Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/t/tipp/tipp_1.0+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/tipp-1.0+dfsg-2wvek4j_y/tipp_1.0+dfsg-2_amd64.buildinfo Get source package info: tipp=1.0+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/tipp/1.0+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=ant=1.10.11-1 antlr=2.7.7+dfsg-12 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-8 binutils-common=2.37-8 binutils-x86-64-linux-gnu=2.37-8 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20211016 ca-certificates-java=20190909 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-10 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 default-jre=2:1.11-72 default-jre-headless=2:1.11-72 dh-autoreconf=20 dh-python=5.20211114 dh-strip-nondeterminism=1.12.0-2 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.2.0-10 gcc=4:11.2.0-2 gcc-11=11.2.0-10 gcc-11-base=11.2.0-10 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 groovy=2.4.21-1 gzip=1.10-4 hmmer=3.3.2+dfsg-1 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 ivy=2.5.0-2 java-common=0.72 junit4=4.13.1-2 libacl1=2.3.1-1 libantlr-java=2.7.7+dfsg-12 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-10 libasm-java=9.2-1 libasound2=1.2.5.1-1 libasound2-data=1.2.5.1-1 libatomic1=11.2.0-10 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libavahi-client3=0.8-5 libavahi-common-data=0.8-5 libavahi-common3=0.8-5 libbinutils=2.37-8 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbsf-java=1:2.4.0-8 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-10 libcom-err2=1.46.4-1 libcommons-beanutils-java=1.9.4-1 libcommons-cli-java=1.4-2 libcommons-collections3-java=3.2.2-2 libcommons-lang-java=2.6-9 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-8 libctf0=2.37-8 libcups2=2.3.3op2-7 libdb5.3=5.3.28+dfsg1-0.8 libdbus-1-3=1.12.20-3 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdivsufsort3=2.0.1-5 libdpkg-perl=1.20.9 libdrm-amdgpu1=2.4.108-1 libdrm-common=2.4.108-1 libdrm-intel1=2.4.108-1 libdrm-nouveau2=2.4.108-1 libdrm-radeon1=2.4.108-1 libdrm2=2.4.108-1 libedit2=3.1-20210910-1 libel-api-java=3.0.0-3 libelf1=0.185-2 libexpat1=2.4.1-3 libezmorph-java=1.0.6-4 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.0-2 libfontconfig1=2.13.1-4.2 libfreetype6=2.11.0+dfsg-1 libgcc-11-dev=11.2.0-10 libgcc-s1=11.2.0-10 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgif7=5.1.9-2 libgl1=1.3.4-2+b1 libgl1-mesa-dri=21.2.5-1 libglapi-mesa=21.2.5-1 libglib2.0-0=2.70.1-1 libglvnd0=1.3.4-2+b1 libglx-mesa0=21.2.5-1 libglx0=1.3.4-2+b1 libgmp10=2:6.2.1+dfsg-2 libgnutls30=3.7.2-2 libgomp1=11.2.0-10 libgoogle-gson-java=2.8.8-1 libgpg-error0=1.42-3 libgraphite2-3=1.3.14-1 libgsl25=2.7+dfsg-2 libgslcblas0=2.7+dfsg-2 libgssapi-krb5-2=1.18.3-7 libhamcrest-java=1.3-9 libharfbuzz0b=2.7.4-1 libhawtjni-runtime-java=1.17-1 libhogweed6=3.7.3-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-10 libjansi-java=1.18-1 libjansi-native-java=1.8-1 libjaxen-java=1.1.6-4 libjenkins-json-java=2.4-jenkins-3-6 libjline2-java=2.14.6-4 libjpeg62-turbo=1:2.1.1-2 libjson-java=2.4-3.1 libjsp-api-java=2.3.4-3 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblcms2-2=2.12~rc1-2 libllvm12=1:12.0.1-16 liblmdb0=0.9.24-1 liblsan0=11.2.0-10 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmbedcrypto3=2.16.9-0.1 libmbedtls12=2.16.9-0.1 libmbedx509-0=2.16.9-0.1 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.32-1 libnss3=2:3.72-2 liboro-java=2.0.8a-14 libp11-kit0=0.24.0-5 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpciaccess0=0.16-1 libpcre2-8-0=10.39-2 libpcre3=2:8.39-13 libpcsclite1=1.9.4-1 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpng16-16=1.6.37-3 libpython3-stdlib=3.9.8-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libqdox-java=1.12.1-3 libquadmath0=11.2.0-10 libreadline8=8.1-2 libseccomp2=2.5.2-2 libselinux1=3.3-1 libsensors-config=1:3.6.0-7 libsensors5=1:3.6.0-7 libservlet-api-java=4.0.1-2 libservlet3.1-java=1:4.0.1-2 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-10 libstdc++6=11.2.0-10 libsub-override-perl=0.09-2 libsystemd0=249.6-2 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-10 libubsan1=11.2.0-10 libuchardet0=0.0.7-1 libudev1=249.6-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libvulkan1=1.2.189.0-2 libwebsocket-api-java=1.1-2 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libx11-xcb1=2:1.7.2-2+b1 libxau6=1:1.0.9-1 libxcb-dri2-0=1.14-3 libxcb-dri3-0=1.14-3 libxcb-glx0=1.14-3 libxcb-present0=1.14-3 libxcb-shm0=1.14-3 libxcb-sync1=1.14-3 libxcb-xfixes0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxerces2-java=2.12.1-1 libxext6=2:1.3.4-1 libxfixes3=1:5.0.3-2 libxi6=2:1.8-1 libxml-commons-external-java=1.4.01-5 libxml-commons-resolver1.1-java=1.2-11 libxml2=2.9.12+dfsg-5 libxom-java=1.2.10-2 libxpp3-java=1.1.4c-3 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxstream-java=1.4.18-2 libxtst6=2:1.2.3-1 libxxf86vm1=1:1.1.4-1+b2 libz3-4=4.8.12-1+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.16-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncbi-blast+=2.11.0+ds-1 ncbi-data=6.1.20170106+dfsg1-9 ncurses-base=6.2+20210905-1 ncurses-bin=6.3-1 openjdk-11-jre=11.0.13+8-1 openjdk-11-jre-headless=11.0.13+8-1 openssl=1.1.1l-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 pplacer=1.1~alpha19-5 python3=3.9.8-1 python3-dendropy=4.5.2-1 python3-distutils=3.9.9-2 python3-lib2to3=3.9.9-2 python3-minimal=3.9.8-1 python3-pkg-resources=58.2.0-1 python3-setuptools=58.2.0-1 python3.9=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sepp=4.5.1+really4.5.1+dfsg-2 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 ucf=3.0043 util-linux=2.37.2-4 x11-common=1:7.7+23 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211123T025155Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211123T025155Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211126T150138Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211115T152612Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d tipp=1.0+dfsg-2 && mkdir -p /build/tipp-ULiuuf && dpkg-source --no-check -x /*.dsc /build/tipp-ULiuuf/tipp-1.0+dfsg && chown -R builduser:builduser /build/tipp-ULiuuf" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tipp-ULiuuf/tipp-1.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637165968" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/tipp-ULiuuf /tmp/tipp-1.0+dfsg-2wvek4j_y bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.w2YAnM68uL as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.w2YAnM68uL Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1013 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4669 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211123T025155Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211123T025155Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211126T150138Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211115T152612Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.w2YAnM68uL Get:1 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages [12.0 MB] Fetched 35.2 MB in 29s (1202 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.w2YAnM68uL I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d tipp=1.0+dfsg-2 && mkdir -p /build/tipp-ULiuuf && dpkg-source --no-check -x /*.dsc /build/tipp-ULiuuf/tipp-1.0+dfsg && chown -R builduser:builduser /build/tipp-ULiuuf"' exec /tmp/mmdebstrap.w2YAnM68uL Reading package lists... NOTICE: 'tipp' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tipp.git Please use: git clone https://salsa.debian.org/med-team/tipp.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 79.1 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main tipp 1.0+dfsg-2 (dsc) [2040 B] Get:2 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main tipp 1.0+dfsg-2 (tar) [67.1 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211123T025155Z bookworm/main tipp 1.0+dfsg-2 (diff) [10.0 kB] Fetched 79.1 kB in 0s (835 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'tipp_1.0+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting tipp in /build/tipp-ULiuuf/tipp-1.0+dfsg dpkg-source: info: unpacking tipp_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking tipp_1.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying setup.patch dpkg-source: info: applying use_debian_packaged_guppy_from_pplacer.patch dpkg-source: info: applying change_java_version_for_ant.patch dpkg-source: info: applying java_build.patch dpkg-source: info: applying configuration_files_in_etc_and_per_user.patch dpkg-source: info: applying using_python3_interpreter.patch dpkg-source: info: applying tipp_metagenomics.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tipp-ULiuuf/tipp-1.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637165968" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.w2YAnM68uL dpkg-buildpackage: info: source package tipp dpkg-buildpackage: info: source version 1.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_auto_clean I: pybuild base:237: python3.9 setup.py clean running clean removing '/build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -f -rf tools/bundled rm -f -rf tools/merge/build rm -f tipp.config find . -name "*.class" -delete find . -name "*.jar" -delete make[1]: Leaving directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild debian/rules override_dh_auto_configure make[1]: Entering directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_auto_configure I: pybuild base:237: python3.9 setup.py config running config # Building the jar for tipp. cd tools/merge && \ CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant -f tipp.xml Buildfile: /build/tipp-ULiuuf/tipp-1.0+dfsg/tools/merge/tipp.xml clean: compile: [mkdir] Created dir: /build/tipp-ULiuuf/tipp-1.0+dfsg/tools/merge/classes [javac] /build/tipp-ULiuuf/tipp-1.0+dfsg/tools/merge/tipp.xml:32: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 23 source files to /build/tipp-ULiuuf/tipp-1.0+dfsg/tools/merge/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] /build/tipp-ULiuuf/tipp-1.0+dfsg/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Trees.java:32: warning: SunGraphicsEnvironment is internal proprietary API and may be removed in a future release [javac] import sun.java2d.SunGraphicsEnvironment; [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 warnings jar: [jar] Building jar: /build/tipp-ULiuuf/tipp-1.0+dfsg/tools/merge/tippJsonMerger.jar BUILD SUCCESSFUL Total time: 3 seconds # Creating the config files. BLAST="/usr/bin/blastn" python3 setup.py tipp running tipp Creating main TIPP config file at /build/tipp-ULiuuf/tipp-1.0+dfsg/.tipp/tipp.config and tools at /build/tipp-ULiuuf/tipp-1.0+dfsg/.tipp Warning! REFERENCE variable is not defined. If you plan to run TIPP for abundance profiling, then have REFERENCE pointed to Reference directory. You can also change your config to point to the Reference directory by including the following line in your config: [reference] path=/location/of/reference_directory/ make[1]: Leaving directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3 setup.py build running build running build_py creating /build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build/tipp copying tipp/__init__.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build/tipp copying tipp/exhaustive_tipp.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build/tipp copying tipp/metagenomics.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build/tipp running build_scripts creating build creating build/scripts-3.9 copying and adjusting run_abundance.py -> build/scripts-3.9 copying and adjusting run_tipp.py -> build/scripts-3.9 copying and adjusting run_tipp_tool.py -> build/scripts-3.9 changing mode of build/scripts-3.9/run_abundance.py from 644 to 755 changing mode of build/scripts-3.9/run_tipp.py from 644 to 755 changing mode of build/scripts-3.9/run_tipp_tool.py from 644 to 755 dh: command-omitted: The call to "dh_auto_test -a -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_auto_install I: pybuild base:237: /usr/bin/python3 setup.py install --root /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp running install running build running build_py running build_scripts running install_lib creating /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr creating /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib creating /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9 creating /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages creating /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp copying /build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build/tipp/__init__.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp copying /build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build/tipp/exhaustive_tipp.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp copying /build/tipp-ULiuuf/tipp-1.0+dfsg/.pybuild/cpython3_3.9/build/tipp/metagenomics.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp byte-compiling /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp/exhaustive_tipp.py to exhaustive_tipp.cpython-39.pyc byte-compiling /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp/metagenomics.py to metagenomics.cpython-39.pyc running install_data copying home.path -> /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/ running install_egg_info running egg_info creating tipp.egg-info writing tipp.egg-info/PKG-INFO writing dependency_links to tipp.egg-info/dependency_links.txt writing requirements to tipp.egg-info/requires.txt writing top-level names to tipp.egg-info/top_level.txt writing manifest file 'tipp.egg-info/SOURCES.txt' reading manifest file 'tipp.egg-info/SOURCES.txt' writing manifest file 'tipp.egg-info/SOURCES.txt' Copying tipp.egg-info to /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/lib/python3.9/dist-packages/tipp-1.1.0.egg-info Skipping SOURCES.txt running install_scripts creating /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/bin copying build/scripts-3.9/run_abundance.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/bin copying build/scripts-3.9/run_tipp.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/bin copying build/scripts-3.9/run_tipp_tool.py -> /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/bin changing mode of /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/bin/run_abundance.py to 755 changing mode of /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/bin/run_tipp.py to 755 changing mode of /build/tipp-ULiuuf/tipp-1.0+dfsg/debian/tipp/usr/bin/run_tipp_tool.py to 755 # Deleting upstream configuration file, which we are not packaging. rm -f debian/tipp/usr/home.path make[1]: Leaving directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_installman --language=C make[1]: Leaving directory '/build/tipp-ULiuuf/tipp-1.0+dfsg' dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package tipp: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'tipp' in '../tipp_1.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tipp_1.0+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/tipp-ULiuuf /tmp/tipp-1.0+dfsg-2wvek4j_y I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: hsperfdata_builduser I: removing tempdir /tmp/mmdebstrap.w2YAnM68uL... I: success in 608.3474 seconds md5: tipp_1.0+dfsg-2_amd64.deb: OK sha1: tipp_1.0+dfsg-2_amd64.deb: OK sha256: tipp_1.0+dfsg-2_amd64.deb: OK Checksums: OK