Mon Feb 24 20:16:55 UTC 2025 I: starting to build gatk-bwamem/trixie/amd64 on jenkins on '2025-02-24 20:16' Mon Feb 24 20:16:55 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_25/31112/console.log Mon Feb 24 20:16:55 UTC 2025 I: Downloading source for trixie/gatk-bwamem=1.0.4+dfsg2-3 --2025-02-24 20:16:55-- http://deb.debian.org/debian/pool/main/g/gatk-bwamem/gatk-bwamem_1.0.4%2bdfsg2-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2498 (2.4K) [text/prs.lines.tag] Saving to: ‘gatk-bwamem_1.0.4+dfsg2-3.dsc’ 0K .. 100% 413M=0s 2025-02-24 20:16:55 (413 MB/s) - ‘gatk-bwamem_1.0.4+dfsg2-3.dsc’ saved [2498/2498] Mon Feb 24 20:16:55 UTC 2025 I: gatk-bwamem_1.0.4+dfsg2-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gatk-bwamem Binary: libgatk-bwamem-java, libgatk-bwamem-jni Architecture: any all Version: 1.0.4+dfsg2-3 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet Homepage: https://github.com/broadinstitute/gatk-bwamem-jni/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/gatk-bwamem Vcs-Git: https://salsa.debian.org/med-team/gatk-bwamem.git Build-Depends: debhelper-compat (= 13), default-jdk-headless, gradle-debian-helper, libsimde-dev, maven-repo-helper, testng , zlib1g-dev Package-List: libgatk-bwamem-java deb java optional arch=all libgatk-bwamem-jni deb java optional arch=any Checksums-Sha1: 514dfb2510d7c8d5d5f90707dc3f47dfeae7287b 144424 gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz c27d5ad7ee506407448891b75f3d155bd795dd47 21360 gatk-bwamem_1.0.4+dfsg2.orig.tar.xz afe41b692a607ca654338005ed13ef6f701c6aa4 10456 gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz Checksums-Sha256: 954d5d5aae624ce0faa4c9c3d30e91490dd93ce41b2205d84042c3391d35093a 144424 gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz 767c56d136ab24f1fc0511b4a5dcf927ba0028fa140c61e97da10dd57291d798 21360 gatk-bwamem_1.0.4+dfsg2.orig.tar.xz ce78146c4c6a08d9891e033c50bf88e60cda4d0ef7ea09f48fde28b97597fea0 10456 gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz Files: d0b90d3400ed4ccc469367c4dfbd9bca 144424 gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz ed2b395e5416b1bf2b6902acedd61c80 21360 gatk-bwamem_1.0.4+dfsg2.orig.tar.xz acf6ac69dcb09904bd5b12096e198075 10456 gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYATxsACgkQPCZ2P2xn 5uIHmRAAqxg8qmLyOcHjtd/RsYPHXWcQ9onT9ezZ5OZGHQ6PGtrFY2U8xgyhO6XE 2ZY4y1sGAu0cq/WFeBveKL+H3UsCgwgWFMBvShTaNbjJ8YMbAMaB12vyKu9i7cnX tu7NG6CioZ4DhZdU++7kakATB5K46FlFTgekzZF3VYt3ZJrKzdkNzpQx4uec/mN0 cg1C6pTTgZRF3Qiiy9A113DDP64ZWaAUrU80GHrIiriY4uqz/v1DkKOzD4vG3vRT DrWRDFq9ChG9YsuSBHAEp7Fgkn+LBB8o1bAbGNRsz53IqUpZjYvj6bF78zHVfPCo MCxJlYNAAuyfKxbGrsXD247AXad9VnK5mUaZ1oZy7M17/BWTW4Xrw/B+yKeaYJtz yq8ScLaZyuWOZXHqMBJg+rkLzbd/9Iw3x7HHRqtNwhicsuJIyGmf1E8hHOcIiKyA yYbHqJZNSu6ETMLYcpWFXo3+TNiagGWqPM42N00KtS+kfKQkkWGCQpGQ0QzJVzCF GoZxuyJliMgeC4xVoA/0aaM7gU133Hbwmex+LJlBU0ItA2iNLHiTD+vGWWHaAI/U 8QNkhH4UE3wQPdvH4TNAMkuH+rKi25iCd7fV3Fra+Hcg4/7iQ/ZbpFIvkZ1fmuqV P8lOJSH474UNIkG2Qp9gsA94Osn+CHdoRBV/7UOBOYk/4JsG4/c= =Td7x -----END PGP SIGNATURE----- Mon Feb 24 20:16:55 UTC 2025 I: Checking whether the package is not for us Mon Feb 24 20:16:55 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Mon Feb 24 20:16:55 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Mon Feb 24 20:22:06 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 24 08:16:58 -12 2025 I: pbuilder-time-stamp: 1740428218 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gatk-bwamem_1.0.4+dfsg2-3.dsc] I: copying [./gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz] I: copying [./gatk-bwamem_1.0.4+dfsg2.orig.tar.xz] I: copying [./gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gatk-bwamem_1.0.4+dfsg2-3.dsc: unsupported subcommand dpkg-source: info: extracting gatk-bwamem in 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+dfsg2-3.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/452723/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='878c76e9ab9b41689779f3ca2cf69777' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='452723' 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.6G1Fftig/pbuilderrc_gjrM --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6G1Fftig/b1 --logfile b1/build.log gatk-bwamem_1.0.4+dfsg2-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/452723/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), default-jdk-headless, gradle-debian-helper, libsimde-dev, maven-repo-helper, testng, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19802 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-headless; however: Package default-jdk-headless is not installed. pbuilder-satisfydepends-dummy depends on gradle-debian-helper; however: Package gradle-debian-helper is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on maven-repo-helper; however: Package maven-repo-helper is not installed. pbuilder-satisfydepends-dummy depends on testng; however: Package testng is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-optional{a} antlr{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bnd{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk-headless{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gradle{a} gradle-debian-helper{a} groff-base{a} groovy{a} intltool-debian{a} ivy{a} java-common{a} java-wrappers{a} junit4{a} libantlr-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libasm-java{a} libatinject-jsr330-api-java{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libbsf-java{a} libbsh-java{a} libcdi-api-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libdd-plist-java{a} libdebhelper-perl{a} libdom4j-java{a} libeclipse-jdt-annotation-java{a} libel-api-java{a} libelf1t64{a} liberror-prone-java{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfindbugs-java{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgoogle-gson-java{a} libgradle-core-java{a} libgradle-plugins-java{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libhawtjni-runtime-java{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libjansi-java{a} libjansi-native-java{a} libjansi1-java{a} libjarjar-java{a} libjatl-java{a} libjavaewah-java{a} libjaxen-java{a} libjcifs-java{a} libjcip-annotations-java{a} libjcommander-java{a} libjetty9-java{a} libjformatstring-java{a} libjgit-java{a} libjline2-java{a} libjna-java{a} libjna-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjsch-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjunixsocket-java{a} libjunixsocket-jni{a} libjzlib-java{a} libkryo-java{a} liblcms2-2{a} liblightcouch-java{a} liblog4j2-java{a} liblogback-java{a} libmagic-mgc{a} libmagic1t64{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libminlog-java{a} libmongodb-java{a} libnative-platform-java{a} libnative-platform-jni{a} libnekohtml-java{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libpcsclite1{a} libpipeline1{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-interpolation-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpolyglot-maven-java{a} libqdox-java{a} libreflectasm-java{a} librhino-java{a} libservlet-api-java{a} libsimde-dev{a} libsimple-http-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libtool{a} libuchardet0{a} libunistring5{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwebsocket-api-java{a} libxbean-reflect-java{a} libxerces2-java{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxpp3-java{a} libxstream-java{a} libxz-java{a} libyaml-snake-java{a} m4{a} man-db{a} maven-repo-helper{a} openjdk-21-jdk-headless{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} sensible-utils{a} testng{a} unzip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libasound2t64 libbindex-java libcups2t64 libfontconfig1 libfreetype6 libgpars-groovy-java libharfbuzz0b libltdl-dev libmail-sendmail-perl libreflectasm-java-doc lynx wget 0 packages upgraded, 168 newly installed, 0 to remove and 0 not upgraded. Need to get 235 MB of archives. After unpacking 523 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.108-1 [1393 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.1-1 [56.0 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [41.7 MB] Get: 21 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.15-1 [2163 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.15-1 [456 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libantlr-java all 2.7.7+dfsg-14 [458 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 antlr all 2.7.7+dfsg-14 [8376 B] Get: 26 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.5 [8848 B] Get: 33 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libfelix-framework-java all 4.6.1-3 [577 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libfelix-gogo-runtime-java all 0.16.2-2 [117 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 38 http://deb.debian.org/debian trixie/main amd64 libosgi-core-java all 8.0.0-2 [182 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libjansi-native-java all 1.8-2 [26.0 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libjansi1-java all 1.18-3.1 [66.6 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libjline2-java all 2.14.6-5 [151 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libyaml-snake-java all 1.33-2 [321 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 bnd all 5.0.1-5 [10.1 MB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 55 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk-headless amd64 21.0.6+7-1 [82.8 MB] Get: 65 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 66 http://deb.debian.org/debian trixie/main amd64 ivy all 2.5.2-1 [1295 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7.1-1 [391 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 71 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libqdox-java all 1.12.1-4 [173 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libxpp3-java all 1.1.4c-4 [294 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libxstream-java all 1.4.21-1 [567 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 groovy all 2.4.21-10 [12.8 MB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 81 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libjarjar-java all 1.4+svn142-12 [205 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libjna-jni amd64 5.15.0-1 [64.7 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libjna-java all 5.15.0-1 [238 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libbcprov-java all 1.77-1 [5300 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libjunixsocket-jni amd64 2.6.1-1 [18.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.29-2 [25.5 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libjunixsocket-java all 2.6.1-1 [264 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libjzlib-java all 1.1.3-3 [79.4 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libjsch-java all 0.2.19-1 [513 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libminlog-java all 1.3.1-1 [7808 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 libobjenesis-java all 3.4-1 [41.1 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libkryo-java all 2.20-8 [161 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 liblogback-java all 1:1.2.11-6 [701 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libnative-platform-jni amd64 0.14-6 [11.5 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libnative-platform-java all 0.14-6 [69.8 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libgradle-core-java all 4.4.1-22 [4318 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libbcpg-java all 1.77-1 [428 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libbcel-java all 6.10.0-1 [674 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libjformatstring-java all 0.10~20131207-3 [34.8 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libfindbugs-java all 3.1.0~preview2-4 [3535 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 129 http://deb.debian.org/debian trixie/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libjatl-java all 0.2.3-2 [30.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libjcifs-java all 1.3.19+dfsg-1 [414 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libjavaewah-java all 1.2.3-1 [159 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libjetty9-java all 9.4.56-1 [2964 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libjgit-java all 6.7.0-2 [3152 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 143 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 147 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 150 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 159 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libjcommander-java all 1.71-4 [73.0 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 testng all 6.9.12-4 [795 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libgradle-plugins-java all 4.4.1-22 [5245 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 gradle all 4.4.1-22 [400 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 gradle-debian-helper all 2.4 [24.5 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 235 MB in 5s (49.8 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19802 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.4.1-1_amd64.deb ... Unpacking openssl (3.4.1-1) ... Selecting previously unselected package ca-certificates. 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Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../015-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../016-libnspr4_2%3a4.36-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.36-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../017-libnss3_2%3a3.108-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.108-1) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../018-libpcsclite1_2.3.1-1_amd64.deb ... Unpacking libpcsclite1:amd64 (2.3.1-1) ... Selecting previously unselected package openjdk-21-jre-headless:amd64. Preparing to unpack .../019-openjdk-21-jre-headless_21.0.6+7-1_amd64.deb ... Unpacking openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... Selecting previously unselected package default-jre-headless. 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Unpacking junit4 (4.13.2-5) ... Selecting previously unselected package libfelix-framework-java. Preparing to unpack .../034-libfelix-framework-java_4.6.1-3_all.deb ... Unpacking libfelix-framework-java (4.6.1-3) ... Selecting previously unselected package libfelix-gogo-runtime-java. Preparing to unpack .../035-libfelix-gogo-runtime-java_0.16.2-2_all.deb ... Unpacking libfelix-gogo-runtime-java (0.16.2-2) ... Selecting previously unselected package libosgi-annotation-java. Preparing to unpack .../036-libosgi-annotation-java_8.1.0-1_all.deb ... Unpacking libosgi-annotation-java (8.1.0-1) ... Selecting previously unselected package libosgi-core-java. Preparing to unpack .../037-libosgi-core-java_8.0.0-2_all.deb ... Unpacking libosgi-core-java (8.0.0-2) ... Selecting previously unselected package libfelix-resolver-java. Preparing to unpack .../038-libfelix-resolver-java_1.16.0-1_all.deb ... Unpacking libfelix-resolver-java (1.16.0-1) ... 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Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libqdox-java (1.12.1-4) ... Setting up libicu72:amd64 (72.1-6) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up libsimple-http-java (4.1.21-1.1) ... Setting up bsdextrautils (2.40.4-4) ... Setting up java-common (0.76) ... Setting up libjcip-annotations-java (20060626-6) ... Setting up libobjenesis-java (3.4-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up liblogback-java (1:1.2.11-6) ... Setting up libminlog-java (1.3.1-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libasm-java (9.7.1-1) ... Setting up libdd-plist-java (1.20-1.1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libel-api-java (3.0.0-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up file (1:5.45-3+b1) ... Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ... Setting up libfelix-gogo-runtime-java (0.16.2-2) ... Setting up libjzlib-java (1.1.3-3) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-5) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libreflectasm-java (1.11.9+dfsg-4) ... Setting up librhino-java (1.7.15-1) ... Setting up autotools-dev (20220109.1) ... Setting up libbsf-java (1:2.4.0-8) ... Setting up libosgi-annotation-java (8.1.0-1) ... Setting up libjformatstring-java (0.10~20131207-3) ... Setting up libjavaewah-java (1.2.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.29-2) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (33-2) ... Setting up libxpp3-java (1.1.4c-4) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libkryo-java (2.20-8) ... Setting up libxz-java (1.9-1) ... Setting up autopoint (0.23.1-1) ... Setting up libjunixsocket-jni (2.6.1-1) ... Setting up libfelix-framework-java (4.6.1-3) ... Setting up libpcsclite1:amd64 (2.3.1-1) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libnative-platform-jni (0.14-6) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libbcpg-java (1.77-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libantlr-java (2.7.7+dfsg-14) ... Setting up libyaml-snake-java (1.33-2) ... Setting up openssl (3.4.1-1) ... Setting up libcdi-api-java (1.2-4) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libjatl-java (0.2.3-2) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libnative-platform-java (0.14-6) ... Setting up libosgi-core-java (8.0.0-2) ... Setting up libxstream-java (1.4.21-1) ... Setting up libnekohtml-java (1.9.22.noko2-0.1) ... Setting up gettext (0.23.1-1) ... Setting up libjetty9-java (9.4.56-1) ... Setting up java-wrappers (0.5) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up libtool (2.5.4-3) ... Setting up libmaven-parent-java (43-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libnss3:amd64 (2:3.108-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libjunixsocket-java (2.6.1-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up testng (6.9.12-4) ... Setting up libjna-jni (5.15.0-1) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up libjansi-native-java (1.8-2) ... Setting up groff-base (1.23.0-7) ... Setting up libjna-java (5.15.0-1) ... Setting up libjansi1-java (1.18-3.1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libwagon-file-java (3.5.3-1) ... Setting up libcommons-codec-java (1.17.1-1) ... Setting up libjline2-java (2.14.6-5) ... Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libcommons-io-java (2.18.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmaven-resolver-java (1.9.22-1) ... Setting up libbcel-java (6.10.0-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libfindbugs-java (3.1.0~preview2-4) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up debhelper (13.24.1) ... Setting up libjsch-java (0.2.19-1) ... Setting up libjgit-java (6.7.0-2) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libmaven3-core-java (3.9.9-1) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up antlr (2.7.7+dfsg-14) ... Setting up ivy (2.5.2-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up groovy (2.4.21-10) ... update-alternatives: using /usr/share/groovy/bin/groovy to provide /usr/bin/groovy (groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyc to provide /usr/bin/groovyc (groovyc) in auto mode update-alternatives: using /usr/share/groovy/bin/grape to provide /usr/bin/grape (grape) in auto mode update-alternatives: using /usr/share/groovy/bin/startGroovy to provide /usr/bin/startGroovy (startGroovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovysh to provide /usr/bin/groovysh (groovysh) in auto mode update-alternatives: using /usr/share/groovy/bin/java2groovy to provide /usr/bin/java2groovy (java2groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyConsole to provide /usr/bin/groovyConsole (groovyConsole) in auto mode update-alternatives: using /usr/share/groovy/bin/groovydoc to provide /usr/bin/groovydoc (groovydoc) in auto mode Setting up openjdk-21-jdk-headless:amd64 (21.0.6+7-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up maven-repo-helper (1.11) ... Setting up ant-optional (1.10.15-1) ... Setting up bnd (5.0.1-5) ... Setting up default-jdk-headless (2:1.21-76) ... Setting up libgradle-core-java (4.4.1-22) ... Setting up libgradle-plugins-java (4.4.1-22) ... Setting up gradle (4.4.1-22) ... Setting up gradle-debian-helper (2.4) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/ && 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 > ../gatk-bwamem_1.0.4+dfsg2-3_source.changes dpkg-buildpackage: info: source package gatk-bwamem dpkg-buildpackage: info: source version 1.0.4+dfsg2-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4\+dfsg2/.gradle /build/reproducible-path/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:21: override_dh_auto_clean] Error 1 (ignored) # Cleaning the C part cd src/main/c/ && make clean make[2]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c' rm -rf bwaComponent *.o *.so make[2]: Leaving directory '/build/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4+dfsg2' dh_clean debian/rules binary dh binary --with maven_repo_helper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/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+dfsg2-3\"/" 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/reproducible-path/gatk-bwamem-1.0.4+dfsg2' dh_auto_build 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=20 jar openjdk version "21.0.6" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6+7-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6+7-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -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 4.178 secs. The client will now receive all logging from the daemon (pid: 475764). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-475764.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 20 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2edea44f Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2edea44f Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@582aeafd Starting Build Compiling initialization script '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3f41495f Compiling initialization script '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build.gradle'. Compiling build file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@71a6bb1c Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@582aeafd Creating new cache for taskHistory, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@39118ab4 Creating new cache for outputFiles, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@234189fd :compileJava (Thread[#64,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.034 secs. Up-to-date check for task ':compileJava' took 0.179 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[#64,Task worker for ':',5,main]) completed. Took 4.7 secs. :buildBwaLib (Thread[#64,Task worker for ':',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 0.006 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-21-openjdk-amd64 -> /usr/lib/jvm/java-21-openjdk-amd64 as JAVA_HOME Starting process 'command 'make''. Working directory: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c Command: make Successfully started process 'command 'make'' make[1]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -Wdate-time -D_FORTIFY_SOURCE=2 -c -o jnibwa.o jnibwa.c make CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux" LDFLAGS="-Wl,-z,relro -Wl,-z,now" -C bwaComponent libbwa.a make[2]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c/bwaComponent' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o rope.c: In function 'rope_restore_node': rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function 'rope_restore': rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-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/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c' :buildBwaLib (Thread[#64,Task worker for ':',5,main]) completed. Took 21.263 secs. :processResources (Thread[#64,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/reproducible-path/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[#64,Task worker for ':',5,main]) completed. Took 0.018 secs. :classes (Thread[#64,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[#64,Task worker for ':',5,main]) completed. Took 0.001 secs. :debianMavenPom (Thread[#64,Task worker for ':',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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/debian/gatk-bwamem-jni.pom :debianMavenPom (Thread[#64,Task worker for ':',5,main]) completed. Took 0.508 secs. :jar (Thread[#64,Task worker for ':',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 0.059 secs. It is not up-to-date because: No history is available. :jar (Thread[#64,Task worker for ':',5,main]) completed. Took 0.237 secs. BUILD SUCCESSFUL in 51s 4 actionable tasks: 4 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2' # The shared lib should be looked for in its build directory. LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$(readlink -f src/main/c)" dh_auto_test 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=20 test openjdk version "21.0.6" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6+7-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6+7-Debian-1, mixed mode, sharing) Initialized native services in: /build/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -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 3.623 secs. The client will now receive all logging from the daemon (pid: 489751). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-489751.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 20 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4f42121 Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4f42121 Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@c7e4ff5 Starting Build Creating new cache for metadata-1.1/results, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@74155b66 Settings evaluated using settings file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build.gradle'. 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 'test' from project : Creating new cache for annotation-processors, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@7cb7e253 Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@c7e4ff5 Creating new cache for taskHistory, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@74f108e8 Creating new cache for outputFiles, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@567e0051 :compileJava (Thread[#64,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.016 secs. Skipping task ':compileJava' as it is up-to-date (took 0.09 secs). :compileJava UP-TO-DATE :compileJava (Thread[#64,Task worker for ':',5,main]) completed. Took 0.343 secs. :buildBwaLib (Thread[#64,Task worker for ':',5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. Skipping task ':buildBwaLib' as it is up-to-date (took 0.008 secs). :buildBwaLib UP-TO-DATE :buildBwaLib (Thread[#64,Task worker for ':',5,main]) completed. Took 0.013 secs. :processResources (Thread[#64,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/reproducible-path/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[#64,Task worker for ':',5,main]) completed. Took 0.006 secs. :classes (Thread[#64,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[#64,Task worker for ':',5,main]) completed. Took 0.001 secs. :compileTestJava (Thread[#64,Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@5eb61429 Loading the Maven rules... Replacing org.testng:testng:jar:6.9.6 -> org.testng:testng:jar:debian Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Up-to-date check for task ':compileTestJava' took 1.415 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. :compileTestJava (Thread[#64,Task worker for ':',5,main]) completed. Took 3.58 secs. :processTestResources (Thread[#64,Task worker for ':',5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. Up-to-date check for task ':processTestResources' took 0.017 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[#64,Task worker for ':',5,main]) completed. Took 0.07 secs. :testClasses (Thread[#64,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[#64,Task worker for ':',5,main]) completed. Took 0.0 secs. :test (Thread[#79,Task worker for ':' Thread 16,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. Up-to-date check for task ':test' took 0.141 secs. It is not up-to-date because: No history is available. Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath13685800801249995163txt -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs Gradle Test Executor 1 finished executing tests. Results: SUCCESS (7 tests, 7 successes, 0 failures, 0 skipped) Finished generating test XML results (0.05 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test Generating HTML test report... Finished generating test html results (0.114 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test :test (Thread[#79,Task worker for ':' Thread 16,5,main]) completed. Took 4.599 secs. BUILD SUCCESSFUL in 27s 5 actionable tasks: 3 executed, 2 up-to-date make[1]: Leaving directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install dh_install mh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libgatk-bwamem-java: substitution variable ${java:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in '../libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.deb'. dpkg-deb: building package 'libgatk-bwamem-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb'. dpkg-deb: building package 'libgatk-bwamem-java' in '../libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo dpkg-genchanges --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/452723 and its subdirectories I: Current time: Mon Feb 24 08:22:05 -12 2025 I: pbuilder-time-stamp: 1740428525 Mon Feb 24 20:22:06 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon Feb 24 20:22:06 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon Feb 24 20:24:30 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon Feb 24 20:24:30 UTC 2025 I: gatk-bwamem_1.0.4+dfsg2-3_amd64.changes: Format: 1.8 Date: Sun, 24 Mar 2024 17:03:31 +0100 Source: gatk-bwamem Binary: libgatk-bwamem-java libgatk-bwamem-jni libgatk-bwamem-jni-dbgsym Architecture: all amd64 Version: 1.0.4+dfsg2-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libgatk-bwamem-java - interface to call Heng Li's bwa mem aligner from Java code libgatk-bwamem-jni - interface to call Heng Li's bwa mem aligner from Java code (jni) Changes: gatk-bwamem (1.0.4+dfsg2-3) unstable; urgency=medium . * Team upload. * d/rules: make sure the openmp-simd compiler flag is used. * d/patches/hardening: improve with the help of blhc. * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: e795bfd4562f9c2d41b25b646aaf09a0adc6571f 9903 gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo d526c2c80a095488556006464acb033b7a1e9f28 23816 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb faf733f422ac8bca9afc616b216c0d807ce6e7af 237204 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.deb 5c4c1ecb28bc9dc31d75ca50daa6b3a407842420 93496 libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Checksums-Sha256: 5328932def99b614a533f43485592b6db5b1a8583062b3dfe907858ec889e350 9903 gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo af8a0bc7512ce05bf22f73889743e240a3d76b10dcad881774f1462464a48613 23816 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 8199d77f73030c882d01e056d6dfc9380c760e586129e50709f194ec877e3019 237204 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.deb abe75c9a3301649227de72c7189db6d7dec02889c52ea12268664bcae0f373ed 93496 libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Files: 7a182d599eb290385f323749208f7a98 9903 java optional gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo cdf4dec502883b98f3296874b15138a7 23816 java optional libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 8788bcd9b64f9ee3b1c65056507841a1 237204 debug optional libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.deb d91a87adf5977405fbc9142bf7a2a7f0 93496 java optional libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Mon Feb 24 20:24:31 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_25-31112.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.6G1Fftig/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.6G1Fftig/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.6G1Fftig/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.6G1Fftig/b1/gatk-bwamem_1.0.4+dfsg2-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.6G1Fftig/b2/gatk-bwamem_1.0.4+dfsg2-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 241ms CPU time consumed: 240ms Mon Feb 24 20:24:32 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Mon Feb 24 20:24:32 UTC 2025 I: gatk-bwamem from trixie built successfully and reproducibly on amd64. Mon Feb 24 20:24:33 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Feb 24 20:24:33 UTC 2025 I: Submitting 12K b1/gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo.asc Mon Feb 24 20:24:35 UTC 2025 I: Submitting 12K b2/gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo.asc Mon Feb 24 20:24:37 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Feb 24 20:24:37 UTC 2025 I: Done submitting .buildinfo files. Mon Feb 24 20:24:37 UTC 2025 I: Removing signed gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo.asc files: removed './b1/gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo.asc' removed './b2/gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo.asc'