts-lyx all 2.3.6-1 [205 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2 [147 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libimagequant0 i386 2.12.2-1.1 [32.4 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 liblbfgsb0 i386 3.0+dfsg.3-9 [28.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 liblcms2-2 i386 2.12~rc1-2 [161 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libpython3.9 i386 3.9.2-1 [1715 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libpython3.9-dev i386 3.9.2-1 [3822 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libpython3-dev i386 3.9.2-3 [21.7 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1 [269 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libwebpdemux2 i386 0.6.1-2.1 [88.2 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libwebpmux3 i386 0.6.1-2.1 [99.0 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 python3-six all 1.16.0-1 [17.1 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 python3-cycler all 0.10.0-3 [8084 B] Get: 84 http://deb.debian.org/debian bullseye/main i386 python3-dateutil all 2.8.1-5 [81.7 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 python3-decorator all 4.4.2-2 [15.8 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 python3.9-dev i386 3.9.2-1 [515 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 python3-dev i386 3.9.2-3 [24.8 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 python3-kiwisolver i386 1.3.1-1+b1 [58.5 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 python3-pyparsing all 2.4.7-1 [109 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 python3-pil i386 8.1.2+dfsg-0.2 [444 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 python3-matplotlib i386 3.3.4-1 [4165 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 python3-tz all 2021.1-1 [34.8 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 python3-pandas-lib i386 1.1.5+dfsg-2 [3182 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 python3-patsy all 0.5.1-3 [172 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 python3-pubsub all 4.0.3-4 [46.6 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 python3-scipy i386 1.6.0-2 [11.9 MB] Get: 101 http://deb.debian.org/debian bullseye/main i386 python3-setuptools all 52.0.0-4 [366 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 python3-statsmodels-lib i386 0.12.2-1 [1256 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 python3-statsmodels all 0.12.2-1 [4455 kB] Fetched 74.0 MB in 1s (56.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ... 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Selecting previously unselected package python3-minimal. (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 ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. 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Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../03-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../06-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. 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Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-pubsub (4.0.3-4) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-dateutil (2.8.1-5) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up libpython3-dev:i386 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-statsmodels-lib:i386 (0.12.2-1) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-pandas-lib:i386 (1.1.5+dfsg-2) ... Setting up python3-patsy (0.5.1-3) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up python3-statsmodels (0.12.2-1) ... Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (1280 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 28813 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... 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I: Building the package I: Running cd /build/tnseq-transit-3.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package tnseq-transit dpkg-buildpackage: info: source version 3.2.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird betreten dh_auto_clean I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf tests_invalid_data rm -rf tnseq_transit.egg-info make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird verlassen dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild debian/rules override_dh_auto_configure make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird betreten mkdir -p tests_invalid_data mv tests/H37Rv.fna tests_invalid_data dh_auto_configure I: pybuild base:232: python3.9 setup.py config running config make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird verlassen dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/__main__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/tpp_gui.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/tpp_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/tnseq_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/norm_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/fileDisplay.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/images.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/view_trash.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/__main__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/stat_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/draw_trash.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/transit_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/qcDisplay.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/trash.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/transit_gui.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert copying src/pytransit/convert/gff_to_prot_table.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert copying src/pytransit/convert/base.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert copying src/pytransit/convert/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/tn5gaps.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/gumbel.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/normalize.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/base.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/pathway_enrichment.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/binomial.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/zinb.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/griffin.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/tnseq_stats.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/hmm.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/example.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/resampling.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/rankproduct.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/gi.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/corrplot.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/utest.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/anova.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/heatmap.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/norm.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/igv.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/base.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/mean_counts.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/combined_wig.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/prot_table.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export running egg_info creating tnseq_transit.egg-info writing tnseq_transit.egg-info/PKG-INFO writing dependency_links to tnseq_transit.egg-info/dependency_links.txt writing entry points to tnseq_transit.egg-info/entry_points.txt writing requirements to tnseq_transit.egg-info/requires.txt writing top-level names to tnseq_transit.egg-info/top_level.txt writing manifest file 'tnseq_transit.egg-info/SOURCES.txt' reading manifest file 'tnseq_transit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'VERSION' warning: no files found matching '*.html' under directory 'src/pytransit/doc/build/html' warning: no files found matching '*.png' under directory 'src/pytransit/doc/build/html/_images' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_modules' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_static' writing manifest file 'tnseq_transit.egg-info/SOURCES.txt' creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/COG_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_associated_Rvs-3-11-18.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_associated_Rvs.csv -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_term_names.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv.sanger_associated_RVS.csv -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv_COG_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv_GO_terms.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv_sanger_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/README.md -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep3.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_glycerol_combined.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/gene_ontology.1_2.3-11-18.obo -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/samples_metadata_cg.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/samples_metadata_cg_covar.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/samples_metadata_cg_interactions.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/sanger_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/smeg_GO_terms.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/BCG.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/BCG.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37Rv.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37Rv.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD_mod3.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvMA2.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvMA2.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/genomes.html -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/mc2_155_tamu.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/mc2_155_tamu.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes debian/rules override_dh_auto_test make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird betreten dh_auto_test -- --system=custom --test-args="PYTHONPATH=tests {interpreter} -m unittest -v tests/*.py" I: pybuild base:232: PYTHONPATH=tests python3.9 -m unittest -v tests/*.py /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:648: SyntaxWarning: "is" with a literal. Did you mean "=="? if vars.num_replicons is 1: /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:651: SyntaxWarning: "is" with a literal. Did you mean "=="? elif len(vars.replicon_ids) is 1 and vars.replicon_ids[0].strip() == 'auto': test_Binomial (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1287: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1214: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:518: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(self.annotation): ResourceWarning: Enable tracemalloc to get the object allocation traceback #################### tests.test_analysis_methods.TestMethods.test_Binomial #################### [binomial] Starting Binomial Method [binomial] Getting Data [binomial] Setting Parameters [binomial] Setting Initial Values [binomial] Running Binomial Method... 0.2% [binomial] Running Binomial Method... 0.3% [binomial] Running Binomial Method... 0.4% [binomial] Running Binomial Method... 0.5% [binomial] Running Binomial Method... 0.5% [binomial] Running Binomial Method... 0.6% [binomial] 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Running Binomial Method... 38.0% [binomial] Running Binomial Method... 38.1% [binomial] Running Binomial Method... 38.2% [binomial] Running Binomial Method... 38.3% [binomial] Running Binomial Method... 38.4% [binomial] Running Binomial Method... 38.5% [binomial] Running Binomial Method... 38.5% [binomial] Running Binomial Method... 38.6% [binomial] Running Binomial Method... 38.7% [binomial] Running Binomial Method... 38.8% [binomial] Running Binomial Method... 38.9% [binomial] Running Binomial Method... 39.0% [binomial] Running Binomial Method... 39.1% [binomial] Running Binomial Method... 39.2% [binomial] Running Binomial Method... 39.3% [binomial] Running Binomial Method... 39.4% [binomial] Running Binomial Method... 39.5% [binomial] Running Binomial Method... 39.5% [binomial] Running Binomial Method... 39.6% [binomial] Running Binomial Method... 39.7% [binomial] Running Binomial Method... 39.8% [binomial] Running Binomial Method... 39.9% [binomial] Running Binomial Method... 40.0% 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Method... 60.6% [binomial] Running Binomial Method... 60.7% [binomial] Running Binomial Method... 60.8% [binomial] Running Binomial Method... 60.9% [binomial] Running Binomial Method... 61.0% [binomial] Running Binomial Method... 61.1% [binomial] Running Binomial Method... 61.2% [binomial] Running Binomial Method... 61.3% [binomial] Running Binomial Method... 61.4% [binomial] Running Binomial Method... 61.5% [binomial] Running Binomial Method... 61.5% [binomial] Running Binomial Method... 61.6% [binomial] Running Binomial Method... 61.7% [binomial] Running Binomial Method... 61.8% [binomial] Running Binomial Method... 61.9% [binomial] Running Binomial Method... 62.0% [binomial] Running Binomial Method... 62.1% [binomial] Running Binomial Method... 62.2% [binomial] Running Binomial Method... 62.3% [binomial] Running Binomial Method... 62.4% [binomial] Running Binomial Method... 62.5% [binomial] Running Binomial Method... 62.5% [binomial] Running Binomial Method... 62.6% [binomial] Running Binomial Method... 62.7% [binomial] Running Binomial Method... 62.8% [binomial] Running Binomial Method... 62.9% [binomial] Running Binomial Method... 63.0% [binomial] Running Binomial Method... 63.1% [binomial] Running Binomial Method... 63.2% [binomial] Running Binomial Method... 63.3% [binomial] Running Binomial Method... 63.4% [binomial] Running Binomial Method... 63.5% [binomial] Running Binomial Method... 63.5% [binomial] Running Binomial Method... 63.6% [binomial] Running Binomial Method... 63.7% [binomial] Running Binomial Method... 63.8% [binomial] Running Binomial Method... 63.9% [binomial] Running Binomial Method... 64.0% [binomial] Running Binomial Method... 64.1% [binomial] Running Binomial Method... 64.2% [binomial] Running Binomial Method... 64.3% [binomial] Running Binomial Method... 64.4% [binomial] Running Binomial Method... 64.5% [binomial] Running Binomial Method... 64.5% [binomial] Running Binomial Method... 64.6% [binomial] Running Binomial Method... 64.7% 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Running Binomial Method... 68.9% [binomial] Running Binomial Method... 69.0% [binomial] Running Binomial Method... 69.1% [binomial] Running Binomial Method... 69.2% [binomial] Running Binomial Method... 69.3% [binomial] Running Binomial Method... 69.4% [binomial] Running Binomial Method... 69.5% [binomial] Running Binomial Method... 69.5% [binomial] Running Binomial Method... 69.6% [binomial] Running Binomial Method... 69.7% [binomial] Running Binomial Method... 69.8% [binomial] Running Binomial Method... 69.9% [binomial] Running Binomial Method... 70.0% [binomial] Running Binomial Method... 70.1% [binomial] Running Binomial Method... 70.2% [binomial] Running Binomial Method... 70.3% [binomial] Running Binomial Method... 70.4% [binomial] Running Binomial Method... 70.5% [binomial] Running Binomial Method... 70.5% [binomial] Running Binomial Method... 70.6% [binomial] Running Binomial Method... 70.7% [binomial] Running Binomial Method... 70.8% [binomial] Running Binomial Method... 70.9% 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Running Binomial Method... 75.1% [binomial] Running Binomial Method... 75.2% [binomial] Running Binomial Method... 75.3% [binomial] Running Binomial Method... 75.4% [binomial] Running Binomial Method... 75.5% [binomial] Running Binomial Method... 75.5% [binomial] Running Binomial Method... 75.6% [binomial] Running Binomial Method... 75.7% [binomial] Running Binomial Method... 75.8% [binomial] Running Binomial Method... 75.9% [binomial] Running Binomial Method... 76.0% [binomial] Running Binomial Method... 76.1% [binomial] Running Binomial Method... 76.2% [binomial] Running Binomial Method... 76.3% [binomial] Running Binomial Method... 76.4% [binomial] Running Binomial Method... 76.5% [binomial] Running Binomial Method... 76.5% [binomial] Running Binomial Method... 76.6% [binomial] Running Binomial Method... 76.7% [binomial] Running Binomial Method... 76.8% [binomial] Running Binomial Method... 76.9% [binomial] Running Binomial Method... 77.0% [binomial] Running Binomial Method... 77.1% 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Method... 79.2% [binomial] Running Binomial Method... 79.3% [binomial] Running Binomial Method... 79.4% [binomial] Running Binomial Method... 79.5% [binomial] Running Binomial Method... 79.5% [binomial] Running Binomial Method... 79.6% [binomial] Running Binomial Method... 79.7% [binomial] Running Binomial Method... 79.8% [binomial] Running Binomial Method... 79.9% [binomial] Running Binomial Method... 80.0% [binomial] Running Binomial Method... 80.1% [binomial] Running Binomial Method... 80.2% [binomial] Running Binomial Method... 80.3% [binomial] Running Binomial Method... 80.4% [binomial] Running Binomial Method... 80.5% [binomial] Running Binomial Method... 80.5% [binomial] Running Binomial Method... 80.6% [binomial] Running Binomial Method... 80.7% [binomial] Running Binomial Method... 80.8% [binomial] Running Binomial Method... 80.9% [binomial] Running Binomial Method... 81.0% [binomial] Running Binomial Method... 81.1% [binomial] Running Binomial Method... 81.2% [binomial] Running Binomial Method... 81.3% [binomial] Running Binomial Method... 81.4% [binomial] Running Binomial Method... 81.5% [binomial] Running Binomial Method... 81.5% [binomial] Running Binomial Method... 81.6% [binomial] Running Binomial Method... 81.7% [binomial] Running Binomial Method... 81.8% [binomial] Running Binomial Method... 81.9% [binomial] Running Binomial Method... 82.0% [binomial] Running Binomial Method... 82.1% [binomial] Running Binomial Method... 82.2% [binomial] Running Binomial Method... 82.3% [binomial] Running Binomial Method... 82.4% [binomial] Running Binomial Method... 82.5% [binomial] Running Binomial Method... 82.5% [binomial] Running Binomial Method... 82.6% [binomial] Running Binomial Method... 82.7% [binomial] Running Binomial Method... 82.8% [binomial] Running Binomial Method... 82.9% [binomial] Running Binomial Method... 83.0% [binomial] Running Binomial Method... 83.1% [binomial] Running Binomial Method... 83.2% [binomial] Running Binomial Method... 83.3% 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Running Binomial Method... 99.8% [binomial] Running Binomial Method... 99.9% [binomial] Running Binomial Method... 100.0% ok test_GI (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback [binomial] [binomial] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [binomial] Finished Binomial Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_GI #################### [gi] Starting Genetic Interactions Method [gi] Getting Data [gi] Normalizing using: TTR [gi] Running GI Method... 2% [gi] Running Export Method... 0.0% [gi] Running GI Method... 4% [gi] Running Export Method... 2.0% [gi] Running GI Method... 6% [gi] Running Export Method... 4.0% [gi] Running GI Method... 8% [gi] Running Export Method... 6.0% [gi] Running GI Method... 10% [gi] Running Export Method... 8.0% [gi] Running GI Method... 12% [gi] Running Export Method... 10.0% [gi] Running GI Method... 14% [gi] Running Export 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<_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='w' encoding='UTF-8'> method() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_Griffin (tests.test_analysis_methods.TestMethods) ... 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sigma_s) * (1-w1)) [griffin] [griffin] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [griffin] Finished Griffin Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_Gumbel #################### [gumbel] Reading Annotation [gumbel] Getting Data [gumbel] Doing Regression [gumbel] Setting Initial Class [gumbel] Running Gumbel Method... 0.2% [gumbel] Running Gumbel Method... 0.3% [gumbel] Running Gumbel Method... 0.4% [gumbel] Running Gumbel Method... 0.5% [gumbel] Running Gumbel Method... 0.5% [gumbel] Running Gumbel Method... 0.6% [gumbel] Running Gumbel Method... 0.7% [gumbel] Running Gumbel Method... 0.8% [gumbel] Running Gumbel Method... 0.9% [gumbel] Running Gumbel Method... 1.0% [gumbel] Running Gumbel Method... 1.1% [gumbel] Running Gumbel Method... 1.2% [gumbel] Running Gumbel Method... 1.3% [gumbel] Running Gumbel Method... 1.4% [gumbel] Running Gumbel Method... 1.5% [gumbel] Running Gumbel Method... 1.5% [gumbel] Running 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Method... 95.0% [gumbel] Running Gumbel Method... 95.1% [gumbel] Running Gumbel Method... 95.2% [gumbel] Running Gumbel Method... 95.3% [gumbel] Running Gumbel Method... 95.4% [gumbel] Running Gumbel Method... 95.5% [gumbel] Running Gumbel Method... 95.5% [gumbel] Running Gumbel Method... 95.6% [gumbel] Running Gumbel Method... 95.7% [gumbel] Running Gumbel Method... 95.8% [gumbel] Running Gumbel Method... 95.9% [gumbel] Running Gumbel Method... 96.0% [gumbel] Running Gumbel Method... 96.1% [gumbel] Running Gumbel Method... 96.2% [gumbel] Running Gumbel Method... 96.3% [gumbel] Running Gumbel Method... 96.4% [gumbel] Running Gumbel Method... 96.5% [gumbel] Running Gumbel Method... 96.5% [gumbel] Running Gumbel Method... 96.6% [gumbel] Running Gumbel Method... 96.7% [gumbel] Running Gumbel Method... 96.8% [gumbel] Running Gumbel Method... 96.9% [gumbel] Running Gumbel Method... 97.0% [gumbel] Running Gumbel Method... 97.1% [gumbel] Running Gumbel Method... 97.2% [gumbel] Running Gumbel Method... 97.3% [gumbel] Running Gumbel Method... 97.4% [gumbel] Running Gumbel Method... 97.5% [gumbel] Running Gumbel Method... 97.5% [gumbel] Running Gumbel Method... 97.6% [gumbel] Running Gumbel Method... 97.7% [gumbel] Running Gumbel Method... 97.8% [gumbel] Running Gumbel Method... 97.9% [gumbel] Running Gumbel Method... 98.0% [gumbel] Running Gumbel Method... 98.1% [gumbel] Running Gumbel Method... 98.2% [gumbel] Running Gumbel Method... 98.3% [gumbel] Running Gumbel Method... 98.4% [gumbel] Running Gumbel Method... 98.5% [gumbel] Running Gumbel Method... 98.5% [gumbel] Running Gumbel Method... 98.6% [gumbel] Running Gumbel Method... 98.7% [gumbel] Running Gumbel Method... 98.8% [gumbel] Running Gumbel Method... 98.9% [gumbel] Running Gumbel Method... 99.0% [gumbel] Running Gumbel Method... 99.1% [gumbel] Running Gumbel Method... 99.2% [gumbel] Running Gumbel Method... 99.3% [gumbel] Running Gumbel Method... 99.4% [gumbel] Running Gumbel Method... 99.5% [gumbel] Running Gumbel Method... 99.5% [gumbel] Running Gumbel Method... 99.6% [gumbel] Running Gumbel Method... 99.7% [gumbel] Running Gumbel Method... 99.8% [gumbel] Running Gumbel Method... 99.9% [gumbel] Running Gumbel Method... 100.0% ok test_HMM (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/analysis/hmm.py:194: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.wig' mode='r' encoding='UTF-8'> T = len([1 for line in open(ctrldata[0]).readlines() if not line.startswith("#")]) ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback [gumbel] [gumbel] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [gumbel] Finished Gumbel Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_HMM #################### [hmm] Starting HMM Method [hmm] Getting Data [hmm] Normalizing using: TTR [hmm] Running HMM Method... 2.5% [hmm] Running HMM Method... 5.0% [hmm] Running HMM Method... 7.5% [hmm] Running HMM Method... 10.0% [hmm] Running HMM Method... 12.5% [hmm] Running HMM Method... 15.0% [hmm] Running HMM Method... 17.5% [hmm] Running HMM Method... 20.0% [hmm] Running HMM Method... 22.5% [hmm] Running HMM Method... 25.0% [hmm] Running HMM Method... 27.5% [hmm] Running HMM Method... 30.0% [hmm] Running HMM Method... 32.5% [hmm] Running HMM Method... 35.0% [hmm] Running HMM Method... 37.5% [hmm] Running HMM Method... 40.0% [hmm] Running HMM Method... 42.5% [hmm] Running HMM Method... 45.0% [hmm] Running HMM Method... 47.5% [hmm] Running HMM Method... 50.0% [hmm] Running HMM Method... 50.0% [hmm] Running HMM Method... 52.5% [hmm] Running HMM Method... 55.0% [hmm] Running HMM Method... 57.5% [hmm] Running HMM Method... 60.0% [hmm] Running HMM Method... 62.5% [hmm] Running HMM Method... 65.0% [hmm] Running HMM Method... 67.5% [hmm] Running HMM Method... 70.0% [hmm] Running HMM Method... 72.5% [hmm] Running HMM Method... 75.0% [hmm] Running HMM Method... 77.5% [hmm] Running HMM Method... 80.0% [hmm] Running HMM Method... 82.5% [hmm] Running HMM Method... 85.0% [hmm] Running HMM Method... 87.5% [hmm] Running HMM Method... 90.0% [hmm] Running HMM Method... 92.5% [hmm] Running HMM Method... 95.0% [hmm] Running HMM Method... 97.5% ok test_anova (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(fname): ResourceWarning: Enable tracemalloc to get the object allocation traceback [hmm] [hmm] Finished HMM - Sites Method [hmm] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [hmm] Creating HMM Genes Level Output [hmm] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput_genes.txt [hmm] Finished HMM Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_anova #################### [anova] Starting Anova analysis [anova] Getting Data [anova] Normalizing using: TTR [anova] Running Anova [anova] Running Anova Method... 2.0% [anova] Running Anova Method... 3.9% [anova] Running Anova Method... 5.9% [anova] Running Anova Method... 7.8% [anova] Running Anova Method... 9.8% [anova] Running Anova Method... 11.8% [anova] Running Anova Method... 13.7% [anova] Running Anova Method... 15.7% [anova] Running Anova Method... 17.6% [anova] Running Anova Method... 19.6% [anova] Running Anova Method... 21.6% [anova] Running Anova Method... 23.5% [anova] Running Anova Method... 25.5% [anova] Running Anova Method... 27.5% [anova] Running Anova Method... 29.4% [anova] Running Anova Method... 31.4% [anova] Running Anova Method... 33.3% [anova] Running Anova Method... 35.3% [anova] Running Anova Method... 37.3% [anova] Running Anova Method... 39.2% [anova] Running Anova Method... 41.2% [anova] Running Anova Method... 43.1% [anova] Running Anova Method... 45.1% [anova] Running Anova Method... 47.1% [anova] Running Anova Method... 49.0% [anova] Running Anova Method... 51.0% [anova] Running Anova Method... 52.9% [anova] Running Anova Method... 54.9% [anova] Running Anova Method... 56.9% [anova] Running Anova Method... 58.8% [anova] Running Anova Method... 60.8% [anova] Running Anova Method... 62.7% [anova] Running Anova Method... 64.7% [anova] Running Anova Method... 66.7% [anova] Running Anova Method... 68.6% [anova] Running Anova Method... 70.6% [anova] Running Anova Method... 72.5% [anova] Running Anova Method... 74.5% [anova] Running Anova Method... 76.5% [anova] Running Anova Method... 78.4% [anova] Running Anova Method... 80.4% [anova] Running Anova Method... 82.4% [anova] Running Anova Method... 84.3% [anova] Running Anova Method... 86.3% [anova] Running Anova Method... 88.2% [anova] Running Anova Method... 90.2% [anova] Running Anova Method... 92.2% [anova] Running Anova Method... 94.1% [anova] Running Anova Method... 96.1% [anova] Running Anova Method... 98.0% [anova] Running Anova Method... 100.0% /build/tnseq-transit-3.2.1/tests/transit_test.py:89: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='r' encoding='UTF-8'> for line in open(fname): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_resampling (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1287: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1214: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:518: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(self.annotation): ResourceWarning: Enable tracemalloc to get the object allocation traceback [anova] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [anova] Finished Anova analysis [anova] Time: 0.5s Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Performing LOESS Correction [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Performing LOESS Correction [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% /build/tnseq-transit-3.2.1/tests/transit_test.py:89: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='r' encoding='UTF-8'> for line in open(fname): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_resampling_adaptive (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/stat_tools.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray DATA[K] = numpy.array([L1[K], L2[K]]) /build/tnseq-transit-3.2.1/tests/../src/pytransit/stat_tools.py:515: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray E[L] = numpy.array([perm[:n1], perm[n1:]]) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_adaptive #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_combined_wig (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_combined_wig #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_histogram (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method 38 36 Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_histogram #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_multistrain (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing histogram files Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_multistrain #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Multiple annotation files found [resampling] Mapping ctrl data to /build/tnseq-transit-3.2.1/tests/data/test.prot_table, exp data to /build/tnseq-transit-3.2.1/tests/data/test.prot_table [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_utest (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing histogram files Removing output file... #################### tests.test_analysis_methods.TestMethods.test_utest #################### [utest] Starting Mann-Whitney U-test Method [utest] Getting Data [utest] Normalizing using: TTR [utest] Running Mann-Whitney U-test Method... 2.0% [utest] Running Mann-Whitney U-test Method... 3.9% [utest] Running Mann-Whitney U-test Method... 5.9% [utest] Running Mann-Whitney U-test Method... 7.8% [utest] Running Mann-Whitney U-test Method... 9.8% [utest] Running Mann-Whitney U-test Method... 11.8% [utest] Running Mann-Whitney U-test Method... 13.7% [utest] Running Mann-Whitney U-test Method... 15.7% [utest] Running Mann-Whitney U-test Method... 17.6% [utest] Running Mann-Whitney U-test Method... 19.6% [utest] Running Mann-Whitney U-test Method... 21.6% [utest] Running Mann-Whitney U-test Method... 23.5% [utest] Running Mann-Whitney U-test Method... 25.5% [utest] Running Mann-Whitney U-test Method... 27.5% [utest] Running Mann-Whitney U-test Method... 29.4% [utest] Running Mann-Whitney U-test Method... 31.4% [utest] Running Mann-Whitney U-test Method... 33.3% [utest] Running Mann-Whitney U-test Method... 35.3% [utest] Running Mann-Whitney U-test Method... 37.3% [utest] Running Mann-Whitney U-test Method... 39.2% [utest] Running Mann-Whitney U-test Method... 41.2% [utest] Running Mann-Whitney U-test Method... 43.1% [utest] Running Mann-Whitney U-test Method... 45.1% [utest] Running Mann-Whitney U-test Method... 47.1% [utest] Running Mann-Whitney U-test Method... 49.0% [utest] Running Mann-Whitney U-test Method... 51.0% [utest] Running Mann-Whitney U-test Method... 52.9% [utest] Running Mann-Whitney U-test Method... 54.9% [utest] Running Mann-Whitney U-test Method... 56.9% [utest] Running Mann-Whitney U-test Method... 58.8% [utest] Running Mann-Whitney U-test Method... 60.8% [utest] Running Mann-Whitney U-test Method... 62.7% [utest] Running Mann-Whitney U-test Method... 64.7% [utest] Running Mann-Whitney U-test Method... 66.7% [utest] Running Mann-Whitney U-test Method... 68.6% [utest] Running Mann-Whitney U-test Method... 70.6% [utest] Running Mann-Whitney U-test Method... 72.5% [utest] Running Mann-Whitney U-test Method... 74.5% [utest] Running Mann-Whitney U-test Method... 76.5% [utest] Running Mann-Whitney U-test Method... 78.4% [utest] Running Mann-Whitney U-test Method... 80.4% [utest] Running Mann-Whitney U-test Method... 82.4% [utest] Running Mann-Whitney U-test Method... 84.3% [utest] Running Mann-Whitney U-test Method... 86.3% [utest] Running Mann-Whitney U-test Method... 88.2% [utest] Running Mann-Whitney U-test Method... 90.2% [utest] Running Mann-Whitney U-test Method... 92.2% [utest] Running Mann-Whitney U-test Method... 94.1% [utest] Running Mann-Whitney U-test Method... 96.1% [utest] Running Mann-Whitney U-test Method... 98.0% [utest] Running Mann-Whitney U-test Method... 100.0% ok test_zinb (tests.test_analysis_methods.TestMethods) ... skipped 'requires R, rpy2' test_zinb_covariates (tests.test_analysis_methods.TestMethods) ... skipped 'requires R, rpy2' test_zinb_interactions (tests.test_analysis_methods.TestMethods) ... skipped 'requires R, rpy2' test_TTR (tests.test_norm_methods.TestNormMethods) ... ok test_nonorm (tests.test_norm_methods.TestNormMethods) ... ok test_resampling_NZMean (tests.test_norm_methods.TestNormMethods) ... [utest] [utest] Performing Benjamini-Hochberg Correction [utest] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [utest] Finished Mann-Whitney U-test Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_TTR #################### #################### tests.test_norm_methods.TestNormMethods.test_nonorm #################### #################### tests.test_norm_methods.TestNormMethods.test_resampling_NZMean #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: nzmean [resampling] Preprocessing Exp data... [resampling] Normalizing using: nzmean [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_Quantile (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_Quantile #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: quantile [resampling] Preprocessing Exp data... [resampling] Normalizing using: quantile [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% /build/tnseq-transit-3.2.1/tests/transit_test.py:75: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_resampling_TTR (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_TTR #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_TotReads (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_TotReads #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: totreads [resampling] Preprocessing Exp data... [resampling] Normalizing using: totreads [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_ZINFNB (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_ZINFNB #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: zinfnb [resampling] Preprocessing Exp data... [resampling] Normalizing using: zinfnb [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_nonorm (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_nonorm #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Preprocessing Exp data... [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_cleanargs_flag_arguments_w_quotes (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_flag_arguments_with_double_dash (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_flag_without_arguments (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_negative_arguments (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_positional_arguments (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_positional_arguments_w_quotes (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_file_types (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_genes_creation_fromdata (tests.test_pytransit_tools.TestTnSeqTools) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1287: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/genomes/H37Rv.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1214: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/genomes/H37Rv.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:518: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/genomes/H37Rv.prot_table' mode='r' encoding='UTF-8'> for line in open(self.annotation): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_genes_creation_fromwig (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_normalization (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_read_data (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_tpp_flag_primer (tests.test_tpp.TestTPP) ... skipped 'requires local data file' test_tpp_multicontig_auto_replicon_ids (tests.test_tpp.TestTPP) ... [tn_preprocess] running pre-processing on /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq and [tn_preprocess] protocol: Sassetti [tn_preprocess] transposon type: Himar1 [tn_preprocess] One reference genome specified: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna, containing 3 records. [tn_preprocess] Autogenerating replicon_ids... [tn_preprocess] extracting reads... [tn_preprocess] fastq2reads: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq -> /build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1 /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:85: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq' mode='r' encoding='UTF-8'> for line in open(infile): ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] assuming single-ended reads [tn_preprocess] creating /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 [tn_preprocess] prefix sequence: [tn_preprocess] Looking for start of Tn prefix within P,Q = [0,20] /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:276: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1' mode='r' encoding='UTF-8'> for line in open(infile): ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] mapping reads using BWA...(this takes a couple of minutes) [tn_preprocess] /usr/bin/bwa index /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna b'[bwa_index] Pack FASTA... 0.06 sec' b'[bwa_index] Construct BWT for the packed sequence...' b'[bwa_index] 0.99 seconds elapse.' b'[bwa_index] Update BWT... 0.04 sec' b'[bwa_index] Pack forward-only FASTA... 0.04 sec' b'[bwa_index] Construct SA from BWT and Occ... 0.74 sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa index /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna' b'[main] Real time: 1.924 sec; CPU: 1.872 sec' b'' [tn_preprocess] /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 > /build/tnseq-transit-3.2.1/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' b'[M::mem_process_seqs] Processed 2500 reads in 0.211 CPU sec, 0.210 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1' b'[main] Real time: 0.223 sec; CPU: 0.221 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:378: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna' mode='r' encoding='UTF-8'> for line in open(filename): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:560: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.sam' mode='r' encoding='UTF-8'> for line in open(sam): ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_1.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_2.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_3.wig /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:1108: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1' mode='r' encoding='UTF-8'> for line in open(vars.reads1): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:1117: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1' mode='r' encoding='UTF-8'> read_length = get_read_length(vars.base + ".reads1") ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:1118: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1' mode='r' encoding='UTF-8'> mean_r1_genomic = get_genomic_portion(vars.base + ".trimmed1") ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp.tn_stats [tn_preprocess] Done. ok test_tpp_multicontig_empty_prefix (tests.test_tpp.TestTPP) ... [tn_preprocess] running pre-processing on /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq and [tn_preprocess] protocol: Sassetti [tn_preprocess] transposon type: Himar1 [tn_preprocess] One reference genome specified: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna, containing 3 records. [tn_preprocess] extracting reads... [tn_preprocess] fastq2reads: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq -> /build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1 [tn_preprocess] assuming single-ended reads [tn_preprocess] creating /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 [tn_preprocess] prefix sequence: [tn_preprocess] Looking for start of Tn prefix within P,Q = [0,20] [tn_preprocess] mapping reads using BWA...(this takes a couple of minutes) [tn_preprocess] /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 > /build/tnseq-transit-3.2.1/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' b'[M::mem_process_seqs] Processed 2500 reads in 0.205 CPU sec, 0.205 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1' b'[main] Real time: 0.301 sec; CPU: 0.215 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_a.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_b.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_c.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp.tn_stats [tn_preprocess] Done. ok test_tpp_noflag_primer (tests.test_tpp.TestTPP) ... skipped 'requires local data file' test_tpp_protocol_mme1 (tests.test_tpp.TestTPP) ... skipped 'requires local data file' ---------------------------------------------------------------------- Ran 39 tests in 144.829s OK (skipped=6) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_arguments_w_quotes #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_arguments_with_double_dash #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_without_arguments #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_negative_arguments #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_positional_arguments #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_positional_arguments_w_quotes #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_file_types #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_genes_creation_fromdata #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_genes_creation_fromwig #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_normalization #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_read_data #################### #################### tests.test_tpp.TestTPP.test_tpp_multicontig_auto_replicon_ids #################### # title: Tn-Seq Pre-Processor # date: 08/19/2022 11:02:42 # command: python python3.9 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti # bwa flags: # read1: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq # read2: # ref_genome: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna # replicon_ids: 1,2,3 # total_reads (or read pairs): 2500 # trimmed_reads (reads with valid Tn prefix, and insert size>20bp): 2512 # reads1_mapped: 2116 # reads2_mapped: 0 # mapped_reads (both R1 and R2 map into genome, and R2 has a proper barcode): 2116 # read_count (TA sites only, for Himar1): # 1: 63 # 2: 0 # 3: 0 # template_count: # 1: 63 # 2: 0 # 3: 0 # template_ratio (reads per template): # 1: 1.00 # 2: 0.00 # 3: 0.00 # TA_sites: # 1: 89994 # 2: 646 # 3: 664 # TAs_hit: # 1: 63 # 2: 0 # 3: 0 # density: # 1: 0.001 # 2: 0.000 # 3: 0.000 # max_count (among templates): # 1: 1 # 2: 0 # 3: 0 # max_site (coordinate): # 1: 4977050 # 2: 57441 # 3: 38111 # NZ_mean (among templates): # 1: 1.0 # 2: 0.0 # 3: 0.0 # FR_corr (Fwd templates vs. Rev templates): # 1: -0.000 # 2: nan # 3: nan # BC_corr (reads vs. templates, summed over both strands): # 1: nan # 2: nan # 3: nan # primer_matches: 36 reads (1.4%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1) # vector_matches: 36 reads (1.4%) contain CTAGACCGTCCAGTCTGGCAGGCCGGAAAC (phiMycoMarT7) # adapter_matches: 57 reads (2.3%) contain GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (Illumina/TruSeq index) # misprimed_reads: 17 reads (0.7%) contain Himar1 prefix but don't end in TGTTA # read_length: 125 bp # mean_R1_genomic_length: 121.6 bp Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file #################### tests.test_tpp.TestTPP.test_tpp_multicontig_empty_prefix #################### # title: Tn-Seq Pre-Processor # date: 08/19/2022 11:02:44 # command: python python3.9 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti # bwa flags: # read1: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq # read2: # ref_genome: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna # replicon_ids: a,b,c # total_reads (or read pairs): 2500 # trimmed_reads (reads with valid Tn prefix, and insert size>20bp): 2512 # reads1_mapped: 2116 # reads2_mapped: 0 # mapped_reads (both R1 and R2 map into genome, and R2 has a proper barcode): 2116 # read_count (TA sites only, for Himar1): # a: 63 # b: 0 # c: 0 # template_count: # a: 63 # b: 0 # c: 0 # template_ratio (reads per template): # a: 1.00 # b: 0.00 # c: 0.00 # TA_sites: # a: 89994 # b: 646 # c: 664 # TAs_hit: # a: 63 # b: 0 # c: 0 # density: # a: 0.001 # b: 0.000 # c: 0.000 # max_count (among templates): # a: 1 # b: 0 # c: 0 # max_site (coordinate): # a: 4977050 # b: 57441 # c: 38111 # NZ_mean (among templates): # a: 1.0 # b: 0.0 # c: 0.0 # FR_corr (Fwd templates vs. Rev templates): # a: -0.000 # b: nan # c: nan # BC_corr (reads vs. templates, summed over both strands): # a: nan # b: nan # c: nan # primer_matches: 36 reads (1.4%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1) # vector_matches: 36 reads (1.4%) contain CTAGACCGTCCAGTCTGGCAGGCCGGAAAC (phiMycoMarT7) # adapter_matches: 57 reads (2.3%) contain GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (Illumina/TruSeq index) # misprimed_reads: 17 reads (0.7%) contain Himar1 prefix but don't end in TGTTA # read_length: 125 bp # mean_R1_genomic_length: 121.6 bp Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird verlassen create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/tnseq-transit-3.2.1/debian/tnseq-transit running install running build running build_py running egg_info writing tnseq_transit.egg-info/PKG-INFO writing dependency_links to tnseq_transit.egg-info/dependency_links.txt writing entry points to tnseq_transit.egg-info/entry_points.txt writing requirements to tnseq_transit.egg-info/requires.txt writing top-level names to tnseq_transit.egg-info/top_level.txt reading manifest file 'tnseq_transit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'VERSION' warning: no files found matching '*.html' under directory 'src/pytransit/doc/build/html' warning: no files found matching '*.png' under directory 'src/pytransit/doc/build/html/_images' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_modules' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_static' writing manifest file 'tnseq_transit.egg-info/SOURCES.txt' running install_lib creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9 creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/__main__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/tpp_gui.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/tpp_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/tnseq_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/norm_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/fileDisplay.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert/gff_to_prot_table.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert/base.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/tn5gaps.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/gumbel.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/normalize.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/base.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/pathway_enrichment.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/binomial.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/zinb.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/griffin.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/tnseq_stats.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/hmm.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/example.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/resampling.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/rankproduct.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/gi.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/corrplot.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/utest.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/anova.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/heatmap.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/norm.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv_GO_terms.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/glycerol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/COG_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv_COG_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/samples_metadata_cg_covar.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_term_names.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_associated_Rvs.csv -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/sanger_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv.sanger_associated_RVS.csv -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/samples_metadata_cg.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/glycerol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_glycerol_combined.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/gene_ontology.1_2.3-11-18.obo -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/smeg_GO_terms.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv_sanger_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_rep3.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/README.md -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_associated_Rvs-3-11-18.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/samples_metadata_cg_interactions.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/glycerol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/images.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/view_trash.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/__main__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/stat_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/draw_trash.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvMA2.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvBD.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37Rv.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/mc2_155_tamu.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37Rv.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/BCG.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/mc2_155_tamu.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvMA2.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvBD_mod3.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/genomes.html -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/BCG.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvBD.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/transit_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/qcDisplay.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/trash.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/igv.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/base.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/mean_counts.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/combined_wig.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/prot_table.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/transit_gui.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/__main__.py to __main__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/tpp_gui.py to tpp_gui.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/tpp_tools.py to tpp_tools.cpython-39.pyc /usr/lib/python3.9/dist-packages/pytpp/tpp_tools.py:648: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/pytpp/tpp_tools.py:651: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/tnseq_tools.py to tnseq_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/norm_tools.py to norm_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/fileDisplay.py to fileDisplay.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert/gff_to_prot_table.py to gff_to_prot_table.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert/base.py to base.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/tn5gaps.py to tn5gaps.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/gumbel.py to gumbel.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/normalize.py to normalize.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/base.py to base.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/pathway_enrichment.py to pathway_enrichment.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/binomial.py to binomial.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/zinb.py to zinb.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/griffin.py to griffin.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/tnseq_stats.py to tnseq_stats.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/hmm.py to hmm.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/example.py to example.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/resampling.py to resampling.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/rankproduct.py to rankproduct.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/gi.py to gi.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/corrplot.py to corrplot.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/utest.py to utest.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/anova.py to anova.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/heatmap.py to heatmap.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/norm.py to norm.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/images.py to images.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/view_trash.py to view_trash.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/__main__.py to __main__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/stat_tools.py to stat_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/draw_trash.py to draw_trash.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/transit_tools.py to transit_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/qcDisplay.py to qcDisplay.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/trash.py to trash.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/igv.py to igv.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/base.py to base.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/mean_counts.py to mean_counts.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/combined_wig.py to combined_wig.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/prot_table.py to prot_table.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/transit_gui.py to transit_gui.cpython-39.pyc running install_egg_info Copying tnseq_transit.egg-info to /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/tnseq_transit-3.2.1.egg-info Skipping SOURCES.txt running install_scripts Installing tpp script to /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/bin Installing transit script to /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/bin debian/rules override_dh_install make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird betreten dh_install mv debian/tnseq-transit/usr/bin/tpp debian/tnseq-transit/usr/bin/transit-tpp make[1]: Verzeichnis „/build/tnseq-transit-3.2.1“ wird verlassen dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: Paket »tnseq-transit« wird in »../tnseq-transit_3.2.1-1_i386.deb« gebaut. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tnseq-transit_3.2.1-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/35737/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/35737/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/35737 and its subdirectories I: Current time: Fri Aug 19 11:03:09 +14 2022 I: pbuilder-time-stamp: 1660856589