Diff of the two buildlogs: -- --- b1/build.log 2023-04-14 02:45:49.188299325 +0000 +++ b2/build.log 2023-04-14 03:12:26.705332617 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 13 14:12:51 -12 2023 -I: pbuilder-time-stamp: 1681438371 +I: Current time: Thu May 16 23:08:53 +14 2024 +I: pbuilder-time-stamp: 1715850533 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./cnvkit_0.9.9.orig.tar.gz] I: copying [./cnvkit_0.9.9-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Oct 14 18:51:53 2021 -12 +gpgv: Signature made Fri Oct 15 20:51:53 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key @@ -31,11 +31,20 @@ dpkg-source: info: applying controldir I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/5568/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4273/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-arm64. +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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/4273/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4273/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME='pbuilder2' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' @@ -45,38 +54,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='5568' + PPID='4273' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.1lfsPxIA/pbuilderrc_OFiD --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1lfsPxIA/b1 --logfile b1/build.log cnvkit_0.9.9-2.dsc' + 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/r-b-build.1lfsPxIA/pbuilderrc_5fUy --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1lfsPxIA/b2 --logfile b2/build.log --extrapackages usrmerge cnvkit_0.9.9-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink12-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 11 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/5568/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 14 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4273/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -354,7 +363,7 @@ Get: 208 http://deb.debian.org/debian bookworm/main arm64 r-base-core arm64 4.2.2.20221110-2 [25.7 MB] Get: 209 http://deb.debian.org/debian bookworm/main arm64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get: 210 http://deb.debian.org/debian bookworm/main arm64 r-bioc-dnacopy arm64 1.72.3-1 [375 kB] -Fetched 174 MB in 4s (47.9 MB/s) +Fetched 174 MB in 4s (40.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-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 ... 19616 files and directories currently installed.) @@ -1238,8 +1247,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/cnvkit-0.9.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cnvkit_0.9.9-2_source.changes +I: user script /srv/workspace/pbuilder/4273/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/4273/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/cnvkit-0.9.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cnvkit_0.9.9-2_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.9-2 dpkg-buildpackage: info: source distribution unstable @@ -1249,12 +1267,12 @@ debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt binnengegaan cd test && /usr/bin/make clean || /bin/true -make[2]: Entering directory '/build/cnvkit-0.9.9/test' +make[2]: Map '/build/cnvkit-0.9.9/test' wordt binnengegaan # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf -make[2]: Leaving directory '/build/cnvkit-0.9.9/test' +make[2]: Map '/build/cnvkit-0.9.9/test' wordt verlaten if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:240: python3.11 setup.py clean @@ -1264,7 +1282,7 @@ 'build/scripts-3.11' does not exist -- can't clean it rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info -make[1]: Leaving directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -1275,7 +1293,7 @@ I: pybuild base:240: python3.11 setup.py config running config debian/rules override_dh_auto_build -make[1]: Entering directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt binnengegaan [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ @@ -1376,15 +1394,15 @@ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py -make[1]: Leaving directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt binnengegaan cd test && /usr/bin/make -make[2]: Entering directory '/build/cnvkit-0.9.9/test' +make[2]: Map '/build/cnvkit-0.9.9/test' wordt binnengegaan python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cb7v8779 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-21cp5gyj because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Created directory build/ Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions @@ -1399,7 +1417,7 @@ python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-z9cvyqe2 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-90jniec2 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Number of target and antitarget files: 3, 3 No FASTA reference genome provided; skipping GC, RM calculations @@ -1772,7 +1790,7 @@ python3 ../cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yjqu575k because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-l8tq6i71 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-5_5 Keeping 6308 of 6646 bins @@ -1791,20 +1809,20 @@ python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-z31ydxw_ because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-q_9yx4aj because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vdic7ciu because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2kbzpwio because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ppldonyd because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-kaktf6k5 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-9_2 Keeping 6308 of 6646 bins @@ -1823,20 +1841,20 @@ python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-412el_as because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9mkifv8m because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-d59n3jyi because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-170rnqb7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9erdu04e because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h4y605zv because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_1 Keeping 6308 of 6646 bins @@ -1855,20 +1873,20 @@ python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bq8bhv_2 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qlll2lvx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-l_mszmep because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tsos7ph0 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-x61s7zh5 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ef63pt63 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_2 Keeping 6308 of 6646 bins @@ -1887,20 +1905,20 @@ python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xx3_l58v because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k5ff34sb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-88o__utw because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_dw4kji1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-kl845efw because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4q8dbyay because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_3 Keeping 6308 of 6646 bins @@ -1919,20 +1937,20 @@ python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ofx2aoga because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dtks8c1q because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t9hkfezx because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0v3j657l because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8m6bwz5s because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cv9hjojj because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_4 Keeping 6308 of 6646 bins @@ -1951,7 +1969,7 @@ python3 ../cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-mfecmq9s because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4jz8b6xs because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_5 Keeping 6308 of 6646 bins @@ -1970,7 +1988,7 @@ python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-frp5plge because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gskl4b01 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 8 / 49 bins on chromosome chrY @@ -1978,7 +1996,7 @@ python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ls0lcqlx because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-e4slwezo because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 1 / 949 bins on chromosome chr6 @@ -1987,7 +2005,7 @@ python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dxdmz60r because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-slnu7g4_ because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 6 / 49 bins on chromosome chrY @@ -1995,7 +2013,7 @@ python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wlextxhz because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ujpo55je because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 7 / 49 bins on chromosome chrY @@ -2003,7 +2021,7 @@ python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2ts8v0oi because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a8h3pkc3 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 11 / 49 bins on chromosome chrY @@ -2011,7 +2029,7 @@ python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2_fc8rz9 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1tse8skh because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 8 / 49 bins on chromosome chrY @@ -2019,7 +2037,7 @@ python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9wpc98k3 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vane_35t because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 6 / 49 bins on chromosome chrY @@ -2027,48 +2045,48 @@ python3 ../cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y2z76usu because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-023aqkwi because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-5_5-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-om_6hm_d because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bw__8d2t because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Smoothing overshot at 3 / 97 indices: (-19.887157566382847, -3.337830278732136) vs. original (-19.2826, -0.27873) Wrote p2-9_2-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yoqohm7o because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9nj0cidl because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 1480 probes and 0 selected genes in region chr1 Wrote p2-9_2-chr1-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-frrw9eu3 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-kbmv954a because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 201 probes and 0 selected genes in region chr21 Wrote p2-9_2-chr21-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fsfdegem because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-767wkwgi because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 330 probes and 13 selected genes in region chr9:149999-45000000 Wrote p2-9_2-chr9p-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ma8f1k1j because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_drey8rb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 179 probes and 2 selected genes in region chr9:0-14504268 Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-oxa40f3_ because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-swd3fmmd because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Detected file format: bed Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 @@ -2078,7 +2096,7 @@ python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-g5fng14l because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-12ag5pa8 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. @@ -2181,7 +2199,7 @@ python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wxuq7jid because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k37l6j59 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. @@ -2284,7 +2302,7 @@ python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-w2n7y9bz because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1gj2n4oq because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. @@ -2387,7 +2405,7 @@ python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-os86tqb3 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-n_mgrs6b because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. @@ -2490,35 +2508,35 @@ python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-trfwl0io because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j4e0e9ea because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female Wrote p2-5_5-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1lcncq_w because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ixblknnk because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female Wrote p2-9_2-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-mc8jy7v6 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ja4ktj1o because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female Wrote p2-20_1-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fyz40vt9 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-6a45nf80 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female Wrote p2-20_2-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rnw6yonv because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-erdawkr4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. @@ -2583,7 +2601,7 @@ python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-acwie4k3 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fk_xtcbk because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. @@ -2698,7 +2716,7 @@ python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9ebx_g9f because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-l716xm7g because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. @@ -2791,7 +2809,7 @@ python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ycovxoum because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nqtb46ts because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. @@ -2900,7 +2918,7 @@ python3 ../cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fxjoip2w because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lr4qzkua because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female Treating sample p2-9_2 as female @@ -2913,14 +2931,14 @@ python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nh4sfo0n because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tg5ui82x because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Found 15 gene breakpoints Wrote p2-9_2-breaks.txt python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vy6y2ai2 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-va1o3zbl because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. @@ -3028,37 +3046,37 @@ python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7tt5q4py because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vdgvxpzz because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote gender-picard.txt python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h_1wfskj because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-01dbrlv4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-all.cdt python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3xypj60h because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2sur_fqa because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-all-jtv.txt python3 ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-15jl7z82 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7c0tavi6 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-all.seg python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_vuqqrud because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3w36kj39 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-9_2.nexus python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-km5yprqb because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wgmc_tgh because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Selected test sample NA12882 and control sample NA12878 Loaded 3654 records; skipped: 514 somatic, 394 depth @@ -3072,7 +3090,7 @@ python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-blte58zl because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-op5da79u because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female Rescaling sample with purity 0.65, ploidy 2 @@ -3080,7 +3098,7 @@ python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5mand3cl because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-oalokat3 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female Rescaling sample with purity 0.65, ploidy 2 @@ -3088,7 +3106,7 @@ python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-pxzdlmqq because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9lq6dfmo because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female Rescaling sample with purity 0.65, ploidy 2 @@ -3096,7 +3114,7 @@ python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ek8gsjj3 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3srnxzqh because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female Rescaling sample with purity 0.65, ploidy 2 @@ -3104,7 +3122,7 @@ python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lr3i2_t8 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-274d3mb0 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_3 as female Rescaling sample with purity 0.65, ploidy 2 @@ -3112,7 +3130,7 @@ python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zjttegz5 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fk75zfss because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 @@ -3120,7 +3138,7 @@ python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-surx79wv because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0tdbtbzd because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 @@ -3128,7 +3146,7 @@ python3 ../cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-uzs2m755 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fmd8f8gd because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5.call as female Treating sample p2-9_2.call as female @@ -3141,7 +3159,7 @@ python3 ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-uus3ux56 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-30rva112 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2.call as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. @@ -3152,7 +3170,7 @@ python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fq4graan because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7w9lff8r because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} @@ -3165,7 +3183,7 @@ --ci --pi --sem --smooth-bootstrap /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a15ld0io because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-kabyyy8w because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} @@ -3176,7 +3194,7 @@ --ci -b 50 -a 0.5 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8pwmilyz because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3rd9djn1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} @@ -3186,7 +3204,7 @@ python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-55x06xdm because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p2co5qyw because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} @@ -3196,7 +3214,7 @@ python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-c_383xh7 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-toumlaf7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} @@ -3206,7 +3224,7 @@ python3 ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vey5e2cu because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y1e_tgjn because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} @@ -3229,19 +3247,19 @@ /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote p2-20-metrics.tsv -make[2]: Leaving directory '/build/cnvkit-0.9.9/test' +make[2]: Map '/build/cnvkit-0.9.9/test' wordt verlaten cd test && /usr/bin/make clean || /bin/true -make[2]: Entering directory '/build/cnvkit-0.9.9/test' +make[2]: Map '/build/cnvkit-0.9.9/test' wordt binnengegaan # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf -make[2]: Leaving directory '/build/cnvkit-0.9.9/test' +make[2]: Map '/build/cnvkit-0.9.9/test' wordt verlaten rm -Rf test/build test/*.tsv -make[1]: Leaving directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install -make[1]: Entering directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt binnengegaan [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ @@ -3413,7 +3431,7 @@ copying build/scripts-3.11/cnvkit-reference2targets -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-skg_convert -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin -changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/snpfilter.sh to 755 +changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/snpfilter.sh to 775 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 @@ -3428,7 +3446,7 @@ PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.9 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wexsnid7 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k3gvctnb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.9 --help-option='-h' \ @@ -3438,7 +3456,7 @@ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py -make[1]: Leaving directory '/build/cnvkit-0.9.9' +make[1]: Map '/build/cnvkit-0.9.9' wordt verlaten dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild @@ -3459,7 +3477,7 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.9-2_arm64.deb'. +dpkg-deb: pakket 'cnvkit' wordt gebouwd in '../cnvkit_0.9.9-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../cnvkit_0.9.9-2_arm64.buildinfo dpkg-genchanges --build=binary -O../cnvkit_0.9.9-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3467,12 +3485,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/4273/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4273/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/5568 and its subdirectories -I: Current time: Thu Apr 13 14:45:48 -12 2023 -I: pbuilder-time-stamp: 1681440348 +I: removing directory /srv/workspace/pbuilder/4273 and its subdirectories +I: Current time: Thu May 16 23:35:25 +14 2024 +I: pbuilder-time-stamp: 1715852125