Thu May 16 14:16:51 UTC 2024 I: starting to build gatk-bwamem/trixie/arm64 on jenkins on '2024-05-16 14:16' Thu May 16 14:16:51 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_22/11615/console.log Thu May 16 14:16:51 UTC 2024 I: Downloading source for trixie/gatk-bwamem=1.0.4+dfsg2-3 --2024-05-16 14:16:52-- 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% 354M=0s 2024-05-16 14:16:52 (354 MB/s) - ‘gatk-bwamem_1.0.4+dfsg2-3.dsc’ saved [2498/2498] Thu May 16 14:16:52 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----- Thu May 16 14:16:52 UTC 2024 I: Checking whether the package is not for us Thu May 16 14:16:52 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu May 16 14:16:52 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu May 16 14:18:30 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 16 02:16:54 -12 2024 I: pbuilder-time-stamp: 1715869014 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/531355/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='4dffc1d981654671a011774ce4efd970' 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='531355' 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.0F9iWarw/pbuilderrc_D9Qr --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.0F9iWarw/b1 --logfile b1/build.log gatk-bwamem_1.0.4+dfsg2-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 14 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/531355/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: arm64 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 ... 19744 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} libjzlib-java{a} libkryo-java{a} liblcms2-2{a} liblogback-java{a} libmagic-mgc{a} libmagic1t64{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libminlog-java{a} 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} libsub-override-perl{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-17-jdk-headless{a} openjdk-17-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, 162 newly installed, 0 to remove and 0 not upgraded. Need to get 216 MB of archives. After unpacking 485 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 java-common all 0.75 [6640 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.99-1 [1293 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpcsclite1 arm64 2.0.3-1 [50.3 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jre-headless arm64 17.0.11+9-1 [42.8 MB] Get: 21 http://deb.debian.org/debian trixie/main arm64 default-jre-headless arm64 2:1.17-75 [3068 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 ant all 1.10.14-1 [2162 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 ant-optional all 1.10.14-1 [455 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libantlr-java all 2.7.7+dfsg-13 [458 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 antlr all 2.7.7+dfsg-13 [8272 B] Get: 26 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28 [157 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 java-wrappers all 0.4 [8916 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 junit4 all 4.13.2-4 [349 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 38 http://deb.debian.org/debian trixie/main arm64 libosgi-core-java all 8.0.0-2 [182 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libjansi-native-java all 1.8-2 [26.0 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libjansi1-java all 1.18-3 [66.5 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libjline2-java all 2.14.6-5 [151 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libxz-java all 1.9-1 [143 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libyaml-snake-java all 1.33-2 [321 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 bnd all 5.0.1-5 [10.1 MB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 56 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jdk-headless arm64 17.0.11+9-1 [70.6 MB] Get: 65 http://deb.debian.org/debian trixie/main arm64 default-jdk-headless arm64 2:1.17-75 [1108 B] Get: 66 http://deb.debian.org/debian trixie/main arm64 ivy all 2.5.2-1 [1295 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libasm-java all 9.7-1 [394 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libqdox-java all 1.12.1-3 [172 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libxstream-java all 1.4.20-1 [565 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 groovy all 2.4.21-10 [12.8 MB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 81 http://deb.debian.org/debian trixie/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libjarjar-java all 1.4+svn142-12 [205 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libjna-jni arm64 5.14.0-1 [61.5 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libjna-java all 5.14.0-1 [237 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libjzlib-java all 1.1.3-3 [79.4 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libjsch-java all 0.1.55-1 [298 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libminlog-java all 1.3.0-1.1 [7928 B] Get: 98 http://deb.debian.org/debian trixie/main arm64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libkryo-java all 2.20-7 [158 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 liblogback-java all 1:1.2.11-5 [701 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libnative-platform-jni arm64 0.14-6 [11.4 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libnative-platform-java all 0.14-6 [69.8 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libgradle-core-java all 4.4.1-20 [4293 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libbcprov-java all 1.77-1 [5300 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libbcpg-java all 1.77-1 [428 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libjaxen-java all 1.1.6-4 [214 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libbcel-java all 6.5.0-2 [634 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 121 http://deb.debian.org/debian trixie/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libjcifs-java all 1.3.19-2 [394 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.26-2 [25.3 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libjavaewah-java all 1.2.3-1 [159 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libjetty9-java all 9.4.54-1 [2980 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libjgit-java all 4.11.9-2 [2534 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libmaven-parent-java all 35-1 [6140 B] Get: 137 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 141 http://deb.debian.org/debian trixie/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 144 http://deb.debian.org/debian trixie/main arm64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 153 http://deb.debian.org/debian trixie/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 testng all 6.9.12-4 [795 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libgradle-plugins-java all 4.4.1-20 [5206 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 gradle all 4.4.1-20 [398 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 gradle-debian-helper all 2.4 [24.5 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Fetched 216 MB in 1s (205 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 ... 19744 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.2.1-3_arm64.deb ... Unpacking openssl (3.2.1-3) ... 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_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... 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Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../015-libjpeg62-turbo_1%3a2.1.5-3_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../016-libnspr4_2%3a4.35-1.1+b1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.35-1.1+b1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../017-libnss3_2%3a3.99-1_arm64.deb ... Unpacking libnss3:arm64 (2:3.99-1) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../018-libpcsclite1_2.0.3-1_arm64.deb ... Unpacking libpcsclite1:arm64 (2.0.3-1) ... Selecting previously unselected package openjdk-17-jre-headless:arm64. Preparing to unpack .../019-openjdk-17-jre-headless_17.0.11+9-1_arm64.deb ... Unpacking openjdk-17-jre-headless:arm64 (17.0.11+9-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../020-default-jre-headless_2%3a1.17-75_arm64.deb ... Unpacking default-jre-headless (2:1.17-75) ... Selecting previously unselected package ant. Preparing to unpack .../021-ant_1.10.14-1_all.deb ... Unpacking ant (1.10.14-1) ... Selecting previously unselected package ant-optional. Preparing to unpack .../022-ant-optional_1.10.14-1_all.deb ... Unpacking ant-optional (1.10.14-1) ... Selecting previously unselected package libantlr-java. Preparing to unpack .../023-libantlr-java_2.7.7+dfsg-13_all.deb ... Unpacking libantlr-java (2.7.7+dfsg-13) ... Selecting previously unselected package antlr. Preparing to unpack .../024-antlr_2.7.7+dfsg-13_all.deb ... Unpacking antlr (2.7.7+dfsg-13) ... Selecting previously unselected package m4. Preparing to unpack .../025-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../026-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package unzip. Preparing to unpack .../030-unzip_6.0-28_arm64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package java-wrappers. Preparing to unpack .../031-java-wrappers_0.4_all.deb ... Unpacking java-wrappers (0.4) ... 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_4.13.2-4_all.deb ... Unpacking junit4 (4.13.2-4) ... 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) ... Selecting previously unselected package libhawtjni-runtime-java. Preparing to unpack .../039-libhawtjni-runtime-java_1.18-1_all.deb ... Unpacking libhawtjni-runtime-java (1.18-1) ... Selecting previously unselected package libjansi-native-java. Preparing to unpack .../040-libjansi-native-java_1.8-2_all.deb ... Unpacking libjansi-native-java (1.8-2) ... Selecting previously unselected package libjansi1-java. Preparing to unpack .../041-libjansi1-java_1.18-3_all.deb ... Unpacking libjansi1-java (1.18-3) ... Selecting previously unselected package libjline2-java. Preparing to unpack .../042-libjline2-java_2.14.6-5_all.deb ... Unpacking libjline2-java (2.14.6-5) ... Selecting previously unselected package libosgi-compendium-java. Preparing to unpack .../043-libosgi-compendium-java_7.0.0-1_all.deb ... Unpacking libosgi-compendium-java (7.0.0-1) ... Selecting previously unselected package libslf4j-java. Preparing to unpack .../044-libslf4j-java_1.7.32-1_all.deb ... 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Setting up libjsr305-java (0.1~+svn49-11) ... Setting up libsimple-http-java (4.1.21-1.1) ... Setting up bsdextrautils (2.40-8) ... Setting up java-common (0.75) ... 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) ... Setting up liblogback-java (1:1.2.11-5) ... Setting up libminlog-java (1.3.0-1.1) ... 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 (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libasm-java (9.7-1) ... Setting up libdd-plist-java (1.20-1.1) ... Setting up gettext-base (0.21-14+b1) ... 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) ... 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:arm64 (0.191-1+b1) ... 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 libjsch-java (0.1.55-1) ... 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:arm64 (1:2.1.5-3) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libnspr4:arm64 (2:4.35-1.1+b1) ... Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.26-2) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (29-2) ... 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 (1.26-1) ... 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 (5.14.0-1) ... Setting up autopoint (0.21-14) ... Setting up libfelix-framework-java (4.6.1-2.1) ... Setting up libpcsclite1:arm64 (2.0.3-1) ... 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 (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up libjna-java (5.14.0-1) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libsub-override-perl (0.10-1) ... 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-13) ... Setting up libyaml-snake-java (1.33-2) ... Setting up openssl (3.2.1-3) ... Setting up libcdi-api-java (1.2-3) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... 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 (1.13.1-1) ... 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 (1.4.20-1) ... Setting up libnekohtml-java (1.9.22.noko2-0.1) ... Setting up gettext (0.21-14+b1) ... Setting up libjetty9-java (9.4.54-1) ... Setting up java-wrappers (0.4) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up libtool (2.4.7-7) ... Setting up libmaven-parent-java (35-1) ... 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:arm64 (2:3.99-1) ... Setting up libcommons-lang-java (2.6-10) ... 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 libbcel-java (6.5.0-2) ... Setting up testng (6.9.12-4) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up libjansi-native-java (1.8-2) ... Setting up groff-base (1.23.0-4) ... 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 (1.16.0-1) ... Setting up libjline2-java (2.14.6-5) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmaven-resolver-java (1.6.3-1) ... Setting up openjdk-17-jre-headless:arm64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libjgit-java (4.11.9-2) ... Setting up debhelper (13.15.3) ... 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 (3.8.7-2) ... Processing triggers for libc-bin (2.38-10) ... 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-13) ... Setting up openjdk-17-jdk-headless:arm64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ivy (2.5.2-1) ... Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... 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 default-jre-headless (2:1.17-75) ... Setting up maven-repo-helper (1.11) ... Setting up ant-optional (1.10.14-1) ... Setting up bnd (5.0.1-5) ... Setting up default-jdk-headless (2:1.17-75) ... 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 arm64 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=12 jar openjdk version "17.0.11" 2024-04-16 OpenJDK Runtime Environment (build 17.0.11+9-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.11+9-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-17-openjdk-arm64/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 1.044 secs. The client will now receive all logging from the daemon (pid: 546718). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-546718.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 12 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@585aa1f 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@585aa1f 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@3c1339bb 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@a65fb0 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@4bb342 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@3c1339bb 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@148add6c 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@1e1a233b :compileJava (Thread[Task worker for ':' Thread 5,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.004 secs. Up-to-date check for task ':compileJava' took 0.04 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. :compileJava (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 1.177 secs. :buildBwaLib (Thread[Task worker for ':' Thread 5,5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. Up-to-date check for task ':buildBwaLib' took 0.001 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-17-openjdk-arm64 -> /usr/lib/jvm/java-17-openjdk-arm64 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -Wdate-time -D_FORTIFY_SOURCE=2 -c -o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -Wdate-time -D_FORTIFY_SOURCE=2 -c -o jnibwa.o jnibwa.c make CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux" LDFLAGS="-Wl,-z,relro -Wl,-z,now" -C bwaComponent libbwa.a make[2]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c/bwaComponent' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o rope.c: In function 'rope_restore_node': rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function 'rope_restore': rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-arm64/include -I/usr/lib/jvm/java-17-openjdk-arm64/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[Task worker for ':' Thread 5,5,main]) completed. Took 12.604 secs. :processResources (Thread[Task worker for ':' Thread 5,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/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[Task worker for ':' Thread 5,5,main]) completed. Took 0.012 secs. :classes (Thread[Task worker for ':' Thread 5,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.001 secs. :debianMavenPom (Thread[Task worker for ':' Thread 5,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 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[Task worker for ':' Thread 5,5,main]) completed. Took 0.169 secs. :jar (Thread[Task worker for ':' Thread 5,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.011 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':' Thread 5,5,main]) completed. Took 0.108 secs. BUILD SUCCESSFUL in 19s 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=12 test openjdk version "17.0.11" 2024-04-16 OpenJDK Runtime Environment (build 17.0.11+9-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.11+9-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-17-openjdk-arm64/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 2.106 secs. The client will now receive all logging from the daemon (pid: 550513). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-550513.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 12 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@1be33a5d 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@1be33a5d 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@69b07db8 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@5b5a235b 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@439f6cf 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@69b07db8 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@135f0f49 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@718e609 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.016 secs. Skipping task ':compileJava' as it is up-to-date (took 0.051 secs). :compileJava UP-TO-DATE :compileJava (Thread[Task worker for ':',5,main]) completed. Took 0.189 secs. :buildBwaLib (Thread[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 0.006 secs). :buildBwaLib UP-TO-DATE :buildBwaLib (Thread[Task worker for ':',5,main]) completed. Took 0.011 secs. :processResources (Thread[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[Task worker for ':',5,main]) completed. Took 0.006 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. :compileTestJava (Thread[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@2cb3004a Loading the Maven rules... Replacing org.testng:testng:jar:6.9.6 -> org.testng:testng:jar:debian Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Up-to-date check for task ':compileTestJava' took 1.214 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[Task worker for ':',5,main]) completed. Took 3.289 secs. :processTestResources (Thread[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 0.016 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.15 secs. :testClasses (Thread[Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. :test (Thread[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 0.138 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-17-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath11976984105962847348txt -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 WARNING: A terminally deprecated method in java.lang.System has been called WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar) WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker WARNING: System::setSecurityManager will be removed in a future release Gradle Test Executor 1 finished executing tests. Results: SUCCESS (7 tests, 7 successes, 0 failures, 0 skipped) Finished generating test XML results (0.027 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test Generating HTML test report... Finished generating test html results (0.039 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test :test (Thread[Task worker for ':',5,main]) completed. Took 2.019 secs. BUILD SUCCESSFUL in 16s 5 actionable tasks: 3 executed, 2 up-to-date make[1]: Leaving directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install dh_install mh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libgatk-bwamem-java: substitution variable ${java:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libgatk-bwamem-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_arm64.deb'. dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in '../libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo dpkg-genchanges --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_arm64.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/531355 and its subdirectories I: Current time: Thu May 16 02:18:29 -12 2024 I: pbuilder-time-stamp: 1715869109 Thu May 16 14:18:31 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Thu May 16 14:18:31 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Thu May 16 14:19:58 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Thu May 16 14:19:58 UTC 2024 I: gatk-bwamem_1.0.4+dfsg2-3_arm64.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 arm64 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: 5aa23a754e89ec47a455dbc8358933df78e49050 9935 gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo 7d2fea4ea09aa716de6abca3d3547e42ad48cece 23784 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 32fe40f9722d45fffd11898ffd05a5aaa2ae985a 233604 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_arm64.deb bd8ea47defa73f0ffc2cfe9a0431acfbc0c55945 84012 libgatk-bwamem-jni_1.0.4+dfsg2-3_arm64.deb Checksums-Sha256: ddf7ce654d8e72e011cf223acc218b9f3a5c7af0ae202191836b256a1f90cce7 9935 gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo 14cb67f2febac9289079376fc1f616db75ca0a43025ae0008eaaa67e0b00ac33 23784 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 73fa9ae8babf4ae4a83a653ae6ee55b670a96fbf8d8f5adfaaa3457410a19ab7 233604 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_arm64.deb 0d828c36d1edf45f4ce338e567781c2705e012aa2716feb483fcf7bcd2bb8b86 84012 libgatk-bwamem-jni_1.0.4+dfsg2-3_arm64.deb Files: 38231ad8ef5cde82fa57207b6e934edb 9935 java optional gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo 5e78db754307cf46e9a0a1eb98cec816 23784 java optional libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 9ae45dd34c968b74d2fa8be85aefde21 233604 debug optional libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_arm64.deb 4459111c6df7292d39e1a242818bcdcc 84012 java optional libgatk-bwamem-jni_1.0.4+dfsg2-3_arm64.deb Thu May 16 14:20:00 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_22-11615.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.0F9iWarw/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0F9iWarw/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0F9iWarw/gatk-bwamem_1.0.4+dfsg2-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0F9iWarw/b1/gatk-bwamem_1.0.4+dfsg2-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.0F9iWarw/b2/gatk-bwamem_1.0.4+dfsg2-3_arm64.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: 0.452s) 0.452s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 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: 856ms CPU time consumed: 857ms Thu May 16 14:20:01 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Thu May 16 14:20:01 UTC 2024 I: gatk-bwamem from trixie built successfully and reproducibly on arm64. Thu May 16 14:20:02 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 16 14:20:02 UTC 2024 I: Submitting 12K b1/gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo.asc Thu May 16 14:20:03 UTC 2024 I: Submitting 12K b2/gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo.asc Thu May 16 14:20:04 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 16 14:20:04 UTC 2024 I: Done submitting .buildinfo files. Thu May 16 14:20:04 UTC 2024 I: Removing signed gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo.asc files: removed './b1/gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo.asc' removed './b2/gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo.asc'