debspawn 0.6.5 on fennel at 2024-10-17 11:19:33 UTC-0700 gpgv: Signature made Sun 25 Aug 2024 09:49:00 AM PDT gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for /var/lib/lkspark/workspaces/45ffa331-9b4e-406f-b013-c151f5de7840/mapdamage_2.2.2+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting mapdamage in mapdamage-2.2.2+dfsg dpkg-source: info: unpacking mapdamage_2.2.2+dfsg.orig.tar.xz dpkg-source: info: unpacking mapdamage_2.2.2+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_seqtk.patch ╔═══════════════════════╗ ║ Package build ║ ╚═══════════════════════╝ Package: mapdamage Version: 2.2.2+dfsg-1 Distribution: landing Architecture: amd64 Free space in workspace: 64.4GiB ┌───────────────────────────────────────┐ │ Preparing container for build │ └───────────────────────────────────────┘ Get:1 https://repo.pureos.net/pureos landing InRelease [9625 B] Get:2 https://repo.pureos.net/pureos landing/main all Packages [3883 kB] Get:3 https://repo.pureos.net/pureos landing/main amd64 Packages [4392 kB] Fetched 8285 kB in 2s (4215 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: gpgv 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/218 kB of archives. After this operation, 1024 B disk space will be freed. debconf: delaying package configuration, since apt-utils is not installed (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 ... 13780 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.44-1_amd64.deb ... Unpacking gpgv (2.2.44-1) over (2.2.43-8+b1) ... Setting up gpgv (2.2.44-1) ... Reading package lists... Building dependency tree... Reading state information... build-essential is already the newest version (12.10). dpkg-dev is already the newest version (1.21.22pureos1). fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌───────────────────────────────────────────────┐ │ Installing package build-dependencies │ └───────────────────────────────────────────────┘ Note, using directory './' to get the build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libcairo2 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdebhelper-perl libdeflate0 libelf1t64 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libicu72 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libmagic-mgc libmagic1t64 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 m4 man-db media-types netbase po-debconf python3 python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-pkg-resources python3-pysam python3-setuptools python3-typeguard python3-typing-extensions python3-zipp python3.12 r-base-core r-cran-cli r-cran-codetools r-cran-colorspace r-cran-fansi r-cran-farver r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-isoband r-cran-iterators r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common sensible-utils seqtk ucf unzip x11-common xdg-utils zip 0 upgraded, 161 newly installed, 0 to remove and 0 not upgraded. Need to get 4580 kB/108 MB of archives. After this operation, 280 MB of additional disk space will be used. Get:1 https://repo.pureos.net/pureos landing/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:2 https://repo.pureos.net/pureos landing/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:3 https://repo.pureos.net/pureos landing/main amd64 python3-pysam amd64 0.22.1+ds-2+b1 [3474 kB] Get:4 https://repo.pureos.net/pureos landing/main amd64 r-cran-gam amd64 1.22-5-1 [395 kB] Get:5 https://repo.pureos.net/pureos landing/main all r-cran-inline all 0.3.19-2 [129 kB] Get:6 https://repo.pureos.net/pureos landing/main amd64 seqtk amd64 1.4-2 [34.6 kB] Fetched 4580 kB in 1s (5869 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package media-types. (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 ... 13779 files and directories currently installed.) Preparing to unpack .../000-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../002-libncursesw6_6.5-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2) ... 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Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... 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Processing triggers for libc-bin (2.40-3) ... ┌───────────────┐ │ Build │ └───────────────┘ dpkg-buildpackage: info: source package mapdamage dpkg-buildpackage: info: source version 2.2.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: host architecture amd64  dpkg-source --before-build .  debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/srv/build/mapdamage-2.2.2+dfsg' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f mapdamage/_version.py rm -f mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Length_plot.pdf mapdamage/tests/results/Length_plot.pdf rm -f mapdamage/tests/fake1.fasta.fai mapdamage/tests/results/3pGtoA_freq.txt mapdamage/tests/results/5pCtoT_freq.txt mapdamage/tests/results/Runtime_log.txt mapdamage/tests/results/dnacomp.txt mapdamage/tests/results/lgdistribution.txt mapdamage/tests/results/misincorporation.txt mapdamage/tests/test.rescaled.sam make[1]: Leaving directory '/srv/build/mapdamage-2.2.2+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild  debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules override_dh_auto_test make[1]: Entering directory '/srv/build/mapdamage-2.2.2+dfsg' cd mapdamage && \ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/srv/build/mapdamage-2.2.2+dfsg/bin \ PYTHONPATH=/srv/build/mapdamage-2.2.2+dfsg/.pybuild/cpython3_3.12/build \ python3 mp_test.py Missing the following R libraries 'Rcpp' and 'RcppGSL' The Bayesian estimation has been disabled Started with the command: /srv/build/mapdamage-2.2.2+dfsg/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats Reading from 'tests/test.bam' Writing results to 'tests/results/' pdf tests/results/Fragmisincorporation_plot.pdf generated additional tests/results/Length_plot.pdf generated Successful run .. ---------------------------------------------------------------------- Ran 2 tests in 2.900s OK make[1]: Leaving directory '/srv/build/mapdamage-2.2.2+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/mapdamage/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /srv/build/mapdamage-2.2.2+dfsg/debian/mapdamage dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/srv/build/mapdamage-2.2.2+dfsg' dh_python3 --no-ext-rename make[1]: Leaving directory '/srv/build/mapdamage-2.2.2+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/srv/build/mapdamage-2.2.2+dfsg' dh_fixperms find debian -name checkLibraries.R -exec chmod +x \{\} \; find debian -name runGeneral.R -exec chmod +x \{\} \; make[1]: Leaving directory '/srv/build/mapdamage-2.2.2+dfsg' dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'mapdamage' in '../mapdamage_2.2.2+dfsg-1_all.deb'.  dpkg-genbuildinfo --build=binary -O../mapdamage_2.2.2+dfsg-1_amd64.buildinfo  dpkg-genchanges -DDistribution=landing --build=binary -mDebian Med Packaging Team -eDebian Med Packaging Team -O../mapdamage_2.2.2+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included)  dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) This build required 698.1KiB of dedicated disk space. ┌────────────────────────────────────┐ │ Retrieving build artifacts │ └────────────────────────────────────┘ Copied 4 files. Done.