Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gatk-bwamem/gatk-bwamem_1.0.4+dfsg2-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gatk-bwamem-1.0.4+dfsg2-2jeq921w9/gatk-bwamem_1.0.4+dfsg2-2_amd64.buildinfo Get source package info: gatk-bwamem=1.0.4+dfsg2-2 Source URL: http://snapshot.notset.fr/mr/package/gatk-bwamem/1.0.4+dfsg2-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=ant=1.10.12-3 ant-optional=1.10.12-3 antlr=2.7.7+dfsg-12 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6.1 binutils=2.38.90.20220713-2 binutils-common=2.38.90.20220713-2 binutils-x86-64-linux-gnu=2.38.90.20220713-2 bnd=5.0.1-3 bsdextrautils=2.38-5 bsdutils=1:2.38-5 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 ca-certificates-java=20220719 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-5 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.8 debianutils=5.7-0.2 default-jdk-headless=2:1.11-72 default-jre-headless=2:1.11-72 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.9 dpkg-dev=1.21.9 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.3.0-5 gcc=4:11.2.0-2 gcc-11=11.3.0-5 gcc-11-base=11.3.0-5 gcc-12-base=12.1.0-7 gettext=0.21-6 gettext-base=0.21-6 gradle=4.4.1-14 gradle-debian-helper=2.3 grep=3.7-1 groff-base=1.22.4-8 groovy=2.4.21-2 gzip=1.12-1 hostname=3.23 init-system-helpers=1.64 intltool-debian=0.35.0+20060710.5 ivy=2.5.0-2 java-common=0.72 java-wrappers=0.3 junit4=4.13.2-1 libacl1=2.3.1-1 libantlr-java=2.7.7+dfsg-12 libaopalliance-java=20070526-6 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-5 libasm-java=9.3-1 libasound2=1.2.7.1-1 libasound2-data=1.2.7.1-1 libatinject-jsr330-api-java=1.0+ds1-5 libatomic1=12.1.0-7 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libavahi-client3=0.8-6 libavahi-common-data=0.8-6 libavahi-common3=0.8-6 libbcel-java=6.5.0-1 libbcpg-java=1.71-1 libbcprov-java=1.71-1 libbinutils=2.38.90.20220713-2 libblkid1=2.38-5 libbrotli1=1.0.9-2+b3 libbsf-java=1:2.4.0-8 libbsh-java=2.0b4-20 libbz2-1.0=1.0.8-5 libc-bin=2.33-8 libc-dev-bin=2.33-8 libc6=2.33-8 libc6-dev=2.33-8 libcap-ng0=0.8.3-1 libcap2=1:2.44-1 libcc1-0=12.1.0-7 libcdi-api-java=1.2-3 libcom-err2=1.46.5-2 libcommons-cli-java=1.4-2 libcommons-codec-java=1.15-1 libcommons-collections3-java=3.2.2-2 libcommons-compress-java=1.21-1 libcommons-io-java=2.11.0-2 libcommons-lang-java=2.6-10 libcommons-lang3-java=3.12.0-2 libcommons-logging-java=1.2-3 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.28-2 libcrypt1=1:4.4.28-2 libctf-nobfd0=2.38.90.20220713-2 libctf0=2.38.90.20220713-2 libcups2=2.4.2-1 libdb5.3=5.3.28+dfsg1-0.10 libdbus-1-3=1.14.0-2 libdd-plist-java=1.20-1.1 libdebconfclient0=0.263 libdebhelper-perl=13.8 libdom4j-java=2.1.3-2 libdpkg-perl=1.21.9 libeclipse-jdt-annotation-java=2.2.600+eclipse4.21-1 libel-api-java=3.0.0-3 libelf1=0.187-1 libexpat1=2.4.8-1 libfelix-framework-java=4.6.1-2.1 libfelix-gogo-runtime-java=0.16.2-1.1 libfelix-resolver-java=1.16.0-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfindbugs-java=3.1.0~preview2-3 libfontconfig1=2.13.1-4.4 libfreetype6=2.12.1+dfsg-3 libgcc-11-dev=11.3.0-5 libgcc-s1=12.1.0-7 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgeronimo-annotation-1.3-spec-java=1.3-1 libgeronimo-interceptor-3.0-spec-java=1.0.1-4 libglib2.0-0=2.72.3-1 libgmp10=2:6.2.1+dfsg1-1 libgnutls30=3.7.6-2 libgomp1=12.1.0-7 libgoogle-gson-java=2.9.0-1 libgpg-error0=1.45-2 libgprofng0=2.38.90.20220713-2 libgradle-core-java=4.4.1-14 libgradle-plugins-java=4.4.1-14 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b2 libguava-java=29.0-6 libguice-java=4.2.3-2 libhamcrest-java=1.3-9 libharfbuzz0b=2.7.4-1+b1 libhawtjni-runtime-java=1.18-1 libhogweed6=3.7.3-1 libhttpclient-java=4.5.13-3 libhttpcore-java=4.4.15-1 libicu71=71.1-3 libidn2-0=2.3.3-1 libisl23=0.25-1 libitm1=12.1.0-7 libjansi-java=2.4.0-1 libjansi-native-java=1.8-1 libjansi1-java=1.18-3 libjarjar-java=1.4+svn142-12 libjatl-java=0.2.3-1.1 libjavaewah-java=1.1.7-1 libjaxen-java=1.1.6-4 libjcifs-java=1.3.19-2 libjcip-annotations-java=20060626-6 libjcommander-java=1.71-3 libjetty9-java=9.4.48-1 libjformatstring-java=0.10~20131207-2.1 libjgit-java=4.11.9-1 libjline2-java=2.14.6-5 libjna-java=5.9.0-1 libjna-jni=5.9.0-1 libjpeg62-turbo=1:2.1.2-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjsch-java=0.1.55-1 libjsoup-java=1.15.1-1 libjsp-api-java=2.3.4-3 libjsr305-java=0.1~+svn49-11 libjzlib-java=1.1.3-2 libk5crypto3=1.19.2-2+b2 libkeyutils1=1.6.3-1 libkrb5-3=1.19.2-2+b2 libkrb5support0=1.19.2-2+b2 libkryo-java=2.20-7 liblcms2-2=2.13.1-1 liblogback-java=1:1.2.11-1 liblsan0=12.1.0-7 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmaven-parent-java=31-2 libmaven-resolver-java=1.6.3-1 libmaven-shared-utils-java=3.3.4-1 libmaven3-core-java=3.6.3-5 libminlog-java=1.3.0-1.1 libmount1=2.38-5 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libnative-platform-java=0.14-5 libnative-platform-jni=0.14-5 libncurses6=6.3+20220423-2 libnekohtml-java=1.9.22-1.1 libnettle8=3.7.3-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.34-1 libnss3=2:3.79-1 libobjenesis-java=3.2-1 libosgi-annotation-java=8.0.1-1 libosgi-compendium-java=7.0.0-1 libosgi-core-java=7.0.0-2 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libpcsclite1=1.9.8-1 libperl5.34=5.34.0-5 libpipeline1=1.5.6-1 libplexus-cipher-java=2.0-1 libplexus-classworlds-java=2.6.0-1 libplexus-component-annotations-java=2.1.1-1 libplexus-container-default-java=2.1.1-1 libplexus-interpolation-java=1.26-1 libplexus-sec-dispatcher-java=2.0-3 libplexus-utils2-java=3.3.0-3 libpng16-16=1.6.37-5 libpolyglot-maven-java=0.8~tobrien+git20120905-10 libqdox-java=1.12.1-3 libquadmath0=12.1.0-7 libreflectasm-java=1.11.6+dfsg-1 librhino-java=1.7.7.2-3 libseccomp2=2.5.4-1 libselinux1=3.4-1 libservlet-api-java=4.0.1-2 libservlet3.1-java=1:4.0.1-2 libsigsegv2=2.14-1 libsimde-dev=0.7.2-6 libsimple-http-java=4.1.21-1.1 libsisu-inject-java=0.3.4-2 libsisu-plexus-java=0.3.4-3 libslf4j-java=1.7.32-1 libsmartcols1=2.38-5 libsqlite3-0=3.39.2-1 libssl3=3.0.4-2 libstdc++-11-dev=11.3.0-5 libstdc++6=12.1.0-7 libsub-override-perl=0.09-3 libsystemd0=251.3-1 libtasn1-6=4.18.0-4 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-4 libtsan0=11.3.0-5 libubsan1=12.1.0-7 libuchardet0=0.0.7-1 libudev1=251.3-1 libunistring2=1.0-1 libuuid1=2.38-5 libwagon-file-java=3.3.4-1 libwagon-http-java=3.3.4-1 libwagon-provider-api-java=3.3.4-1 libwebsocket-api-java=1.1-2 libxbean-reflect-java=4.5-8 libxerces2-java=2.12.2-1 libxml-commons-external-java=1.4.01-5 libxml-commons-resolver1.1-java=1.2-11 libxml2=2.9.14+dfsg-1 libxpp3-java=1.1.4c-3 libxstream-java=1.4.19-1 libxz-java=1.9-1 libyaml-snake-java=1.29-1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.18.5-1 login=1:4.11.1+dfsg1-2 lsb-base=11.2 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 maven-repo-helper=1.11 mawk=1.3.4.20200120-3.1 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 openjdk-11-jdk-headless=11.0.16+8-1 openjdk-11-jre-headless=11.0.16+8-1 openssl=3.0.4-2 patch=2.7.6-7 perl=5.34.0-5 perl-base=5.34.0-5 perl-modules-5.34=5.34.0-5 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 testng=6.9.12-4 ucf=3.0043 unzip=6.0-26 util-linux=2.38-5 util-linux-extra=2.38-5 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --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/20220728T033224Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220728T033224Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220804T151519Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220722T085138Z/ 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 gatk-bwamem=1.0.4+dfsg2-2 && mkdir -p /build/gatk-bwamem-yYaNfi && dpkg-source --no-check -x /*.dsc /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2 && chown -R builduser:builduser /build/gatk-bwamem-yYaNfi" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1658553172" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/gatk-bwamem-yYaNfi /tmp/gatk-bwamem-1.0.4+dfsg2-2jeq921w9 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220722T085138Z 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.vStr8sZDpT 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.vStr8sZDpT Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-5). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 401 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220722T085138Z unstable/main amd64 libfakeroot amd64 1.29-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220722T085138Z unstable/main amd64 fakeroot amd64 1.29-1 [87.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (1105 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 ... 4625 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.29-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.29-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.29-1_amd64.deb ... Unpacking fakeroot (1.29-1) ... Setting up libfakeroot:amd64 (1.29-1) ... Setting up fakeroot (1.29-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-8) ... 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/20220728T033224Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220728T033224Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220804T151519Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220722T085138Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.vStr8sZDpT Get:1 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm InRelease [157 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220804T151519Z unstable InRelease [192 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220722T085138Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main Sources [12.1 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main amd64 Packages [11.5 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220804T151519Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220804T151519Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220804T151519Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220804T151519Z unstable/main amd64 Packages [12.6 MB] Fetched 36.5 MB in 30s (1225 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.vStr8sZDpT I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gatk-bwamem=1.0.4+dfsg2-2 && mkdir -p /build/gatk-bwamem-yYaNfi && dpkg-source --no-check -x /*.dsc /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2 && chown -R builduser:builduser /build/gatk-bwamem-yYaNfi"' exec /tmp/mmdebstrap.vStr8sZDpT Reading package lists... NOTICE: 'gatk-bwamem' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gatk-bwamem.git Please use: git clone https://salsa.debian.org/med-team/gatk-bwamem.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 178 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main gatk-bwamem 1.0.4+dfsg2-2 (dsc) [2498 B] Get:2 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main gatk-bwamem 1.0.4+dfsg2-2 (tar) [144 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main gatk-bwamem 1.0.4+dfsg2-2 (tar) [21.4 kB] Get:4 http://snapshot.notset.fr/archive/debian/20220728T033224Z bookworm/main gatk-bwamem 1.0.4+dfsg2-2 (diff) [10.2 kB] Fetched 178 kB in 0s (963 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gatk-bwamem_1.0.4+dfsg2-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gatk-bwamem in /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2 dpkg-source: info: unpacking gatk-bwamem_1.0.4+dfsg2.orig.tar.xz dpkg-source: info: unpacking gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz dpkg-source: info: unpacking gatk-bwamem_1.0.4+dfsg2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build.patch dpkg-source: info: applying use_bwa_from_component.patch dpkg-source: info: applying fix_heap_block_overrun dpkg-source: info: applying fix_build_on_freebsd.patch dpkg-source: info: applying CVE-2019-10269.patch dpkg-source: info: applying simde dpkg-source: info: applying gcc10.patch dpkg-source: info: applying hurd dpkg-source: info: applying hardening.patch dpkg-source: info: applying missing_obj_files.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1658553172" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.vStr8sZDpT dpkg-buildpackage: info: source package gatk-bwamem dpkg-buildpackage: info: source version 1.0.4+dfsg2-2 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 maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2' dh_auto_clean sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4\+dfsg2/.gradle /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4\+dfsg2/buildSrc/.gradle .m2 if [ -e src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c.save ]; then \ mv src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c.save src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c; \ fi rm src/test/resources/ref.fa.img rm: cannot remove 'src/test/resources/ref.fa.img': No such file or directory make[1]: [debian/rules:19: override_dh_auto_clean] Error 1 (ignored) # Cleaning the C part cd src/main/c/ && make clean make[2]: Entering directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/c' rm -rf bwaComponent *.o *.so make[2]: Leaving directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/c' rm -rf src/main/c/bwaComponent # Replacing the modified build.gradle file having a version number by the original one. if [ -e build.gradle.old ]; then mv build.gradle.old build.gradle; fi make[1]: Leaving directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2' dh_clean debian/rules binary-arch dh binary-arch --with maven_repo_helper dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2' # Putting the version in the JNI file so that is can output version information. cp src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c.save sed -i "s/BWA_COMMIT/\"1.0.4+dfsg2-2\"/" src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c # Copying the component sources to src/main/c for the JNI build mkdir -p src/main/c/bwaComponent/ cp -a bwa-apache2/* src/main/c/bwaComponent/ # Adding a version number in the build.gradle file. cp build.gradle build.gradle.old sed -i "s/\(^group.*\)/\1\nversion = '1.0.4+dfsg2'/ ; s/\+dfsg[[:digit:]]*//" build.gradle dh_auto_configure make[1]: Leaving directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2' dh_auto_build -a mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8 --parallel --max-workers=10 jar Initialized native services in: /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar --add-opens java.base/java.lang=ALL-UNNAMED -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 1.386 secs. The client will now receive all logging from the daemon (pid: 45113). The daemon log file: /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-45113.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 10 worker leases. Creating new cache for fileHashes, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6802a008 Creating new cache for resourceHashesCache, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6802a008 Creating new cache for fileHashes, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@44b00eb9 Starting Build Compiling initialization script '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a83369 Compiling initialization script '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/settings.gradle'. Projects loaded. Root project using build file '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/build.gradle'. Included projects: [root project 'gatk-bwamem-jni'] Keep-alive timer started Adding Debian repository to project 'gatk-bwamem-jni' Parallel execution is an incubating feature. Evaluating root project 'gatk-bwamem-jni' using build file '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/build.gradle'. Compiling build file '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/build.gradle' using BuildScriptTransformer. Adding Maven pom generation to project 'gatk-bwamem-jni' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : Creating new cache for annotation-processors, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@3080fdd2 Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] Creating new cache for resourceHashesCache, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@44b00eb9 Creating new cache for taskHistory, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@2a7e4a0e Creating new cache for outputFiles, path /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@6ae01073 :compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.006 secs. Up-to-date check for task ':compileJava' took 0.044 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. :compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1.724 secs. :buildBwaLib (Thread[Task worker for ':' Thread 5,5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. Up-to-date check for task ':buildBwaLib' took 0.001 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-11-openjdk-amd64 -> /usr/lib/jvm/java-11-openjdk-amd64 as JAVA_HOME Starting process 'command 'make''. Working directory: /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/c Command: make Successfully started process 'command 'make'' make[1]: Entering directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/c' gcc -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -Wdate-time -D_FORTIFY_SOURCE=2 -c -o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c gcc -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -Wdate-time -D_FORTIFY_SOURCE=2 -c -o jnibwa.o jnibwa.c make CFLAGS="-ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux" LDFLAGS="-Wl,-z,relro -Wl,-z,now" -C bwaComponent libbwa.a make[2]: Entering directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/c/bwaComponent' gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o gcc -c -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o bwtindex.o is.o rope.o rle.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/c/bwaComponent' gcc -Wl,-z,relro -Wl,-z,now -ggdb -dynamiclib -shared -o libbwa.so org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.o jnibwa.o bwaComponent/libbwa.a -lm -lz -lpthread make[1]: Leaving directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/c' :buildBwaLib (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 10.833 secs. :processResources (Thread[Task worker for ':' Thread 5,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE :processResources (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.01 secs. :classes (Thread[Task worker for ':' Thread 5,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.002 secs. :debianMavenPom (Thread[Task worker for ':' Thread 5,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.009 secs. It is not up-to-date because: No history is available. Generating pom file /build/gatk-bwamem-yYaNfi/gatk-bwamem-1.0.4+dfsg2/build/debian/gatk-bwamem-jni.pom :debianMavenPom (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.19 secs. :jar (Thread[Task worker for ':' Thread 5,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.01 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.084 secs. BUILD SUCCESSFUL in 20s 4 actionable tasks: 4 executed create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a dh_install -a mh_install -a dh_installdocs -a dh_installchangelogs -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libgatk-bwamem-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-2_amd64.deb'. dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in '../libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../gatk-bwamem_1.0.4+dfsg2-2_amd64.buildinfo dpkg-genchanges --build=any -O../gatk-bwamem_1.0.4+dfsg2-2_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/gatk-bwamem-yYaNfi /tmp/gatk-bwamem-1.0.4+dfsg2-2jeq921w9 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.vStr8sZDpT... I: success in 593.7576 seconds md5: libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-2_amd64.deb: OK md5: libgatk-bwamem-jni_1.0.4+dfsg2-2_amd64.deb: OK sha1: libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-2_amd64.deb: OK sha1: libgatk-bwamem-jni_1.0.4+dfsg2-2_amd64.deb: OK sha256: libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-2_amd64.deb: OK sha256: libgatk-bwamem-jni_1.0.4+dfsg2-2_amd64.deb: OK Checksums: OK