I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 12 08:28:38 -12 2023 I: pbuilder-time-stamp: 1686601718 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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-fermilite_1.2.1+dfsg-2.dsc] I: copying [./gatk-fermilite_1.2.1+dfsg.orig.tar.xz] I: copying [./gatk-fermilite_1.2.1+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Apr 5 08:14:33 2022 -12 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gatk-fermilite_1.2.1+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting gatk-fermilite in gatk-fermilite-1.2.1+dfsg dpkg-source: info: unpacking gatk-fermilite_1.2.1+dfsg.orig.tar.xz dpkg-source: info: unpacking gatk-fermilite_1.2.1+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build.patch dpkg-source: info: applying use_Debian_fml.patch dpkg-source: info: applying rename_bseq1_t.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/266369/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='96550e3c21464579b85e6b36ec0eb721' 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='266369' 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.Mhb8dL1C/pbuilderrc_8XHi --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Mhb8dL1C/b1 --logfile b1/build.log gatk-fermilite_1.2.1+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 6.1.0-9-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.27-1 (2023-05-08) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/266369/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), default-jdk-headless, gradle-debian-helper, libfml-dev, maven-repo-helper, testng dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19591 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 libfml-dev; however: Package libfml-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. 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} fontconfig-config{a} fonts-dejavu-core{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} libasound2{a} libasound2-data{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libbrotli1{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} libcups2{a} libdbus-1-3{a} libdd-plist-java{a} libdebhelper-perl{a} libdom4j-java{a} libeclipse-jdt-annotation-java{a} libel-api-java{a} libelf1{a} liberror-prone-java{a} libexpat1{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libfile-stripnondeterminism-perl{a} libfindbugs-java{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libglib2.0-0{a} libgoogle-gson-java{a} libgradle-core-java{a} libgradle-plugins-java{a} libgraphite2-3{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{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} libmagic1{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} libncurses6{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} libpng16-16{a} libpolyglot-maven-java{a} libqdox-java{a} libreflectasm-java{a} librhino-java{a} libservlet-api-java{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: alsa-topology-conf alsa-ucm-conf curl dbus javascript-common libarchive-cpio-perl libbindex-java libglib2.0-data libgpars-groovy-java libgpm2 libltdl-dev libmail-sendmail-perl libreflectasm-java-doc lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 181 newly installed, 0 to remove and 0 not upgraded. Need to get 386 MB of archives. After unpacking 650 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.9-1 [1416 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 39 http://deb.debian.org/debian bookworm/main amd64 ant all 1.10.13-1 [2161 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 ant-optional all 1.10.13-1 [449 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libantlr-java all 2.7.7+dfsg-12 [458 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 antlr all 2.7.7+dfsg-12 [14.3 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 java-wrappers all 0.4 [8916 B] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libhamcrest-java all 2.2-1 [121 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 junit4 all 4.13.2-3 [348 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libosgi-annotation-java all 8.1.0-1 [9436 B] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libosgi-core-java all 8.0.0-2 [182 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libjansi-native-java all 1.8-1 [26.0 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libjansi1-java all 1.18-3 [66.5 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libjline2-java all 2.14.6-5 [151 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libxz-java all 1.9-1 [143 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libyaml-snake-java all 1.33-2 [321 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 bnd all 5.0.1-3 [9915 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.6+10-1 [230 MB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B] Get: 83 http://deb.debian.org/debian bookworm/main amd64 ivy all 2.5.1-2 [1288 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libasm-java all 9.4-1 [389 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libcommons-cli-java all 1.5.0-1 [60.0 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libjansi-java all 2.4.0-2 [105 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxstream-java all 1.4.20-1 [565 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 groovy all 2.4.21-8 [12.9 MB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libjarjar-java all 1.4+svn142-12 [205 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libjna-jni amd64 5.13.0-2 [63.3 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libjna-java all 5.13.0-2 [236 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libjzlib-java all 1.1.3-2 [80.0 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libjsch-java all 0.1.55-1 [298 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libminlog-java all 1.3.0-1.1 [7928 B] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libobjenesis-java all 3.3-3 [41.3 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libkryo-java all 2.20-7 [158 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 liblogback-java all 1:1.2.11-3 [700 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libnative-platform-jni amd64 0.14-5 [13.0 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libnative-platform-java all 0.14-5 [71.0 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libgradle-core-java all 4.4.1-18 [4286 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libbcprov-java all 1.72-2 [8225 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libbcpg-java all 1.72-2 [383 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libdom4j-java all 2.1.3-2 [310 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libbcel-java all 6.5.0-2 [634 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libjcifs-java all 1.3.19-2 [394 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.26-2 [25.3 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libjavaewah-java all 1.1.7-1 [156 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libjetty9-java all 9.4.50-4 [2962 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libjgit-java all 4.11.9-2 [2534 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libmaven3-core-java all 3.8.7-1 [1572 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libjcommander-java all 1.71-4 [73.0 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 testng all 6.9.12-4 [795 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libgradle-plugins-java all 4.4.1-18 [5212 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 gradle all 4.4.1-18 [398 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 gradle-debian-helper all 2.4 [24.5 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b1 [82.9 kB] Fetched 386 MB in 7s (58.8 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 ... 19591 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.0.9-1_amd64.deb ... Unpacking openssl (3.0.9-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../004-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../007-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../010-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../012-ca-certificates-java_20230103_all.deb ... Unpacking ca-certificates-java (20230103) ... Selecting previously unselected package java-common. Preparing to unpack .../013-java-common_0.74_all.deb ... Unpacking java-common (0.74) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../014-libavahi-common-data_0.8-10_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.8-10) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../015-libavahi-common3_0.8-10_amd64.deb ... Unpacking libavahi-common3:amd64 (0.8-10) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../016-libdbus-1-3_1.14.6-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.14.6-1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../017-libavahi-client3_0.8-10_amd64.deb ... Unpacking libavahi-client3:amd64 (0.8-10) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../018-libcups2_2.4.2-3_amd64.deb ... Unpacking libcups2:amd64 (2.4.2-3) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../019-liblcms2-2_2.14-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.14-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../020-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../021-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../022-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../023-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../024-libfreetype6_2.12.1+dfsg-5_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../025-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../026-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../027-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../028-libnspr4_2%3a4.35-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.35-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../029-libnss3_2%3a3.87.1-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.87.1-1) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../030-libasound2-data_1.2.8-1_all.deb ... Unpacking libasound2-data (1.2.8-1) ... Selecting previously unselected package libasound2:amd64. Preparing to unpack .../031-libasound2_1.2.8-1+b1_amd64.deb ... Unpacking libasound2:amd64 (1.2.8-1+b1) ... Selecting previously unselected package libglib2.0-0:amd64. 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Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libjcommander-java (1.71-4) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libqdox-java (1.12.1-3) ... Setting up libicu72:amd64 (72.1-3) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up libsimple-http-java (4.1.21-1.1) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up java-common (0.74) ... 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 (1.5.0-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up liblogback-java (1:1.2.11-3) ... Setting up libminlog-java (1.3.0-1.1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libgoogle-gson-java (2.10-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libasm-java (9.4-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdd-plist-java (1.20-1.1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libel-api-java (3.0.0-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up file (1:5.44-3) ... 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 (1.1.3-2) ... Setting up libfml0:amd64 (0.1+git20190320.b499514-1+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 (3.2.2-2) ... Setting up libasound2-data (1.2.8-1) ... 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 (1.1.7-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.26-2) ... Setting up libjansi-java (2.4.0-2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.14.6-1) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... 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 (5.13.0-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libfelix-framework-java (4.6.1-2.1) ... Setting up libpcsclite1:amd64 (1.9.9-2) ... Setting up libhamcrest-java (2.2-1) ... 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:amd64 (1:1.2.13.dfsg-1) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libxml-commons-external-java (1.4.01-5) ... Setting up libjna-java (5.13.0-2) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libnative-platform-jni (0.14-5) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libbcpg-java (1.72-2) ... 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-12) ... Setting up libyaml-snake-java (1.33-2) ... Setting up openssl (3.0.9-1) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... 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 (2.1.3-2) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libnative-platform-java (0.14-5) ... 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 (0.21-12) ... Setting up libjetty9-java (9.4.50-4) ... Setting up libfml-dev:amd64 (0.1+git20190320.b499514-1+b1) ... Setting up java-wrappers (0.4) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libmaven-parent-java (35-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.87.1-1) ... 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 (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libbcel-java (6.5.0-2) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up testng (6.9.12-4) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up dwz (0.15-1) ... Setting up libjansi-native-java (1.8-1) ... Setting up groff-base (1.22.4-10) ... Setting up libjansi1-java (1.18-3) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libjline2-java (2.14.6-5) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libcups2:amd64 (2.4.2-3) ... 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 (13.11.4) ... Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20230103) ... 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:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.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: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:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.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_1.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:SZAFIR_ROOT_CA2.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:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.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 junit4 (4.13.2-3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up default-jre-headless (2:1.17-74) ... Setting up maven-repo-helper (1.11) ... Setting up antlr (2.7.7+dfsg-12) ... Setting up bnd (5.0.1-3) ... Setting up libguava-java (31.1-1) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ivy (2.5.1-2) ... Setting up ant (1.10.13-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up groovy (2.4.21-8) ... 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 libguice-java (4.2.3-2) ... Setting up ant-optional (1.10.13-1) ... Setting up default-jdk-headless (2:1.17-74) ... Setting up libgradle-core-java (4.4.1-18) ... Setting up libmaven3-core-java (3.8.7-1) ... Setting up libgradle-plugins-java (4.4.1-18) ... Setting up gradle (4.4.1-18) ... Setting up gradle-debian-helper (2.4) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... 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 (20230103) ... 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/gatk-fermilite-1.2.1+dfsg/ && 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-fermilite_1.2.1+dfsg-2_source.changes dpkg-buildpackage: info: source package gatk-fermilite dpkg-buildpackage: info: source version 1.2.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/gatk-fermilite-1.2.1+dfsg' dh_auto_clean sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/gatk-fermilite-1.2.1\+dfsg/.gradle /build/gatk-fermilite-1.2.1\+dfsg/buildSrc/.gradle .m2 if [ -e src/main/c/org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.c.save ]; then \ mv src/main/c/org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.c.save src/main/c/org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.c; \ fi # Cleaning the C part cd src/main/c/ && make clean make[2]: Entering directory '/build/gatk-fermilite-1.2.1+dfsg/src/main/c' rm -rf fermi-lite *.o *.so make[2]: Leaving directory '/build/gatk-fermilite-1.2.1+dfsg/src/main/c' # Cleaning the custom pom rm debian/pom.xml rm: cannot remove 'debian/pom.xml': No such file or directory make[1]: [debian/rules:20: override_dh_auto_clean] Error 1 (ignored) make[1]: Leaving directory '/build/gatk-fermilite-1.2.1+dfsg' 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/gatk-fermilite-1.2.1+dfsg' # Putting the version of fermi-lite in the JNI file so that is can output version information. cp src/main/c/org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.c src/main/c/org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.c.save fmlVersion=$(dpkg -s libfml-dev | grep "Version" | sed 's/Version: \(.*\)-.*/\1/') && \ sed -i "s/FML_COMMIT/\"$fmlVersion\"/" src/main/c/org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.c # Putting the version number in the custom pom. sed 's/\(VERSION_PACKAGE\)/\11.2.1+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/pom.xml.in > debian/pom.xml dh_auto_configure make[1]: Leaving directory '/build/gatk-fermilite-1.2.1+dfsg' 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-fermilite -Dfile.encoding=UTF-8 --parallel --max-workers=15 jar openjdk version "17.0.6" 2023-01-17 OpenJDK Runtime Environment (build 17.0.6+10-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.6+10-Debian-1, mixed mode, sharing) Initialized native services in: /build/gatk-fermilite-1.2.1+dfsg/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/gatk-fermilite-1.2.1+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 1.013 secs. The client will now receive all logging from the daemon (pid: 272781). The daemon log file: /build/gatk-fermilite-1.2.1+dfsg/.gradle/daemon/4.4.1/daemon-272781.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 15 worker leases. Creating new cache for fileHashes, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@221191e9 Creating new cache for resourceHashesCache, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@221191e9 Creating new cache for fileHashes, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7aad0b5 Starting Build Compiling initialization script '/build/gatk-fermilite-1.2.1+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@677b8309 Compiling initialization script '/build/gatk-fermilite-1.2.1+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/gatk-fermilite-1.2.1+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/gatk-fermilite-1.2.1+dfsg/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/gatk-fermilite-1.2.1+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/gatk-fermilite-1.2.1+dfsg/build.gradle'. Included projects: [root project 'gatk-fermilite'] Keep-alive timer started Adding Debian repository to project 'gatk-fermilite' Parallel execution is an incubating feature. Evaluating root project 'gatk-fermilite' using build file '/build/gatk-fermilite-1.2.1+dfsg/build.gradle'. Compiling build file '/build/gatk-fermilite-1.2.1+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/gatk-fermilite-1.2.1+dfsg/build.gradle' using BuildScriptTransformer. Adding Maven pom generation to project 'gatk-fermilite' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : Creating new cache for annotation-processors, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4024bde6 Tasks to be executed: [task ':compileJava', task ':buildFermiLib', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] Creating new cache for resourceHashesCache, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7aad0b5 Creating new cache for taskHistory, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@ab26034 Creating new cache for outputFiles, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@37afb844 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.005 secs. Up-to-date check for task ':compileJava' took 0.044 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. :compileJava (Thread[Task worker for ':',5,main]) completed. Took 1.367 secs. :buildFermiLib (Thread[Task worker for ':',5,main]) started. :buildFermiLib Putting task artifact state for task ':buildFermiLib' into context took 0.0 secs. Up-to-date check for task ':buildFermiLib' took 0.003 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-17-openjdk-amd64 -> /usr/lib/jvm/java-17-openjdk-amd64 as JAVA_HOME Starting process 'command 'make''. Working directory: /build/gatk-fermilite-1.2.1+dfsg/src/main/c Command: make Successfully started process 'command 'make'' make[1]: Entering directory '/build/gatk-fermilite-1.2.1+dfsg/src/main/c' gcc -g -O2 -Wall -fPIC -I/usr/lib/jvm/java-17-openjdk-amd64/include -I/usr/lib/jvm/java-17-openjdk-amd64/include/linux -Wdate-time -D_FORTIFY_SOURCE=2 -c -o org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.o org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.c gcc -dynamiclib -shared -o libfml.so org_broadinstitute_hellbender_utils_fermi_FermiLiteAssembler.o /usr/lib/x86_64-linux-gnu/libfml.so -lm -lz -lpthread make[1]: Leaving directory '/build/gatk-fermilite-1.2.1+dfsg/src/main/c' :buildFermiLib (Thread[Task worker for ':',5,main]) completed. Took 0.301 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/gatk-fermilite-1.2.1+dfsg/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 0.003 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. :debianMavenPom (Thread[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 0.002 secs. It is not up-to-date because: No history is available. Generating pom file /build/gatk-fermilite-1.2.1+dfsg/build/debian/gatk-fermilite.pom :debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.12 secs. :jar (Thread[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 0.008 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':',5,main]) completed. Took 0.062 secs. BUILD SUCCESSFUL in 7s 4 actionable tasks: 4 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/gatk-fermilite-1.2.1+dfsg' # 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-fermilite -Dfile.encoding=UTF-8 --parallel --max-workers=15 test openjdk version "17.0.6" 2023-01-17 OpenJDK Runtime Environment (build 17.0.6+10-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.6+10-Debian-1, mixed mode, sharing) Initialized native services in: /build/gatk-fermilite-1.2.1+dfsg/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/gatk-fermilite-1.2.1+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 1.036 secs. The client will now receive all logging from the daemon (pid: 275698). The daemon log file: /build/gatk-fermilite-1.2.1+dfsg/.gradle/daemon/4.4.1/daemon-275698.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 15 worker leases. Creating new cache for fileHashes, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@654d7672 Creating new cache for resourceHashesCache, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@654d7672 Creating new cache for fileHashes, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@259e936b Starting Build Creating new cache for metadata-1.1/results, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@5f7d0cfa Settings evaluated using settings file '/build/gatk-fermilite-1.2.1+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/gatk-fermilite-1.2.1+dfsg/build.gradle'. Included projects: [root project 'gatk-fermilite'] Keep-alive timer started Adding Debian repository to project 'gatk-fermilite' Parallel execution is an incubating feature. Evaluating root project 'gatk-fermilite' using build file '/build/gatk-fermilite-1.2.1+dfsg/build.gradle'. Adding Maven pom generation to project 'gatk-fermilite' 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/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d1407d3 Tasks to be executed: [task ':compileJava', task ':buildFermiLib', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] Creating new cache for resourceHashesCache, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@259e936b Creating new cache for taskHistory, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@25650238 Creating new cache for outputFiles, path /build/gatk-fermilite-1.2.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a08e31e :compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.004 secs. Skipping task ':compileJava' as it is up-to-date (took 0.033 secs). :compileJava UP-TO-DATE :compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.074 secs. :buildFermiLib (Thread[Task worker for ':' Thread 2,5,main]) started. :buildFermiLib Putting task artifact state for task ':buildFermiLib' into context took 0.0 secs. Skipping task ':buildFermiLib' as it is up-to-date (took 0.007 secs). :buildFermiLib UP-TO-DATE :buildFermiLib (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.011 secs. :processResources (Thread[Task worker for ':' Thread 2,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/gatk-fermilite-1.2.1+dfsg/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 2,5,main]) completed. Took 0.003 secs. :classes (Thread[Task worker for ':' Thread 2,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. :compileTestJava (Thread[Task worker for ':' Thread 2,5,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/gatk-fermilite-1.2.1+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@22227c49 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 0.647 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 ':' Thread 2,5,main]) completed. Took 1.591 secs. :processTestResources (Thread[Task worker for ':' Thread 2,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. file or directory '/build/gatk-fermilite-1.2.1+dfsg/src/test/resources', not found Skipping task ':processTestResources' as it has no source files and no previous output files. :processTestResources NO-SOURCE :processTestResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.003 secs. :testClasses (Thread[Task worker for ':' Thread 2,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. :test (Thread[Task worker for ':' Thread 2,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. Up-to-date check for task ':test' took 0.096 secs. It is not up-to-date because: No history is available. Starting process 'Gradle Test Executor 1'. Working directory: /build/gatk-fermilite-1.2.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath3819968137910926144txt -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. Gradle Test Executor 1 finished executing tests. 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 Results: SUCCESS (2 tests, 2 successes, 0 failures, 0 skipped) Finished generating test XML results (0.011 secs) into: /build/gatk-fermilite-1.2.1+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (0.022 secs) into: /build/gatk-fermilite-1.2.1+dfsg/build/reports/tests/test :test (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1.545 secs. BUILD SUCCESSFUL in 8s 4 actionable tasks: 2 executed, 2 up-to-date make[1]: Leaving directory '/build/gatk-fermilite-1.2.1+dfsg' 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-fermilite-java: substitution variable ${java:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libgatk-fermilite-java' in '../libgatk-fermilite-java_1.2.1+dfsg-2_all.deb'. dpkg-deb: building package 'libgatk-fermilite-jni' in '../libgatk-fermilite-jni_1.2.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'libgatk-fermilite-jni-dbgsym' in '../libgatk-fermilite-jni-dbgsym_1.2.1+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gatk-fermilite_1.2.1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gatk-fermilite_1.2.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/266369 and its subdirectories I: Current time: Mon Jun 12 08:29:44 -12 2023 I: pbuilder-time-stamp: 1686601784