Sat Dec 21 02:30:30 UTC 2024 I: starting to build gatk-bwamem/trixie/armhf on jenkins on '2024-12-21 02:30' Sat Dec 21 02:30:30 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_32/22281/console.log Sat Dec 21 02:30:30 UTC 2024 I: Downloading source for trixie/gatk-bwamem=1.0.4+dfsg2-3 --2024-12-21 02:30:31-- 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% 298M=0s 2024-12-21 02:30:31 (298 MB/s) - ‘gatk-bwamem_1.0.4+dfsg2-3.dsc’ saved [2498/2498] Sat Dec 21 02:30:31 UTC 2024 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----- Sat Dec 21 02:30:31 UTC 2024 I: Checking whether the package is not for us Sat Dec 21 02:30:31 UTC 2024 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Sat Dec 21 02:30:31 UTC 2024 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Sat Dec 21 02:34:13 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 20 14:30:37 -12 2024 I: pbuilder-time-stamp: 1734748237 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 gpgv: Signature made Sun Mar 24 16:04:43 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gatk-bwamem_1.0.4+dfsg2-3.dsc: no acceptable signature found 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/17425/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='6bad8d4fdfef44ed8deefdd15a182d93' 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='17425' 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.mZmmwOGL/pbuilderrc_xzSq --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.mZmmwOGL/b1 --logfile b1/build.log gatk-bwamem_1.0.4+dfsg2-3.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/17425/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: armhf 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 ... 19674 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} 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-1.6-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} 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, 167 newly installed, 0 to remove and 0 not upgraded. Need to get 223 MB of archives. After unpacking 471 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.3.2-2 [1348 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-6 [1091 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf ca-certificates-java all 20240118 [11.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf java-common all 0.76 [6776 B] Get: 15 http://deb.debian.org/debian trixie/main armhf liblcms2-2 armhf 2.16-2 [131 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libnspr4 armhf 2:4.36-1 [87.8 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libnss3 armhf 2:3.106-1 [1204 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libpcsclite1 armhf 2.3.0-3 [51.7 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf openjdk-21-jre-headless armhf 21.0.5+11-1 [35.6 MB] Get: 21 http://deb.debian.org/debian trixie/main armhf default-jre-headless armhf 2:1.21-76 [3192 B] Get: 22 http://deb.debian.org/debian trixie/main armhf ant all 1.10.15-1 [2163 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf ant-optional all 1.10.15-1 [456 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libantlr-java all 2.7.7+dfsg-14 [458 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf antlr all 2.7.7+dfsg-14 [8376 B] Get: 26 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf unzip armhf 6.0-28 [152 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf java-wrappers all 0.5 [8848 B] Get: 33 http://deb.debian.org/debian trixie/main armhf libhamcrest-java all 2.2-2 [121 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf junit4 all 4.13.2-5 [350 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 38 http://deb.debian.org/debian trixie/main armhf libosgi-core-java all 8.0.0-2 [182 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libjansi-native-java all 1.8-2 [26.0 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libjansi1-java all 1.18-3 [66.5 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libjline2-java all 2.14.6-5 [151 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libslf4j-java all 1.7.32-1 [144 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libxz-java all 1.9-1 [143 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libyaml-snake-java all 1.33-2 [321 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf bnd all 5.0.1-5 [10.1 MB] Get: 49 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 55 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf openjdk-21-jdk-headless armhf 21.0.5+11-1 [78.3 MB] Get: 64 http://deb.debian.org/debian trixie/main armhf default-jdk-headless armhf 2:1.21-76 [1124 B] Get: 65 http://deb.debian.org/debian trixie/main armhf ivy all 2.5.2-1 [1295 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libasm-java all 9.7.1-1 [391 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libapache-pom-java all 33-2 [5852 B] Get: 70 http://deb.debian.org/debian trixie/main armhf libcommons-parent-java all 56-1 [10.8 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libjansi-java all 2.4.1-2 [100 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libqdox-java all 1.12.1-4 [173 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libxpp3-java all 1.1.4c-3 [292 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libxstream-java all 1.4.21-1 [567 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf groovy all 2.4.21-10 [12.8 MB] Get: 79 http://deb.debian.org/debian trixie/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 80 http://deb.debian.org/debian trixie/main armhf libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libcommons-codec-java all 1.17.1-1 [303 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libcommons-io-java all 2.17.0-1 [488 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libcommons-compress-java all 1.27.1-2 [641 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libcommons-lang-java all 2.6-10 [273 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libguava-java all 32.0.1-1 [2708 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libhttpcore-java all 4.4.16-1 [636 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libhttpclient-java all 4.5.14-1 [1247 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libjarjar-java all 1.4+svn142-12 [205 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libjna-jni armhf 5.15.0-1 [60.7 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libjna-java all 5.15.0-1 [238 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libbcprov-java all 1.77-1 [5300 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libjunixsocket-jni armhf 2.6.1-1 [16.1 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libeclipse-jdt-annotation-java all 2.2.700+eclipse4.29-2 [25.5 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libjunixsocket-java all 2.6.1-1 [264 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libmongodb-java all 3.6.3-2 [1901 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf liblog4j2-java all 2.19.0-2 [2310 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libjzlib-java all 1.1.3-3 [79.4 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libjsch-java all 0.2.19-1 [513 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libminlog-java all 1.3.1-1 [7808 B] Get: 105 http://deb.debian.org/debian trixie/main armhf libobjenesis-java all 3.3-3 [41.3 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libkryo-java all 2.20-7 [158 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf liblogback-java all 1:1.2.11-6 [701 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libnative-platform-jni armhf 0.14-6 [10.2 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libnative-platform-java all 0.14-6 [69.8 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libxerces2-java all 2.12.2-1 [1440 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libxbean-reflect-java all 4.5-9 [132 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libgradle-core-java all 4.4.1-20 [4293 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libbcpg-java all 1.77-1 [428 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libbsh-java all 2.0b4-20 [291 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libjaxen-java all 1.1.6-5 [214 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libdom4j-java all 2.1.4-1 [312 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libbcel-java all 6.10.0-1 [674 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf libfindbugs-java all 3.1.0~preview2-4 [3535 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libaopalliance-java all 20070526-7 [8572 B] Get: 127 http://deb.debian.org/debian trixie/main armhf libguice-java all 4.2.3-2 [1435 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf libjcifs-java all 1.3.19-2 [394 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf libjavaewah-java all 1.2.3-1 [159 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf libel-api-java all 3.0.0-3 [64.9 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf libjetty9-java all 9.4.56-1 [2964 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf libjgit-java all 6.7.0-2 [3152 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 140 http://deb.debian.org/debian trixie/main armhf libmaven-parent-java all 43-2 [6252 B] Get: 141 http://deb.debian.org/debian trixie/main armhf libmaven-resolver-1.6-java all 1.6.3-3 [558 kB] Get: 142 http://deb.debian.org/debian trixie/main armhf libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 143 http://deb.debian.org/debian trixie/main armhf libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 144 http://deb.debian.org/debian trixie/main armhf libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 145 http://deb.debian.org/debian trixie/main armhf libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 146 http://deb.debian.org/debian trixie/main armhf libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 147 http://deb.debian.org/debian trixie/main armhf libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 148 http://deb.debian.org/debian trixie/main armhf libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 149 http://deb.debian.org/debian trixie/main armhf libcdi-api-java all 1.2-4 [55.3 kB] Get: 150 http://deb.debian.org/debian trixie/main armhf libsisu-inject-java all 0.3.4-2 [347 kB] Get: 151 http://deb.debian.org/debian trixie/main armhf libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 152 http://deb.debian.org/debian trixie/main armhf libmaven3-core-java all 3.8.8-2 [1579 kB] Get: 153 http://deb.debian.org/debian trixie/main armhf libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 154 http://deb.debian.org/debian trixie/main armhf libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 155 http://deb.debian.org/debian trixie/main armhf librhino-java all 1.7.14-2.1 [1357 kB] Get: 156 http://deb.debian.org/debian trixie/main armhf libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 157 http://deb.debian.org/debian trixie/main armhf libwagon-file-java all 3.5.3-1 [8388 B] Get: 158 http://deb.debian.org/debian trixie/main armhf libjsoup-java all 1.15.3-1 [431 kB] Get: 159 http://deb.debian.org/debian trixie/main armhf libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 160 http://deb.debian.org/debian trixie/main armhf libjcommander-java all 1.71-4 [73.0 kB] Get: 161 http://deb.debian.org/debian trixie/main armhf testng all 6.9.12-4 [795 kB] Get: 162 http://deb.debian.org/debian trixie/main armhf libgradle-plugins-java all 4.4.1-20 [5206 kB] Get: 163 http://deb.debian.org/debian trixie/main armhf gradle all 4.4.1-20 [398 kB] Get: 164 http://deb.debian.org/debian trixie/main armhf maven-repo-helper all 1.11 [142 kB] Get: 165 http://deb.debian.org/debian trixie/main armhf gradle-debian-helper all 2.4 [24.5 kB] Get: 166 http://deb.debian.org/debian trixie/main armhf libsimde-dev all 0.8.2-2 [467 kB] Get: 167 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Fetched 223 MB in 6s (38.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19674 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_3.3.2-2_armhf.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-6_armhf.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-12_armhf.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../010-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../012-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package java-common. Preparing to unpack .../013-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:armhf. Preparing to unpack .../014-liblcms2-2_2.16-2_armhf.deb ... Unpacking liblcms2-2:armhf (2.16-2) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../015-libjpeg62-turbo_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package libnspr4:armhf. Preparing to unpack .../016-libnspr4_2%3a4.36-1_armhf.deb ... Unpacking libnspr4:armhf (2:4.36-1) ... Selecting previously unselected package libnss3:armhf. Preparing to unpack .../017-libnss3_2%3a3.106-1_armhf.deb ... Unpacking libnss3:armhf (2:3.106-1) ... Selecting previously unselected package libpcsclite1:armhf. Preparing to unpack .../018-libpcsclite1_2.3.0-3_armhf.deb ... Unpacking libpcsclite1:armhf (2.3.0-3) ... Selecting previously unselected package openjdk-21-jre-headless:armhf. Preparing to unpack .../019-openjdk-21-jre-headless_21.0.5+11-1_armhf.deb ... Unpacking openjdk-21-jre-headless:armhf (21.0.5+11-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../020-default-jre-headless_2%3a1.21-76_armhf.deb ... Unpacking default-jre-headless (2:1.21-76) ... Selecting previously unselected package ant. Preparing to unpack .../021-ant_1.10.15-1_all.deb ... Unpacking ant (1.10.15-1) ... Selecting previously unselected package ant-optional. Preparing to unpack .../022-ant-optional_1.10.15-1_all.deb ... Unpacking ant-optional (1.10.15-1) ... Selecting previously unselected package libantlr-java. Preparing to unpack .../023-libantlr-java_2.7.7+dfsg-14_all.deb ... Unpacking libantlr-java (2.7.7+dfsg-14) ... Selecting previously unselected package antlr. Preparing to unpack .../024-antlr_2.7.7+dfsg-14_all.deb ... Unpacking antlr (2.7.7+dfsg-14) ... Selecting previously unselected package m4. Preparing to unpack .../025-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../026-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../027-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../028-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../029-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package unzip. Preparing to unpack .../030-unzip_6.0-28_armhf.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package java-wrappers. Preparing to unpack .../031-java-wrappers_0.5_all.deb ... Unpacking java-wrappers (0.5) ... Selecting previously unselected package libhamcrest-java. Preparing to unpack .../032-libhamcrest-java_2.2-2_all.deb ... Unpacking libhamcrest-java (2.2-2) ... Selecting previously unselected package junit4. Preparing to unpack .../033-junit4_4.13.2-5_all.deb ... Unpacking junit4 (4.13.2-5) ... Selecting previously unselected package libfelix-framework-java. Preparing to unpack .../034-libfelix-framework-java_4.6.1-2.1_all.deb ... Unpacking libfelix-framework-java (4.6.1-2.1) ... Selecting previously unselected package libfelix-gogo-runtime-java. Preparing to unpack .../035-libfelix-gogo-runtime-java_0.16.2-1.1_all.deb ... Unpacking libfelix-gogo-runtime-java (0.16.2-1.1) ... 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 libsimple-http-java (4.1.21-1.1) ... Setting up bsdextrautils (2.40.2-12) ... Setting up java-common (0.76) ... Setting up libjcip-annotations-java (20060626-6) ... Setting up libobjenesis-java (3.3-3) ... 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 (13.20) ... Setting up libmagic1t64:armhf (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 (0.22.5-2) ... Setting up m4 (1.4.19-4) ... 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 (0.16.2-1.1) ... Setting up libjzlib-java (1.1.3-3) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libreflectasm-java (1.11.9+dfsg-4) ... Setting up librhino-java (1.7.14-2.1) ... 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 (0.10~20131207-2.1) ... Setting up libjavaewah-java (1.2.3-1) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Setting up libjaxen-java (1.1.6-5) ... Setting up libnspr4:armhf (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-3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libplexus-interpolation-java (1.27-1) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libkryo-java (2.20-7) ... Setting up libxz-java (1.9-1) ... Setting up libjna-jni (5.15.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up libjunixsocket-jni (2.6.1-1) ... Setting up libfelix-framework-java (4.6.1-2.1) ... Setting up libpcsclite1:armhf (2.3.0-3) ... 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:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up libjna-java (5.15.0-1) ... 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 (3.3.2-2) ... Setting up libcdi-api-java (1.2-4) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libjatl-java (0.2.3-1.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 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 (0.22.5-2) ... 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 (2.4.7-8) ... 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 (0.3.4-2) ... Setting up libnss3:armhf (2:3.106-1) ... 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 (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up testng (6.9.12-4) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up libjansi-native-java (1.8-2) ... Setting up groff-base (1.23.0-6) ... Setting up libjansi1-java (1.18-3) ... 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:armhf (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libcommons-io-java (2.17.0-1) ... 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-1.6-java (1.6.3-3) ... Setting up libmaven-resolver-java (1.6.3-1) ... 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 (13.20) ... 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 (4.2.3-2) ... Setting up libmaven3-core-java (3.8.8-2) ... Processing triggers for libc-bin (2.40-4) ... 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: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: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:Security_Communication_Root_CA.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_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.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:armhf (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/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 (4.4.1-20) ... Setting up libgradle-plugins-java (4.4.1-20) ... Setting up gradle (4.4.1-20) ... Setting up gradle-debian-helper (2.4) ... Processing triggers for ca-certificates (20240203) ... 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 armhf 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=3 jar openjdk version "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Debian-1) OpenJDK Server VM (build 21.0.5+11-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-armhf/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 3.159 secs. The client will now receive all logging from the daemon (pid: 23460). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-23460.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 3 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@139025b 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@139025b 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@8f0d52 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@1a64b40 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@1f1f65c 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@8f0d52 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@43cc06 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@1f0d62d :compileJava (Thread[#41,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.016 secs. Up-to-date check for task ':compileJava' took 0.063 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[#41,Task worker for ':',5,main]) completed. Took 4.156 secs. :buildBwaLib (Thread[#41,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 0.002 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-21-openjdk-armhf -> /usr/lib/jvm/java-21-openjdk-armhf 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c: In function 'Java_org_broadinstitute_hellbender_utils_bwa_BwaMemIndex_openIndex': org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c:57:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 57 | return (jlong)jnibwa_openIndex(fd); | ^ org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c: In function 'Java_org_broadinstitute_hellbender_utils_bwa_BwaMemIndex_destroyIndex': org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c:63:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 63 | return jnibwa_destroyIndex((bwaidx_t*)idxAddr); | ^ org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c: In function 'Java_org_broadinstitute_hellbender_utils_bwa_BwaMemIndex_getRefContigNames': org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c:81:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 81 | void* bufMem = jnibwa_getRefContigNames((bwaidx_t*)idxAddr, &bufSize); | ^ org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c: In function 'Java_org_broadinstitute_hellbender_utils_bwa_BwaMemIndex_createAlignments': org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c:122:26: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 122 | bwaidx_t* pIdx = (bwaidx_t*)idxAddr; | ^ 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o bwamem.c: In function 'mem_align1_core': bwamem.c:1072:33: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1072 | err_printf("* %ld chains remain after removing duplicated chains\n", regs.n); | ~~^ ~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o bwamem_pair.c: In function 'mem_pestat': bwamem_pair.c:65:106: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:111: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:116: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:121: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-armhf/include -I/usr/lib/jvm/java-21-openjdk-armhf/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[#41,Task worker for ':',5,main]) completed. Took 30.844 secs. :processResources (Thread[#41,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[#41,Task worker for ':',5,main]) completed. Took 0.006 secs. :classes (Thread[#41,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[#41,Task worker for ':',5,main]) completed. Took 0.002 secs. :debianMavenPom (Thread[#41,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 0.003 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[#41,Task worker for ':',5,main]) completed. Took 0.235 secs. :jar (Thread[#41,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 0.019 secs. It is not up-to-date because: No history is available. :jar (Thread[#41,Task worker for ':',5,main]) completed. Took 0.179 secs. BUILD SUCCESSFUL in 56s 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=3 test openjdk version "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Debian-1) OpenJDK Server VM (build 21.0.5+11-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-armhf/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 3.343 secs. The client will now receive all logging from the daemon (pid: 24473). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-24473.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 3 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@32cda1 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@32cda1 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@649c57 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@1e1102e 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@12a317f 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@649c57 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@123ce09 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@b1ff65 :compileJava (Thread[#41,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.015 secs. Skipping task ':compileJava' as it is up-to-date (took 0.098 secs). :compileJava UP-TO-DATE :compileJava (Thread[#41,Task worker for ':',5,main]) completed. Took 0.214 secs. :buildBwaLib (Thread[#41,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 0.01 secs). :buildBwaLib UP-TO-DATE :buildBwaLib (Thread[#41,Task worker for ':',5,main]) completed. Took 0.022 secs. :processResources (Thread[#41,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[#41,Task worker for ':',5,main]) completed. Took 0.01 secs. :classes (Thread[#41,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[#41,Task worker for ':',5,main]) completed. Took 0.004 secs. :compileTestJava (Thread[#41,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@1b230f9 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 2.096 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[#41,Task worker for ':',5,main]) completed. Took 6.499 secs. :processTestResources (Thread[#41,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 0.038 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[#41,Task worker for ':',5,main]) completed. Took 0.112 secs. :testClasses (Thread[#41,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[#41,Task worker for ':',5,main]) completed. Took 0.002 secs. :test (Thread[#41,Task worker for ':',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 0.376 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-armhf/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath14925027316079609977txt -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 (0.028 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test Generating HTML test report... Finished generating test html results (0.08 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test :test (Thread[#41,Task worker for ':',5,main]) completed. Took 4.513 secs. BUILD SUCCESSFUL in 29s 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged 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_armhf.deb'. dpkg-deb: building package 'libgatk-bwamem-java' in '../libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb'. dpkg-deb: building package 'libgatk-bwamem-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo dpkg-genchanges --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_armhf.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/17425 and its subdirectories I: Current time: Fri Dec 20 14:34:06 -12 2024 I: pbuilder-time-stamp: 1734748446 Sat Dec 21 02:34:15 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32c-armhf-rb.debian.net. Sat Dec 21 02:34:15 UTC 2024 I: Preparing to do remote build '2' on virt32c-armhf-rb.debian.net. Sat Dec 21 02:38:11 UTC 2024 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net. Sat Dec 21 02:38:14 UTC 2024 I: gatk-bwamem_1.0.4+dfsg2-3_armhf.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 armhf 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: fec7a76292197ed6ca27f41677cfe8523a06b024 9928 gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo d526c2c80a095488556006464acb033b7a1e9f28 23816 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 1f0261661c8c7f1c8e457684b7bf18a0912c5ffd 243540 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_armhf.deb 39b3a194dc14962d19227c48cc35f098e778fa36 88988 libgatk-bwamem-jni_1.0.4+dfsg2-3_armhf.deb Checksums-Sha256: 2fe6b67fa06e7957e2e766ae2f8af5a2a0cc476ef75854a136ef9a3e42e933df 9928 gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo af8a0bc7512ce05bf22f73889743e240a3d76b10dcad881774f1462464a48613 23816 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 2f2bc36f23184cc7e2bb2caad7df0b25a2fb4d7463099d32e244cb059cda3d03 243540 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_armhf.deb 3a4eb1ecc84371cff2079493659eb42aac50432609a0feaca643dc489be30582 88988 libgatk-bwamem-jni_1.0.4+dfsg2-3_armhf.deb Files: 40378fe1477ebcfe6adae6e3c9e9533c 9928 java optional gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo cdf4dec502883b98f3296874b15138a7 23816 java optional libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb d1600c8cd8f5713bb9f87131dfa1c15a 243540 debug optional libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_armhf.deb d81feae0f54097f9c1ad7c50f280817a 88988 java optional libgatk-bwamem-jni_1.0.4+dfsg2-3_armhf.deb Sat Dec 21 02:38:15 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_32-22281.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.mZmmwOGL/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.mZmmwOGL/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.mZmmwOGL/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.mZmmwOGL/b1/gatk-bwamem_1.0.4+dfsg2-3_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.mZmmwOGL/b2/gatk-bwamem_1.0.4+dfsg2-3_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.336s) 0.336s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 634ms CPU time consumed: 635ms Sat Dec 21 02:38:16 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Sat Dec 21 02:38:16 UTC 2024 I: gatk-bwamem from trixie built successfully and reproducibly on armhf. Sat Dec 21 02:38:17 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Dec 21 02:38:17 UTC 2024 I: Submitting 12K b1/gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo.asc Sat Dec 21 02:38:17 UTC 2024 I: Submitting 12K b2/gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo.asc Sat Dec 21 02:38:18 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Dec 21 02:38:18 UTC 2024 I: Done submitting .buildinfo files. Sat Dec 21 02:38:18 UTC 2024 I: Removing signed gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo.asc files: removed './b1/gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo.asc' removed './b2/gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo.asc'