Sun Jun 20 15:17:23 UTC 2021 I: starting to build htsjdk/buster/amd64 on jenkins on '2021-06-20 15:17' Sun Jun 20 15:17:23 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_3/1018/console.log Sun Jun 20 15:17:23 UTC 2021 I: Downloading source for buster/htsjdk=2.18.2+dfsg-2 --2021-06-20 15:17:23-- http://deb.debian.org/debian/pool/main/h/htsjdk/htsjdk_2.18.2+dfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2450 (2.4K) Saving to: ‘htsjdk_2.18.2+dfsg-2.dsc’ 0K .. 100% 101M=0s 2021-06-20 15:17:23 (101 MB/s) - ‘htsjdk_2.18.2+dfsg-2.dsc’ saved [2450/2450] Sun Jun 20 15:17:23 UTC 2021 I: htsjdk_2.18.2+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: htsjdk Binary: libhtsjdk-java, libhtsjdk-java-doc Architecture: all Version: 2.18.2+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Olivier Sallou , Vincent Danjean , Andreas Tille Homepage: http://samtools.github.io/htsjdk/ Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/htsjdk Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git Build-Depends: default-jdk (>= 2:1.9), javahelper, gradle-debian-helper, maven-repo-helper, debhelper (>= 12~), libcommons-jexl2-java, libcommons-logging-java, libjaxb-api-java, libjaxb-java, libsnappy-java, libcommons-compress-java, libxz-java (>= 1.5), libngs-java, default-jdk-doc, testng (>= 6.9.9), junit4, libjimfs-java, scala-library Package-List: libhtsjdk-java deb java optional arch=all libhtsjdk-java-doc deb doc optional arch=all Checksums-Sha1: bc025ee84a909243e7d7950671da88ab248a09d6 8461296 htsjdk_2.18.2+dfsg.orig.tar.xz 874bc437a45fe21019931324f9fb61c8e99e91d6 29656 htsjdk_2.18.2+dfsg-2.debian.tar.xz Checksums-Sha256: 1c8b66ba451ee3214b968bb8dd2786d1b35d2f40466bb0b66cbe8cb600d1d8ff 8461296 htsjdk_2.18.2+dfsg.orig.tar.xz 1031f1097c534edf53be3da89dcb888f8d41cab8d78751f51dcc3c8891fcb207 29656 htsjdk_2.18.2+dfsg-2.debian.tar.xz Files: ec28760f3333688562722b651c749107 8461296 htsjdk_2.18.2+dfsg.orig.tar.xz dc408d66ae77ab5fc6c01988cf8cc500 29656 htsjdk_2.18.2+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCAAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlx5rMkOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtERBA//b+LRopfPmHFXm+pyHCwYw7tkQ/vhV5ec6Kud soFRK0lLtlwUhf67OtuopKIe7/dfncq1x6LUrNEf5tJe/6WTY2tPm2AxUM/Rztqw CeS1sKSumpzmABRlL2XTQCtUT+ZS/Kcv24HCZHLj3Sj8Y9dH3McZs8uLsZxvLzQT mMlamc6oiVHiw3HS0PvqxzKc5h9oAma9aKrhpT4T/LuoWMUtjCVV7V8eSjOATWix ZBZWQTzA+R3SMi/BY6CBirikTB1az5YqcYB5SjpfhCMVSN0SeXjWMvkQ9xV5KSb1 tNPepXJmOn36GjyVuDyyawNMiyz9XjN0ArqRyK2pvVQ0te1RV5qt/mrkqsh+7XmP fv4EJQFhCqCqhASiAIFNzmb2QUUn8dg9sJxmC4VuL31Fo+jIJnRJfixFV1hhj6S6 ZXth3WPz92+ySQ6Pxd0lL3LMGBqDnUf48cVeLSje8iriFnHUigZrp0jXX/KbPfst KPTpwiQft6wVJcbku45ZxZmJsWm3SUEKqxCR0gUAtQ+KcdlEfEYMlQo5o0xE43dq AjgDXD6ELWHeR0n5jPJB0hf+zRmZ8vFKRpOcY74KbEAMkQRPnzgFyxw5ZIq75DsQ 4cC/2US0HHuvnOUimE2v6WwmITN1pZyMs+RZyxYZGSsiL6VUYy3xR8B/QbGpTJyP rw0Szm8= =lqSa -----END PGP SIGNATURE----- Sun Jun 20 15:17:23 UTC 2021 I: Checking whether the package is not for us Sun Jun 20 15:17:23 UTC 2021 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sun Jun 20 15:17:23 UTC 2021 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sun Jun 20 15:25:01 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 20 03:17:24 -12 2021 I: pbuilder-time-stamp: 1624202244 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [htsjdk_2.18.2+dfsg-2.dsc] I: copying [./htsjdk_2.18.2+dfsg.orig.tar.xz] I: copying [./htsjdk_2.18.2+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Mar 1 10:06:01 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./htsjdk_2.18.2+dfsg-2.dsc dpkg-source: info: extracting htsjdk in htsjdk-2.18.2+dfsg dpkg-source: info: unpacking htsjdk_2.18.2+dfsg.orig.tar.xz dpkg-source: info: unpacking htsjdk_2.18.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10-build.xml.patch dpkg-source: info: applying 13-skip_network_tests dpkg-source: info: applying 20-fix-version.patch dpkg-source: info: applying 30-disable-scalatest.patch dpkg-source: info: applying 40-fix-java9 dpkg-source: info: applying 50-fix-javadoc dpkg-source: info: applying 60-enable-tests dpkg-source: info: applying 70-removesometests-testng.patch dpkg-source: info: applying 80-2to3.patch dpkg-source: info: applying 90-disable-testftp.patch dpkg-source: info: applying 92-disable-testhttp.patch dpkg-source: info: applying 100-fix-java11 dpkg-source: info: applying 110-debian-lib-version.patch dpkg-source: info: applying disable-network-tests.diff I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13073/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='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d0c328230f6d4b35908e1d4e352eb8e0' 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='13073' 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/tmp.LASAkCP8BM/pbuilderrc_RPM0 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.LASAkCP8BM/b1 --logfile b1/build.log htsjdk_2.18.2+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jun 6 20:23 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/13073/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: default-jdk (>= 2:1.9), javahelper, gradle-debian-helper, maven-repo-helper, debhelper (>= 12~), libcommons-jexl2-java, libcommons-logging-java, libjaxb-api-java, libjaxb-java, libsnappy-java, libcommons-compress-java, libxz-java (>= 1.5), libngs-java, default-jdk-doc, testng (>= 6.9.9), junit4, libjimfs-java, scala-library dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 default-jdk (>= 2:1.9); however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on gradle-debian-helper; however: Package gradle-debian-helper is not installed. pbuilder-satisfydepends-dummy depends on maven-repo-helper; however: Package maven-repo-helper is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libcommons-jexl2-java; however: Package libcommons-jexl2-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however: Package libcommons-logging-java is not installed. pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however: Package libjaxb-api-java is not installed. pbuilder-satisfydepends-dummy depends on libjaxb-java; however: Package libjaxb-java is not installed. pbuilder-satisfydepends-dummy depends on libsnappy-java; however: Package libsnappy-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-compress-java; however: Package libcommons-compress-java is not installed. pbuilder-satisfydepends-dummy depends on libxz-java (>= 1.5); however: Package libxz-java is not installed. pbuilder-satisfydepends-dummy depends on libngs-java; however: Package libngs-java is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-doc; however: Package default-jdk-doc is not installed. pbuilder-satisfydepends-dummy depends on testng (>= 6.9.9); however: Package testng is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 is not installed. pbuilder-satisfydepends-dummy depends on libjimfs-java; however: Package libjimfs-java is not installed. pbuilder-satisfydepends-dummy depends on scala-library; however: Package scala-library 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} bsdmainutils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} gradle{a} gradle-debian-helper{a} groff-base{a} groovy{a} intltool-debian{a} ivy{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} libactivation-java{a} libantlr-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libbsd0{a} libbsf-java{a} libbsh-java{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcroco3{a} libcups2{a} libdbus-1-3{a} libdd-plist-java{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} libexpat1{a} libfastinfoset-java{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfindbugs-java{a} libfontconfig1{a} libfreetype6{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgradle-core-java{a} libgradle-plugins-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhawtjni-runtime-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu63{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libjansi-java{a} libjansi-native-java{a} libjarjar-java{a} libjatl-java{a} libjavaewah-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjcifs-java{a} libjcip-annotations-java{a} libjcommander-java{a} libjformatstring-java{a} libjgit-java{a} libjimfs-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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libkryo-java{a} libksba8{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libllvm7{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libminlog-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libmpdec2{a} libnative-platform-java{a} libnative-platform-jni{a} libncurses6{a} libnekohtml-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-sdk-dev{a} libngs-sdk2{a} libnpth0{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16{a} libpolyglot-maven-java{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libqdox-java{a} libreadline7{a} libreflectasm-java{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libservlet3.1-java{a} libsigsegv2{a} libsimple-http-java{a} libsisu-guice-java{a} libsisu-inject-java{a} libsisu-ioc-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssl1.1{a} libstax-ex-java{a} libstreambuffer-java{a} libstrictures-perl{a} libsub-exporter-progressive-perl{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} liburi-perl{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-sync1{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxpp3-java{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxstream-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libyaml-snake-java{a} lsb-base{a} m4{a} man-db{a} maven-repo-helper{a} mime-support{a} netbase{a} openjdk-11-doc{a} openjdk-11-jdk{a} openjdk-11-jdk-headless{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} scala-library{a} sensible-utils{a} testng{a} ucf{a} unzip{a} wdiff{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: at curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra javascript-common krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libbindex-java libcglib-java libclass-xsaccessor-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpars-groovy-java libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libsub-name-perl libxt-dev licensecheck lintian lynx python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg shared-mime-info strace wget xdg-user-dirs 0 packages upgraded, 330 newly installed, 0 to remove and 0 not upgraded. Need to get 425 MB of archives. After unpacking 1182 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 netbase all 5.6 [19.4 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u6 [844 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.11+9-1~deb10u1 [37.2 MB] Get: 57 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 ant all 1.10.5-2 [2082 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 ant-optional all 1.10.5-2 [379 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libantlr-java all 2.7.7+dfsg-9.2 [459 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 antlr all 2.7.7+dfsg-9.2 [13.9 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 java-wrappers all 0.3 [10.9 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libhamcrest-java all 1.3-9 [388 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 junit4 all 4.12-8 [292 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libfelix-framework-java all 4.6.1-2 [543 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libfelix-gogo-runtime-java all 0.16.2-1 [111 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libosgi-annotation-java all 6.0.0-2 [3698 B] Get: 75 http://deb.debian.org/debian buster/main amd64 libosgi-core-java all 6.0.0-1 [147 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libfelix-resolver-java all 1.14.0-1 [177 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libosgi-compendium-java all 6.0.0-1 [244 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libslf4j-java all 1.7.25-3 [143 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libxz-java all 1.8-2 [141 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libyaml-snake-java all 1.23-1 [270 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 bnd all 3.5.0-4 [7604 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 dctrl-tools amd64 2.24-3 [103 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libglvnd0 amd64 1.1.0-1 [48.6 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libdrm-common all 2.4.97-1 [13.8 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libdrm2 amd64 2.4.97-1 [39.7 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libglapi-mesa amd64 18.3.6-2+deb10u1 [66.3 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libx11-xcb1 amd64 2:1.6.7-1+deb10u2 [191 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libxcb-dri2-0 amd64 1.13.1-2 [101 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libxcb-dri3-0 amd64 1.13.1-2 [100 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libxcb-glx0 amd64 1.13.1-2 [116 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libxcb-present0 amd64 1.13.1-2 [99.1 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libxcb-sync1 amd64 1.13.1-2 [103 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libxdamage1 amd64 1:1.1.4-3+b3 [14.9 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 117 http://deb.debian.org/debian buster/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libdrm-amdgpu1 amd64 2.4.97-1 [27.3 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libdrm-intel1 amd64 2.4.97-1 [69.8 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libdrm-nouveau2 amd64 2.4.97-1 [26.3 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libdrm-radeon1 amd64 2.4.97-1 [31.1 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libllvm7 amd64 1:7.0.1-8+deb10u2 [13.1 MB] Get: 125 http://deb.debian.org/debian buster/main amd64 libsensors-config all 1:3.5.0-3 [31.6 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libsensors5 amd64 1:3.5.0-3 [52.6 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libgl1-mesa-dri amd64 18.3.6-2+deb10u1 [6685 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 libglx-mesa0 amd64 18.3.6-2+deb10u1 [180 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libglx0 amd64 1.1.0-1 [30.0 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libgif7 amd64 5.1.4-3 [43.3 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre amd64 11.0.11+9-1~deb10u1 [174 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 default-jre amd64 2:1.11-71 [1044 B] Get: 139 http://deb.debian.org/debian buster/main amd64 openjdk-11-jdk-headless amd64 11.0.11+9-1~deb10u1 [220 MB] Get: 140 http://deb.debian.org/debian buster/main amd64 default-jdk-headless amd64 2:1.11-71 [1104 B] Get: 141 http://deb.debian.org/debian buster/main amd64 openjdk-11-jdk amd64 11.0.11+9-1~deb10u1 [2665 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 default-jdk amd64 2:1.11-71 [1056 B] Get: 143 http://deb.debian.org/debian buster/main amd64 openjdk-11-doc all 11.0.11+9-1~deb10u1 [13.5 MB] Get: 144 http://deb.debian.org/debian buster/main amd64 default-jdk-doc amd64 2:1.11-71 [10.9 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 libassuan0 amd64 2.5.2-1 [49.4 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 gpgconf amd64 2.2.12-1+deb10u1 [510 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 libksba8 amd64 1.3.5-2 [99.7 kB] Get: 148 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 149 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 151 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 libnpth0 amd64 1.6-1 [18.4 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 dirmngr amd64 2.2.12-1+deb10u1 [712 kB] Get: 154 http://deb.debian.org/debian buster/main amd64 gnupg-l10n all 2.2.12-1+deb10u1 [1010 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 gnupg-utils amd64 2.2.12-1+deb10u1 [861 kB] Get: 156 http://deb.debian.org/debian buster/main amd64 gpg amd64 2.2.12-1+deb10u1 [865 kB] Get: 157 http://deb.debian.org/debian buster/main amd64 pinentry-curses amd64 1.1.0-2 [64.5 kB] Get: 158 http://deb.debian.org/debian buster/main amd64 gpg-agent amd64 2.2.12-1+deb10u1 [617 kB] Get: 159 http://deb.debian.org/debian buster/main amd64 gpg-wks-client amd64 2.2.12-1+deb10u1 [485 kB] Get: 160 http://deb.debian.org/debian buster/main amd64 gpg-wks-server amd64 2.2.12-1+deb10u1 [478 kB] Get: 161 http://deb.debian.org/debian buster/main amd64 gpgsm amd64 2.2.12-1+deb10u1 [604 kB] Get: 162 http://deb.debian.org/debian buster/main amd64 gnupg all 2.2.12-1+deb10u1 [715 kB] Get: 163 http://deb.debian.org/debian buster/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get: 164 http://deb.debian.org/debian buster/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get: 165 http://deb.debian.org/debian buster/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get: 166 http://deb.debian.org/debian buster/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get: 167 http://deb.debian.org/debian buster/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get: 168 http://deb.debian.org/debian buster/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 169 http://deb.debian.org/debian buster/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get: 170 http://deb.debian.org/debian buster/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b1 [11.4 kB] Get: 171 http://deb.debian.org/debian buster/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get: 172 http://deb.debian.org/debian buster/main amd64 libdevel-callchecker-perl amd64 0.008-1 [15.7 kB] Get: 173 http://deb.debian.org/debian buster/main amd64 libparams-classify-perl amd64 0.015-1+b1 [25.5 kB] Get: 174 http://deb.debian.org/debian buster/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 175 http://deb.debian.org/debian buster/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 176 http://deb.debian.org/debian buster/main amd64 librole-tiny-perl all 2.000006-1 [19.4 kB] Get: 177 http://deb.debian.org/debian buster/main amd64 libstrictures-perl all 2.000005-1 [18.3 kB] Get: 178 http://deb.debian.org/debian buster/main amd64 libsub-quote-perl all 2.005001-1 [17.9 kB] Get: 179 http://deb.debian.org/debian buster/main amd64 libmoo-perl all 2.003004-2 [57.4 kB] Get: 180 http://deb.debian.org/debian buster/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get: 181 http://deb.debian.org/debian buster/main amd64 libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get: 182 http://deb.debian.org/debian buster/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get: 183 http://deb.debian.org/debian buster/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get: 184 http://deb.debian.org/debian buster/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 185 http://deb.debian.org/debian buster/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get: 186 http://deb.debian.org/debian buster/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get: 187 http://deb.debian.org/debian buster/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get: 188 http://deb.debian.org/debian buster/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get: 189 http://deb.debian.org/debian buster/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get: 190 http://deb.debian.org/debian buster/main amd64 libhttp-message-perl all 6.18-1 [77.8 kB] Get: 191 http://deb.debian.org/debian buster/main amd64 libhttp-cookies-perl all 6.04-1 [17.8 kB] Get: 192 http://deb.debian.org/debian buster/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 193 http://deb.debian.org/debian buster/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get: 194 http://deb.debian.org/debian buster/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get: 195 http://deb.debian.org/debian buster/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get: 196 http://deb.debian.org/debian buster/main amd64 libnet-http-perl all 6.18-1 [24.5 kB] Get: 197 http://deb.debian.org/debian buster/main amd64 liblwp-protocol-https-perl all 6.07-2 [9242 B] Get: 198 http://deb.debian.org/debian buster/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 199 http://deb.debian.org/debian buster/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 200 http://deb.debian.org/debian buster/main amd64 libwww-perl all 6.36-2 [188 kB] Get: 201 http://deb.debian.org/debian buster/main amd64 patchutils amd64 0.3.4-2 [90.4 kB] Get: 202 http://deb.debian.org/debian buster/main amd64 wdiff amd64 1.2.2-2+b1 [122 kB] Get: 203 http://deb.debian.org/debian buster/main amd64 devscripts amd64 2.19.5+deb10u1 [1046 kB] Get: 204 http://deb.debian.org/debian buster/main amd64 ivy all 2.4.0-5 [1207 kB] Get: 205 http://deb.debian.org/debian buster/main amd64 libasm-java all 7.0-1 [362 kB] Get: 206 http://deb.debian.org/debian buster/main amd64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 207 http://deb.debian.org/debian buster/main amd64 libcommons-cli-java all 1.4-1 [55.2 kB] Get: 208 http://deb.debian.org/debian buster/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 209 http://deb.debian.org/debian buster/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 210 http://deb.debian.org/debian buster/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 211 http://deb.debian.org/debian buster/main amd64 libhawtjni-runtime-java all 1.16-1 [29.9 kB] Get: 212 http://deb.debian.org/debian buster/main amd64 libjansi-native-java all 1.8-1 [26.0 kB] Get: 213 http://deb.debian.org/debian buster/main amd64 libjansi-java all 1.17.1-1 [63.8 kB] Get: 214 http://deb.debian.org/debian buster/main amd64 libjline2-java all 2.14.6-3 [151 kB] Get: 215 http://deb.debian.org/debian buster/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 216 http://deb.debian.org/debian buster/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 217 http://deb.debian.org/debian buster/main amd64 libjsp-api-java all 2.3.4-2+deb10u1 [53.7 kB] Get: 218 http://deb.debian.org/debian buster/main amd64 libel-api-java all 3.0.0-2+deb10u1 [64.9 kB] Get: 219 http://deb.debian.org/debian buster/main amd64 libwebsocket-api-java all 1.1-1+deb10u1 [40.0 kB] Get: 220 http://deb.debian.org/debian buster/main amd64 libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 221 http://deb.debian.org/debian buster/main amd64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 222 http://deb.debian.org/debian buster/main amd64 libxstream-java all 1.4.11.1-1+deb10u2 [539 kB] Get: 223 http://deb.debian.org/debian buster/main amd64 groovy all 2.4.16-2 [12.9 MB] Get: 224 http://deb.debian.org/debian buster/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 225 http://deb.debian.org/debian buster/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 226 http://deb.debian.org/debian buster/main amd64 libcommons-compress-java all 1.18-2+deb10u1 [531 kB] Get: 227 http://deb.debian.org/debian buster/main amd64 libcommons-io-java all 2.6-2 [213 kB] Get: 228 http://deb.debian.org/debian buster/main amd64 libcommons-lang-java all 2.6-8 [273 kB] Get: 229 http://deb.debian.org/debian buster/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 230 http://deb.debian.org/debian buster/main amd64 libguava-java all 19.0-1 [2028 kB] Get: 231 http://deb.debian.org/debian buster/main amd64 libcommons-codec-java all 1.11-1 [271 kB] Get: 232 http://deb.debian.org/debian buster/main amd64 libhttpcore-java all 4.4.11-1 [625 kB] Get: 233 http://deb.debian.org/debian buster/main amd64 libhttpclient-java all 4.5.7-1+deb10u1 [721 kB] Get: 234 http://deb.debian.org/debian buster/main amd64 libjarjar-java all 1.4+svn142-10 [192 kB] Get: 235 http://deb.debian.org/debian buster/main amd64 libjcip-annotations-java all 20060626-5 [12.7 kB] Get: 236 http://deb.debian.org/debian buster/main amd64 libjna-jni amd64 4.5.2-1 [54.2 kB] Get: 237 http://deb.debian.org/debian buster/main amd64 libjna-java all 4.5.2-1 [195 kB] Get: 238 http://deb.debian.org/debian buster/main amd64 libjzlib-java all 1.1.3-2 [80.0 kB] Get: 239 http://deb.debian.org/debian buster/main amd64 libjsch-java all 0.1.55-1 [298 kB] Get: 240 http://deb.debian.org/debian buster/main amd64 libminlog-java all 1.3.0-1 [7618 B] Get: 241 http://deb.debian.org/debian buster/main amd64 libobjenesis-java all 3.0.1-2 [52.5 kB] Get: 242 http://deb.debian.org/debian buster/main amd64 libreflectasm-java all 1.05-4 [17.6 kB] Get: 243 http://deb.debian.org/debian buster/main amd64 libkryo-java all 2.20-6 [151 kB] Get: 244 http://deb.debian.org/debian buster/main amd64 liblogback-java all 1:1.2.3-5 [762 kB] Get: 245 http://deb.debian.org/debian buster/main amd64 libnative-platform-jni amd64 0.14-5 [13.0 kB] Get: 246 http://deb.debian.org/debian buster/main amd64 libnative-platform-java all 0.14-5 [71.0 kB] Get: 247 http://deb.debian.org/debian buster/main amd64 libxml-commons-external-java all 1.4.01-3 [240 kB] Get: 248 http://deb.debian.org/debian buster/main amd64 libxml-commons-resolver1.1-java all 1.2-9 [91.6 kB] Get: 249 http://deb.debian.org/debian buster/main amd64 libxerces2-java all 2.12.0-1 [1440 kB] Get: 250 http://deb.debian.org/debian buster/main amd64 libnekohtml-java all 1.9.22-1 [120 kB] Get: 251 http://deb.debian.org/debian buster/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 252 http://deb.debian.org/debian buster/main amd64 libgradle-core-java all 4.4.1-6 [4242 kB] Get: 253 http://deb.debian.org/debian buster/main amd64 libbcprov-java all 1.60-1 [3258 kB] Get: 254 http://deb.debian.org/debian buster/main amd64 libbcpg-java all 1.60-1 [301 kB] Get: 255 http://deb.debian.org/debian buster/main amd64 libbsh-java all 2.0b4-19 [282 kB] Get: 256 http://deb.debian.org/debian buster/main amd64 libdd-plist-java all 1.20-1 [72.5 kB] Get: 257 http://deb.debian.org/debian buster/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 258 http://deb.debian.org/debian buster/main amd64 libdom4j-java all 2.1.1-2 [310 kB] Get: 259 http://deb.debian.org/debian buster/main amd64 libbcel-java all 6.2-1 [611 kB] Get: 260 http://deb.debian.org/debian buster/main amd64 libjformatstring-java all 0.10~20131207-2 [33.8 kB] Get: 261 http://deb.debian.org/debian buster/main amd64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB] Get: 262 http://deb.debian.org/debian buster/main amd64 libgoogle-gson-java all 2.8.5-3 [225 kB] Get: 263 http://deb.debian.org/debian buster/main amd64 libaopalliance-java all 20070526-6 [9048 B] Get: 264 http://deb.debian.org/debian buster/main amd64 libguice-java all 4.2.1-1 [962 kB] Get: 265 http://deb.debian.org/debian buster/main amd64 libjatl-java all 0.2.3-1 [28.1 kB] Get: 266 http://deb.debian.org/debian buster/main amd64 libjcifs-java all 1.3.19-2 [394 kB] Get: 267 http://deb.debian.org/debian buster/main amd64 libjavaewah-java all 0.7.9-1 [120 kB] Get: 268 http://deb.debian.org/debian buster/main amd64 libjgit-java all 3.7.1-6 [1885 kB] Get: 269 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get: 270 http://deb.debian.org/debian buster/main amd64 libplexus-utils2-java all 3.1.1-1 [249 kB] Get: 271 http://deb.debian.org/debian buster/main amd64 libwagon-provider-api-java all 3.3.1-2 [50.1 kB] Get: 272 http://deb.debian.org/debian buster/main amd64 libmaven-resolver-java all 1.3.1-1 [549 kB] Get: 273 http://deb.debian.org/debian buster/main amd64 libcommons-lang3-java all 3.8-2 [478 kB] Get: 274 http://deb.debian.org/debian buster/main amd64 libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.6 kB] Get: 275 http://deb.debian.org/debian buster/main amd64 libmaven-parent-java all 31-2 [5100 B] Get: 276 http://deb.debian.org/debian buster/main amd64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 277 http://deb.debian.org/debian buster/main amd64 libplexus-cipher-java all 1.7-3 [15.0 kB] Get: 278 http://deb.debian.org/debian buster/main amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 279 http://deb.debian.org/debian buster/main amd64 libplexus-component-annotations-java all 1.7.1-7 [7536 B] Get: 280 http://deb.debian.org/debian buster/main amd64 libplexus-interpolation-java all 1.25-1 [76.8 kB] Get: 281 http://deb.debian.org/debian buster/main amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 282 http://deb.debian.org/debian buster/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 283 http://deb.debian.org/debian buster/main amd64 libcdi-api-java all 1.2-2 [54.5 kB] Get: 284 http://deb.debian.org/debian buster/main amd64 libsisu-inject-java all 0.3.3-1 [347 kB] Get: 285 http://deb.debian.org/debian buster/main amd64 libsisu-plexus-java all 0.3.3-3 [182 kB] Get: 286 http://deb.debian.org/debian buster/main amd64 libmaven3-core-java all 3.6.0-1 [1465 kB] Get: 287 http://deb.debian.org/debian buster/main amd64 libplexus-container-default-java all 1.7.1-7 [194 kB] Get: 288 http://deb.debian.org/debian buster/main amd64 libplexus-container-default1.5-java all 1.7.1-7 [4336 B] Get: 289 http://deb.debian.org/debian buster/main amd64 libpolyglot-maven-java all 0.8~tobrien+git20120905-9 [74.7 kB] Get: 290 http://deb.debian.org/debian buster/main amd64 librhino-java all 1.7.7.1-1 [1160 kB] Get: 291 http://deb.debian.org/debian buster/main amd64 libsimple-http-java all 4.1.21-1 [205 kB] Get: 292 http://deb.debian.org/debian buster/main amd64 libwagon-file-java all 3.3.1-2 [10.7 kB] Get: 293 http://deb.debian.org/debian buster/main amd64 libjsoup-java all 1.10.2-2 [350 kB] Get: 294 http://deb.debian.org/debian buster/main amd64 libwagon-http-java all 3.3.1-2 [50.5 kB] Get: 295 http://deb.debian.org/debian buster/main amd64 libjcommander-java all 1.71-3 [72.7 kB] Get: 296 http://deb.debian.org/debian buster/main amd64 testng all 6.9.12-4 [795 kB] Get: 297 http://deb.debian.org/debian buster/main amd64 libgradle-plugins-java all 4.4.1-6 [5162 kB] Get: 298 http://deb.debian.org/debian buster/main amd64 gradle all 4.4.1-6 [400 kB] Get: 299 http://deb.debian.org/debian buster/main amd64 maven-repo-helper all 1.9.3 [142 kB] Get: 300 http://deb.debian.org/debian buster/main amd64 gradle-debian-helper all 2.0.2 [25.2 kB] Get: 301 http://deb.debian.org/debian buster/main amd64 javahelper all 0.72.9 [96.4 kB] Get: 302 http://deb.debian.org/debian buster/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 303 http://deb.debian.org/debian buster/main amd64 libargs4j-java all 2.33-1 [139 kB] Get: 304 http://deb.debian.org/debian buster/main amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 305 http://deb.debian.org/debian buster/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 306 http://deb.debian.org/debian buster/main amd64 libplexus-io-java all 3.1.1-1 [64.6 kB] Get: 307 http://deb.debian.org/debian buster/main amd64 libsnappy1v5 amd64 1.1.7-1 [17.0 kB] Get: 308 http://deb.debian.org/debian buster/main amd64 libsnappy-jni amd64 1.1.7.2-1 [7148 B] Get: 309 http://deb.debian.org/debian buster/main amd64 libsnappy-java all 1.1.7.2-1 [73.7 kB] Get: 310 http://deb.debian.org/debian buster/main amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 311 http://deb.debian.org/debian buster/main amd64 libsisu-guice-java all 4.2.0-1 [785 kB] Get: 312 http://deb.debian.org/debian buster/main amd64 libsisu-ioc-java all 2.3.0-11 [492 kB] Get: 313 http://deb.debian.org/debian buster/main amd64 libistack-commons-java all 3.0.6-3 [144 kB] Get: 314 http://deb.debian.org/debian buster/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-8 [163 kB] Get: 315 http://deb.debian.org/debian buster/main amd64 libcommons-jexl2-java all 2.1.1-4 [257 kB] Get: 316 http://deb.debian.org/debian buster/main amd64 libdtd-parser-java all 1.2~svn20110404-1 [62.5 kB] Get: 317 http://deb.debian.org/debian buster/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 318 http://deb.debian.org/debian buster/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 319 http://deb.debian.org/debian buster/main amd64 libstreambuffer-java all 1.5.4-1 [71.8 kB] Get: 320 http://deb.debian.org/debian buster/main amd64 librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get: 321 http://deb.debian.org/debian buster/main amd64 libxsom-java all 2.3.0.1-8 [396 kB] Get: 322 http://deb.debian.org/debian buster/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 323 http://deb.debian.org/debian buster/main amd64 librngom-java all 2.3.0.1-8 [288 kB] Get: 324 http://deb.debian.org/debian buster/main amd64 libtxw2-java all 2.3.0.1-8 [134 kB] Get: 325 http://deb.debian.org/debian buster/main amd64 libjaxb-java all 2.3.0.1-8 [1966 kB] Get: 326 http://deb.debian.org/debian buster/main amd64 libjimfs-java all 1.1-5 [191 kB] Get: 327 http://deb.debian.org/debian buster/main amd64 libngs-sdk2 amd64 2.9.3-1 [62.7 kB] Get: 328 http://deb.debian.org/debian buster/main amd64 libngs-sdk-dev amd64 2.9.3-1 [111 kB] Get: 329 http://deb.debian.org/debian buster/main amd64 libngs-java amd64 2.9.3-1 [79.9 kB] Get: 330 http://deb.debian.org/debian buster/main amd64 scala-library all 2.11.12-4 [9589 kB] 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Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.30-1) ... Setting up libsensors-config (1:3.5.0-3) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libngs-sdk2 (2.9.3-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libdd-plist-java (1.20-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libel-api-java (3.0.0-2+deb10u1) ... Setting up scala-library (2.11.12-4) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libplexus-component-annotations-java (1.7.1-7) ... Setting up libnpth0:amd64 (1.6-1) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-9) ... Setting up libfelix-gogo-runtime-java (0.16.2-1) ... Setting up libassuan0:amd64 (2.5.2-1) ... 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Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up libnet-http-perl (6.18-1) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up default-jdk-doc (2:1.11-71) ... Setting up libdevel-callchecker-perl (0.008-1) ... Setting up libcommons-lang-java (2.6-8) ... Setting up libxcb-present0:amd64 (1.13.1-2) ... Setting up libcommons-jexl2-java (2.1.1-4) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libmaven-resolver-java (1.3.1-1) ... Setting up libbcel-java (6.2-1) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up libguava-java (19.0-1) ... Setting up libxcb-sync1:amd64 (1.13.1-2) ... Setting up testng (6.9.12-4) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libstreambuffer-java (1.5.4-1) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libcommons-lang3-java (3.8-2) ... Setting up autoconf (2.69-11) ... Setting up libxcb-dri2-0:amd64 (1.13.1-2) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libfelix-resolver-java (1.14.0-1) ... Setting up librngom-java (2.3.0.1-8) ... Setting up libdrm2:amd64 (2.4.97-1) ... Setting up dwz (0.12-3) ... Setting up libjansi-native-java (1.8-1) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.12-1+deb10u1) ... 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Setting up gettext (0.19.8.1-9) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up gpg-agent (2.2.12-1+deb10u1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.18-2+deb10u1) ... Setting up libhttp-cookies-perl (6.04-1) ... Setting up libcommons-io-java (2.6-2) ... Setting up libdrm-radeon1:amd64 (2.4.97-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b1) ... Setting up gpgsm (2.2.12-1+deb10u1) ... Setting up libdrm-intel1:amd64 (2.4.97-1) ... Setting up libgl1-mesa-dri:amd64 (18.3.6-2+deb10u1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libsisu-ioc-java (2.3.0-11) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libguice-java (4.2.1-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... 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Setting up libsisu-inject-java (0.3.3-1) ... Setting up libsisu-plexus-java (0.3.3-3) ... Setting up gnupg (2.2.12-1+deb10u1) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up libglx-mesa0:amd64 (18.3.6-2+deb10u1) ... Setting up libglx0:amd64 (1.1.0-1) ... Setting up libmaven3-core-java (3.6.0-1) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libgl1:amd64 (1.1.0-1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up default-jre-headless (2:1.11-71) ... Setting up libwww-perl (6.36-2) ... Setting up maven-repo-helper (1.9.3) ... Setting up antlr (2.7.7+dfsg-9.2) ... Setting up dh-autoreconf (19) ... Setting up devscripts (2.19.5+deb10u1) ... Setting up ivy (2.4.0-5) ... Setting up ant (1.10.5-2) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up junit4 (4.12-8) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up groovy (2.4.16-2) ... 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 debhelper (12.1.1) ... Setting up ant-optional (1.10.5-2) ... Setting up bnd (3.5.0-4) ... Setting up libgradle-core-java (4.4.1-6) ... Setting up libgradle-plugins-java (4.4.1-6) ... Setting up javahelper (0.72.9) ... Setting up gradle (4.4.1-6) ... Setting up libistack-commons-java (3.0.6-3) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-8) ... Setting up gradle-debian-helper (2.0.2) ... Setting up libtxw2-java (2.3.0.1-8) ... Setting up libjaxb-java (2.3.0.1-8) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Setting up openjdk-11-jre-headless:amd64 (11.0.11+9-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:amd64 (11.0.11+9-1~deb10u1) ... Setting up openjdk-11-jdk-headless:amd64 (11.0.11+9-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre (2:1.11-71) ... Setting up default-jdk-headless (2:1.11-71) ... Setting up openjdk-11-jdk:amd64 (11.0.11+9-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk (2:1.11-71) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/htsjdk-2.18.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 2.18.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_auto_clean -O--buildsystem=gradle 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/htsjdk-2.18.2\+dfsg/.gradle /build/htsjdk-2.18.2\+dfsg/buildSrc/.gradle .m2 dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper mh_clean -O--buildsystem=gradle dh_clean -O--buildsystem=gradle rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhtsjdk-java.substvars debian/libhtsjdk-java-doc.substvars debian/files rm -fr -- debian/libhtsjdk-java/ debian/tmp/ debian/libhtsjdk-java-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_update_autotools_config -O--buildsystem=gradle dh_autoreconf -O--buildsystem=gradle dh_auto_configure -O--buildsystem=gradle jh_linkjars -O--buildsystem=gradle debian/rules override_dh_auto_build make[1]: Entering directory '/build/htsjdk-2.18.2+dfsg' dh_auto_build -- jar javadoc 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=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=15 jar javadoc Initialized native services in: /build/htsjdk-2.18.2+dfsg/.gradle/native Using 15 worker leases. Creating new cache for fileHashes, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@64beebb7 Creating new cache for resourceHashesCache, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@64beebb7 Creating new cache for fileHashes, path /build/htsjdk-2.18.2+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@30b34287 WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access using Lookup on org.gradle.internal.reflect.JavaMethod (file:/usr/share/gradle/lib/gradle-base-services-4.4.1.jar) to class java.lang.ClassLoader WARNING: Please consider reporting this to the maintainers of org.gradle.internal.reflect.JavaMethod WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Starting Build Compiling initialization script '/build/htsjdk-2.18.2+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@47e51549 Compiling initialization script '/build/htsjdk-2.18.2+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/htsjdk-2.18.2+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/htsjdk-2.18.2+dfsg/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/htsjdk-2.18.2+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/htsjdk-2.18.2+dfsg/build.gradle'. Included projects: [root project 'htsjdk'] Keep-alive timer started Adding Debian repository to project 'htsjdk' Parallel execution is an incubating feature. Evaluating root project 'htsjdk' using build file '/build/htsjdk-2.18.2+dfsg/build.gradle'. Compiling build file '/build/htsjdk-2.18.2+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/htsjdk-2.18.2+dfsg/build.gradle' using BuildScriptTransformer. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/htsjdk-2.18.2+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:2.18.2 Adding Maven pom generation to project 'htsjdk' 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/htsjdk-2.18.2+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@1f70bce5 Selected primary task 'javadoc' from project : Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc'] Creating new cache for resourceHashesCache, path /build/htsjdk-2.18.2+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@30b34287 Creating new cache for taskHistory, path /build/htsjdk-2.18.2+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@17477bbb Creating new cache for outputFiles, path /build/htsjdk-2.18.2+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@5e2718b3 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.008 secs. Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@22e82193 Loading the Maven rules... Replacing org.apache.commons:commons-jexl:jar:2.1.1 -> org.apache.commons:commons-jexl:jar:debian Passing through org.apache.commons:commons-parent:jar:debian Passing through org.apache:apache:jar:debian Replacing commons-logging:commons-logging:jar:1.1.1 -> commons-logging:commons-logging:jar:debian Replacing org.xerial.snappy:snappy-java:jar:1.1.4 -> org.xerial.snappy:snappy-java:jar:debian Replacing org.apache.commons:commons-compress:jar:1.4.1 -> org.apache.commons:commons-compress:jar:debian Replacing org.tukaani:xz:jar:1.5 -> org.tukaani:xz:jar:debian Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 -> gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through javax.xml.bind:jaxb-api:jar:debian Passing through javax.xml.bind:jaxb-api-parent:jar:debian Passing through javax.activation:javax.activation-api:jar:debian javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies. Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian Up-to-date check for task ':compileJava' took 1.372 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. Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. :compileJava (Thread[Task worker for ':',5,main]) completed. Took 11.206 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/htsjdk-2.18.2+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 0.013 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/htsjdk-2.18.2+dfsg/build/debian/htsjdk.pom :debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.056 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 0.031 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':',5,main]) completed. Took 0.376 secs. :javadoc (Thread[Task worker for ':',5,main]) started. :javadoc Putting task artifact state for task ':javadoc' into context took 0.0 secs. Up-to-date check for task ':javadoc' took 0.129 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc''. Working directory: /build/htsjdk-2.18.2+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc @/build/htsjdk-2.18.2+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc'' /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/variant/bcf2/BCF2Codec.java:488: warning - @param argument "bufferedinput" is not a parameter name. /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/filter/IntervalFilter.java:53: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java:59: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/index/DynamicIndexCreator.java:171: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/cram/io/ITF8.java:17: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/cram/io/ITF8.java:31: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java:165: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java:166: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:75: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:453: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/readers/Positional.java:45: warning - invalid usage of tag > javadoc: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/Bin.java:106: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/Bin.java:106: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java:194: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:125: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:150: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/GenomicIndexUtil.java:57: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/QueryInterval.java:18: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:331: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMFileWriterImpl.java:35: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMLineParser.java:221: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:53: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:159: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:159: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:774: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordComparator.java:37: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:39: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:39: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:85: warning - invalid usage of tag < javadoc: warning - invalid usage of tag < javadoc: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java:77: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMSortOrderChecker.java:42: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:655: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:655: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:641: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:642: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:642: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:655: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:655: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:656: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:656: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:1125: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:1125: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMValidationError.java:84: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SAMValidationError.java:84: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:63: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:63: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:64: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:95: warning - invalid usage of tag > javadoc: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/FeatureCodecHeader.java:31: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/tribble/FeatureCodecHeader.java:71: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:143: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:143: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:151: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:151: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:161: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:161: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:170: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:170: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/BlockGunzipper.java:104: warning - Parameter "compressedBlock" is documented more than once. /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/CloserUtil.java:57: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/CloserUtil.java:57: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/CollectionUtil.java:108: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/CollectionUtil.java:108: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning - invalid usage of tag & /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:240: warning - invalid usage of tag {@link #uniqued()#getIntervals() /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:312: warning - invalid usage of tag {@link #uniqued(boolean)#getIntervals() /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:240: warning - invalid usage of tag {@link #uniqued()#getIntervals() /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:312: warning - invalid usage of tag {@link #uniqued(boolean)#getIntervals() /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:331: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java:65: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java:76: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java:65: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java:76: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalListReferenceSequenceMask.java:78: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalTree.java:213: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IntervalTree.java:310: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:118: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:118: warning - invalid usage of tag < /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:165: warning - invalid usage of tag > /build/htsjdk-2.18.2+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:172: warning - invalid usage of tag > 100 warnings :javadoc (Thread[Task worker for ':',5,main]) completed. Took 12.022 secs. BUILD SUCCESSFUL in 30s 4 actionable tasks: 4 executed make[1]: Leaving directory '/build/htsjdk-2.18.2+dfsg' jh_build -O--buildsystem=gradle rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/htsjdk-2.18.2+dfsg' # testng bug 895886: testng: jcommander classes not found dh_auto_build -- 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=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=15 test Initialized native services in: /build/htsjdk-2.18.2+dfsg/.gradle/native Using 15 worker leases. Creating new cache for fileHashes, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@64beebb7 Creating new cache for resourceHashesCache, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@64beebb7 Creating new cache for fileHashes, path /build/htsjdk-2.18.2+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@30b34287 WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access using Lookup on org.gradle.internal.reflect.JavaMethod (file:/usr/share/gradle/lib/gradle-base-services-4.4.1.jar) to class java.lang.ClassLoader WARNING: Please consider reporting this to the maintainers of org.gradle.internal.reflect.JavaMethod WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Starting Build Creating new cache for metadata-1.1/results, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@765ffb14 Settings evaluated using settings file '/build/htsjdk-2.18.2+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/htsjdk-2.18.2+dfsg/build.gradle'. Included projects: [root project 'htsjdk'] Keep-alive timer started Adding Debian repository to project 'htsjdk' Parallel execution is an incubating feature. Evaluating root project 'htsjdk' using build file '/build/htsjdk-2.18.2+dfsg/build.gradle'. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/htsjdk-2.18.2+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:2.18.2 Adding Maven pom generation to project 'htsjdk' 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/htsjdk-2.18.2+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@5ac0bf84 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':findScalaAndJavaTypes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] Creating new cache for resourceHashesCache, path /build/htsjdk-2.18.2+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@30b34287 Creating new cache for taskHistory, path /build/htsjdk-2.18.2+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@1397b141 Creating new cache for outputFiles, path /build/htsjdk-2.18.2+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@34f60be9 :compileJava (Thread[Task worker for ':' Thread 3,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.005 secs. Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.18.2+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@60880349 Loading the Maven rules... Replacing org.apache.commons:commons-jexl:jar:2.1.1 -> org.apache.commons:commons-jexl:jar:debian Passing through org.apache.commons:commons-parent:jar:debian Passing through org.apache:apache:jar:debian Replacing commons-logging:commons-logging:jar:1.1.1 -> commons-logging:commons-logging:jar:debian Replacing org.xerial.snappy:snappy-java:jar:1.1.4 -> org.xerial.snappy:snappy-java:jar:debian Replacing org.apache.commons:commons-compress:jar:1.4.1 -> org.apache.commons:commons-compress:jar:debian Replacing org.tukaani:xz:jar:1.5 -> org.tukaani:xz:jar:debian Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 -> gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through javax.xml.bind:jaxb-api:jar:debian Passing through javax.xml.bind:jaxb-api-parent:jar:debian Passing through javax.activation:javax.activation-api:jar:debian javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies. Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian Skipping task ':compileJava' as it is up-to-date (took 1.037 secs). :compileJava UP-TO-DATE :compileJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 1.095 secs. :processResources (Thread[Task worker for ':' Thread 3,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/htsjdk-2.18.2+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 3,5,main]) completed. Took 0.007 secs. :classes (Thread[Task worker for ':' Thread 3,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.001 secs. :findScalaAndJavaTypes (Thread[Task worker for ':' Thread 3,5,main]) started. :findScalaAndJavaTypes Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.008 secs. Up-to-date check for task ':findScalaAndJavaTypes' took 0.0 secs. It is not up-to-date because: Task has not declared any outputs. Starting process 'command './scripts/checkScalaAndJavaFiles.sh''. Working directory: /build/htsjdk-2.18.2+dfsg Command: ./scripts/checkScalaAndJavaFiles.sh Successfully started process 'command './scripts/checkScalaAndJavaFiles.sh'' :findScalaAndJavaTypes (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.039 secs. :compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Passing through org.scala-lang:scala-library:jar:2.11.x Passing through org.testng:testng:jar:debian Passing through com.google.jimfs:jimfs:jar:debian Passing through com.google.jimfs:jimfs-parent:jar:debian Passing through com.google.guava:guava:jar:debian Passing through com.google.guava:guava-parent:jar:debian Passing through com.sun.xml.bind:jaxb-impl:jar:debian com.sun.xml.bind:jaxb-impl:debian is relocated to org.glassfish.jaxb:jaxb-runtime:debian. Please update your dependencies. Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Passing through org.glassfish.jaxb:jaxb-runtime:jar:debian Passing through com.sun.xml.bind.mvn:jaxb-runtime-parent:jar:debian Passing through com.sun.xml.bind.mvn:jaxb-parent:jar:debian Passing through com.sun.xml.bind:jaxb-bom-ext:jar:debian Passing through org.glassfish.jaxb:jaxb-bom:jar:debian Passing through org.glassfish.jaxb:jaxb-core:jar:debian Passing through org.jvnet.staxex:stax-ex:jar:debian Passing through com.sun.xml.fastinfoset:FastInfoset:jar:debian Passing through com.sun.xml.fastinfoset:fastinfoset-project:jar:debian Passing through org.glassfish.jaxb:txw2:jar:debian Passing through com.sun.xml.bind.mvn:jaxb-txw-parent:jar:debian Passing through com.sun.istack:istack-commons-runtime:jar:debian Passing through com.sun.istack:istack-commons:jar:debian Up-to-date check for task ':compileTestJava' took 2.872 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. Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. :compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 12.032 secs. :processTestResources (Thread[Task worker for ':' Thread 3,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. Up-to-date check for task ':processTestResources' took 0.427 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.935 secs. :testClasses (Thread[Task worker for ':' Thread 3,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. :test (Thread[Task worker for ':' Thread 3,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.001 secs. Up-to-date check for task ':test' took 0.581 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 1'. Working directory: /build/htsjdk-2.18.2+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath15538009979374668143txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -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 suite > Gradle test > htsjdk.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters[0](ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf, variantFilter01.js, 61) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters[1](ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf, variantFilter02.js, 38) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR java.lang.RuntimeException: oops at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_1$0(VariantContextWriterBuilderUnitTest.java:515) at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:540) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_2 STANDARD_ERROR java.lang.RuntimeException: oops at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_2$1(VariantContextWriterBuilderUnitTest.java:521) at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:540) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[5](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstSequence runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 12ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 12ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstOfChr1 runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 11ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 11ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testOpenFile runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testOpenFile runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testOpenFile runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testOpenFile runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testOpenFile runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadPastEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadPastEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadPastEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadPastEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReadPastEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[0](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 12ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 12ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.18.2+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 Time so far: 0 Linear scan total time: 0 queryUnmapped time: 0 Number of unmapped reads:279 Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testRandomQueries STANDARD_OUT Testing query chr11_random:7211102-7392752 ... Testing query chrX_random:2969904-3087323 ... Testing query chr5:9255377-9796767 ... Testing query chr16_random:9067406-9976989 ... Testing query chr6:2164417-9572211 ... Testing query chr8_random:5688357-6576007 ... Testing query chr4_random:4241203-6327831 ... Testing query chr2_random:411082-4462819 ... Testing query chr13_random:145947-4307287 ... Testing query chr15_random:3298214-6356603 ... Testing query chr21:472385-8291032 ... Testing query chr2:4177649-9835176 ... Testing query chr22_random:1490587-8781106 ... Testing query chr14:2167927-6299701 ... Testing query chr7:4700515-5593851 ... Testing query chr22:5016764-7470151 ... Testing query chr22_random:7524398-8627117 ... Testing query chr8:3764754-6977071 ... Testing query chr1_random:1725504-3204042 ... Testing query chr21:2025794-4625889 ... Testing query chr14:1426554-6327490 ... Testing query chrX_random:1992622-9650667 ... Testing query chr4:2669418-7183639 ... Testing query chr10:2967472-3641376 ... Testing query chr10_random:3273594-3427480 ... Testing query chr19_random:4582311-5090524 ... Testing query chr9_random:7218100-8812477 ... Testing query chrX:257134-4337775 ... Testing query chr9_random:713930-3536575 ... Testing query chrX:2523687-4774316 ... Testing query chr21:513221-829881 ... Testing query chr14:6924617-9048044 ... Testing query chr6:4945372-7173211 ... Testing query chr6_random:7501139-9077397 ... Testing query chr19:2934833-5141776 ... Testing query chr9:863231-7545153 ... Testing query chr2:4308042-6742767 ... Testing query chr12:293858-324418 ... Testing query chr6_random:3308674-4557713 ... Testing query chr2_random:6755655-7330097 ... Testing query chr9_random:1234763-6135261 ... Testing query chr17:7042296-7582149 ... Testing query chr18:6749235-8476299 ... Testing query chr22:1198031-6226173 ... Testing query chr22:9446557-9458998 ... Testing query chr15:473293-1136600 ... Testing query chr13:8001267-8034858 ... Testing query chr7_random:12779-8349897 ... Testing query chrX:6476995-9046675 ... Testing query chr22:455684-9901546 ... Testing query chr20:2540726-9004820 ... Testing query chr1:5290124-7772462 ... Testing query chr2_random:4562177-7629291 ... Testing query chr4:5992612-7734912 ... Testing query chr5:1027938-6017856 ... Testing query chr5:3945452-4558863 ... Testing query chr7_random:1434224-8766265 ... Testing query chr13_random:2806926-8471270 ... Testing query chr21:5896937-6230120 ... Testing query chr10_random:2325170-6773979 ... Testing query chr4:768115-9242973 ... Testing query chr9:204376-1523700 ... Testing query chr15:6918456-9920136 ... Testing query chr8:195836-2912231 ... Testing query chr4_random:8569316-9601747 ... Testing query chr14:7539676-8479802 ... Testing query chr17_random:6016149-9676582 ... Testing query chr3:2401075-5926977 ... Testing query chr7:6825835-8610049 ... Testing query chr4:8589977-9226779 ... Testing query chr22_random:881883-9900377 ... Testing query chr19:2282185-2974234 ... Testing query chr2_random:530137-7997036 ... Testing query chr11_random:1524078-8571487 ... Testing query chrX:3561537-3812547 ... Testing query chr7_random:5345040-8399303 ... Testing query chr22:1586323-6546266 ... Testing query chr13:356087-8263221 ... Testing query chr9:6308509-8761532 ... Testing query chr8:3702301-5705153 ... Testing query chr13_random:1656308-4034137 ... Testing query chr3:4684965-7862719 ... Testing query chr19_random:5585589-7312648 ... Testing query chr18:8395777-9280098 ... Testing query chr6_random:738052-6252176 ... Testing query chr5_random:6874632-8838246 ... Testing query chr7_random:4576401-9601286 ... Testing query chr6_random:1277796-9240909 ... Testing query chr22:2128956-7451924 ... Testing query chr9:5866041-7641214 ... Testing query chr6_random:2900603-6324004 ... Testing query chr5:3340073-3878152 ... Testing query chr7_random:6065731-8117472 ... Testing query chr22:6980282-9420307 ... Testing query chr3_random:7896234-9902729 ... Testing query chr4:5226514-9465698 ... Testing query chr11_random:2710966-7297413 ... Testing query chr4:5814391-6477874 ... Testing query chr17:3411447-7945931 ... Testing query chr19_random:1563833-8954930 ... Testing query chr4:2666458-5577064 ... Testing query chrM:2495375-2785830 ... Testing query chr22_random:2741863-7160257 ... Testing query chr20:3030962-4839827 ... Testing query chrX_random:1999206-3290596 ... Testing query chr1_random:7581574-9491516 ... Testing query chr5:8544911-9905206 ... Testing query chr17_random:5247411-8818598 ... Testing query chr18:2206748-2542618 ... Testing query chr6:5560095-6841213 ... Testing query chrX:5584638-8069137 ... Testing query chr2_random:893746-4019636 ... Testing query chr4_random:7220619-8625179 ... Testing query chr17_random:7487783-7745825 ... Testing query chr13_random:140415-4339843 ... Testing query chr22:3465880-9918684 ... Testing query chr16_random:2228554-5218116 ... Testing query chr6:3812651-9020894 ... Testing query chr19:4897072-8152584 ... Testing query chr15_random:2493596-3303830 ... Testing query chr17:7330256-9331563 ... Testing query chr7_random:2372609-7660988 ... Testing query chr21:16468-1408282 ... Testing query chrM:946718-7866529 ... Testing query chr6:636772-5261193 ... Testing query chr4:4081985-5160778 ... Testing query chr4_random:3992937-8001782 ... Testing query chr3_random:4269902-7314671 ... Testing query chr8_random:5398008-9100867 ... Testing query chr11_random:4717946-5886722 ... Testing query chr14:3324888-9762784 ... Testing query chr3_random:447076-2904415 ... Testing query chr18_random:4656587-8830031 ... Testing query chr15_random:2677992-8013872 ... Testing query chr8:8741342-9773821 ... Testing query chrM:638643-3884353 ... Testing query chr6:1102480-2996219 ... Testing query chr13:27071-9001996 ... Testing query chr8_random:133575-8239847 ... Testing query chr4:5119076-7497751 ... Testing query chr6_random:8932876-9157638 ... Testing query chr2:8039126-9556281 ... Testing query chr18:2759483-4424919 ... Testing query chr7_random:2162721-7693312 ... Testing query chr17_random:3212242-7079443 ... Testing query chrX_random:9441944-9675063 ... Testing query chrX:1483850-9503277 ... Testing query chrY:708618-2939362 ... Testing query chr1:1457571-8460228 ... Testing query chrM:5153488-6390263 ... Testing query chr8:2469944-5489240 ... Testing query chr4:2270560-9937550 ... Testing query chr10:1924284-4282155 ... Testing query chrY:5044757-9726553 ... Testing query chr21_random:8138434-8862076 ... Testing query chr17_random:8064209-8585636 ... Testing query chr22:7325448-9656485 ... Testing query chr11:6475178-6915306 ... Testing query chrM:1569370-6357214 ... Testing query chr8_random:1676954-7528262 ... Testing query chr8:3436473-9972209 ... Testing query chr19_random:8309162-8766514 ... Testing query chr7_random:6416981-6735864 ... Testing query chr19:3484685-3801122 ... Testing query chr1:1868925-6151268 ... Testing query chr1:536419-4044558 ... Testing query chr1:2522877-4924643 ... Testing query chr11_random:676633-9128847 ... Testing query chr6_random:3598124-6981657 ... Testing query chr5_random:7166103-8219161 ... Testing query chr19:1684800-5872548 ... Testing query chr1_random:3315026-8441262 ... Testing query chr18_random:2290355-8594736 ... Testing query chr20:3121858-8750525 ... Testing query chr5:1854779-7785465 ... Testing query chr3:2844488-8229201 ... Testing query chr9:98994-6937193 ... Testing query chr7_random:566405-4329525 ... Testing query chrM:3349123-8858299 ... Testing query chr18_random:2476805-3333909 ... Testing query chr5_random:2947230-5023103 ... Testing query chrY:858711-3764404 ... Testing query chrM:3202756-4087290 ... Testing query chr3:2241212-3744434 ... Testing query chr2:294299-2791063 ... Testing query chr16:5636813-7725712 ... Testing query chrY:190457-4183568 ... Testing query chr15_random:1757556-6243468 ... Testing query chr21_random:2404640-9698959 ... Testing query chrY:2899895-8525822 ... Testing query chr14:5316023-9325638 ... Testing query chr5_random:3836137-6496666 ... Testing query chr10_random:1992029-2390509 ... Testing query chr15:2008393-5397033 ... Testing query chr6:3033491-5689013 ... Testing query chr13:4802709-6651494 ... Testing query chr11_random:1126435-2590416 ... Testing query chr14:674415-1741256 ... Testing query chr2:5945864-7917088 ... Testing query chr4:2984861-4376484 ... Testing query chr1_random:5661261-9348854 ... Testing query chr18:2892586-9538492 ... Testing query chr19_random:2666788-6214501 ... Testing query chr5_random:2892340-8892790 ... Testing query chr3:8321138-9156829 ... Testing query chr20:1010051-2675065 ... Testing query chr12:2016127-9734230 ... Testing query chr17:6565364-9842724 ... Testing query chr2_random:1534009-9935421 ... Testing query chr22_random:1798866-3566302 ... Testing query chr9_random:2863862-4098636 ... Testing query chr7_random:6695702-7166373 ... Testing query chr19_random:7774915-8904502 ... Testing query chr4_random:1354793-3060860 ... Testing query chr16_random:680783-7967813 ... Testing query chr22_random:1679274-1962853 ... Testing query chr5:1405068-3861785 ... Testing query chr8_random:6642950-9011653 ... Testing query chr16:1873173-7921837 ... Testing query chr7_random:2750681-9520458 ... Testing query chr16_random:885218-3713066 ... Testing query chr10_random:4952036-9328892 ... Testing query chr1_random:1556041-9207413 ... Testing query chrX:3509058-4668683 ... Testing query chr22_random:5775297-9086853 ... Testing query chr1:1171026-6903635 ... Testing query chr17_random:706069-7256916 ... Testing query chr1:7825983-8559769 ... Testing query chr7_random:7709758-9250068 ... Testing query chr6:4475592-7218806 ... Testing query chr5_random:7263397-7305993 ... Testing query chr16_random:5376132-9863064 ... Testing query chr5:4383593-4921390 ... Testing query chr12:5541381-6329888 ... Testing query chr7_random:297473-6191920 ... Testing query chr7_random:5797186-6007720 ... Testing query chr14:6288978-7147625 ... Testing query chrY:3280527-6071425 ... Testing query chr2_random:341241-9849655 ... Testing query chr18_random:2756400-5124352 ... Testing query chr18_random:3245587-6421468 ... Testing query chr7_random:1108885-7011416 ... Testing query chr19:55506-8032351 ... Testing query chr9_random:507759-1925801 ... Testing query chr21_random:5641470-6291456 ... Testing query chr16_random:2647045-6473932 ... Testing query chr3:8883638-9872842 ... Testing query chr17:2328196-3652679 ... Testing query chr22_random:2297511-5498425 ... Testing query chrX_random:3773240-4693054 ... Testing query chr13:1575245-9070298 ... Testing query chr8_random:5301468-7005527 ... Testing query chr4:6535020-9656212 ... Testing query chr18:5782944-8199590 ... Testing query chr5_random:1102579-7463246 ... Testing query chr5:2779653-6802521 ... Testing query chr10:99615-2172940 ... Testing query chr7:2762506-2870870 ... Testing query chr15_random:981768-8907527 ... Testing query chr16:436530-5189740 ... Testing query chr15:9551545-9569163 ... Testing query chr17_random:432471-8074112 ... Testing query chr8:4845184-5039976 ... Testing query chr7:3531770-6086719 ... Testing query chr17:2693356-7185572 ... Testing query chr6:6650063-9646384 ... Testing query chrY:121317-4718433 ... Testing query chr1_random:1003027-1831870 ... Testing query chr21:8788645-9420609 ... Testing query chr13_random:987064-4341370 ... Testing query chr13_random:842466-5111480 ... Testing query chrM:7654248-8310027 ... Testing query chr2:1532378-3980671 ... Testing query chr16_random:2308350-8259941 ... Testing query chr18_random:7619793-8200073 ... Testing query chr16:908998-6962421 ... Testing query chr1_random:4760134-7897692 ... Testing query chr4_random:351969-2613223 ... Testing query chr16:3482498-9633584 ... Testing query chr22:7907949-9933800 ... Testing query chr15:5854248-7275283 ... Testing query chr14:3664791-8748133 ... Testing query chrX:896137-9572469 ... Testing query chrX:1865390-3062428 ... Testing query chr6:595893-8247348 ... Testing query chr9_random:1425130-4402172 ... Testing query chr7_random:463001-1378501 ... Testing query chr10:5465621-8140677 ... Testing query chr22:4007755-6030817 ... Testing query chr19:2152758-4285738 ... Testing query chrX_random:6197638-7278734 ... Testing query chr8_random:2506286-3132074 ... Testing query chr3:5088917-6346018 ... Testing query chr21_random:709245-2447062 ... Testing query chr7_random:2297450-2733491 ... Testing query chrX_random:75616-6715390 ... Testing query chr14:1451557-9217186 ... Testing query chr22:4216648-4273083 ... Testing query chr22_random:2900019-9495009 ... Testing query chr4:6062237-9450155 ... Testing query chr3_random:2205998-8038523 ... Testing query chr19:4006735-8497976 ... Testing query chrM:4367909-8743630 ... Testing query chr1:3235237-5886681 ... Testing query chr18:2455071-8918070 ... Testing query chr3:715763-7415212 ... Testing query chr2_random:3698070-6718252 ... Testing query chr10:4035923-8780337 ... Testing query chr1_random:4369783-9221375 ... Testing query chr11:3488452-9565235 ... Testing query chrX:3524615-7110878 ... Testing query chr19_random:7779323-8424172 ... Testing query chr15_random:910898-4876910 ... Testing query chr15_random:1015024-3678499 ... Testing query chr9:3393986-9417756 ... Testing query chr18_random:857279-9200045 ... Testing query chr18:1396324-2772435 ... Testing query chr12:5614369-9031405 ... Testing query chr5:3780359-4070909 ... Testing query chr17:4508678-5389778 ... Testing query chr21_random:6972726-7854603 ... Testing query chr12:3182535-8039198 ... Testing query chr10:3951103-7166395 ... Testing query chr5_random:6532707-9837900 ... Testing query chr13_random:7985015-9743703 ... Testing query chr20:6134113-9969678 ... Testing query chrY:1542908-4899134 ... Testing query chr19_random:324180-7673324 ... Testing query chr22_random:4465119-8807791 ... Testing query chr14:4342424-6275354 ... Testing query chr21:3393386-7099240 ... Testing query chr3_random:2130566-2642809 ... Testing query chr1_random:2534189-6047752 ... Testing query chrM:3319509-8627744 ... Testing query chr4_random:7027413-8546790 ... Testing query chr18:5213087-7307044 ... Testing query chrX_random:5138706-7179617 ... Testing query chr21:1746459-3369825 ... Testing query chr17_random:4364489-9952653 ... Testing query chr21_random:2852383-6343308 ... Testing query chr16:1718072-7027200 ... Testing query chr7:2836942-5941970 ... Testing query chr21_random:6013526-6739121 ... Testing query chr6:2041720-8080188 ... Testing query chr20:5614189-8320637 ... Testing query chr18:7510033-9259036 ... Testing query chr7_random:5464431-5858425 ... Testing query chrX_random:2642097-9170108 ... Testing query chr21_random:2372613-7228145 ... Testing query chr7:7643929-8629915 ... Testing query chrM:1496669-3662785 ... Testing query chrM:5816559-7988640 ... Testing query chr4_random:3216837-5344216 ... Testing query chr8_random:7939352-9193364 ... Testing query chr11_random:4477474-7119222 ... Testing query chr22:1795085-7018163 ... Testing query chr2:489045-5507534 ... Testing query chr20:228222-2645827 ... Testing query chr2_random:6696262-7193942 ... Testing query chrX:624678-2022130 ... Testing query chr11_random:7420609-7476969 ... Testing query chr7_random:35741-8947140 ... Testing query chr9:2887670-8574309 ... Testing query chr9_random:5022666-8213630 ... Testing query chr16_random:2811399-8122673 ... Testing query chr19:2563169-2938289 ... Testing query chr15_random:3165794-8354108 ... Testing query chr1_random:4114915-9235471 ... Testing query chr10_random:983161-9480146 ... Testing query chr2:5984445-9861542 ... Testing query chr21:2955353-3709382 ... Testing query chr18:4220403-7713605 ... Testing query chr9:5837376-6191557 ... Testing query chr18:3760903-6211242 ... Testing query chr4:2604919-6869284 ... Testing query chr14:8243966-8657979 ... Testing query chrX:8572226-9566286 ... Testing query chr15_random:1776922-9379642 ... Testing query chr11:6484864-9835462 ... Testing query chr13_random:2265643-8434104 ... Testing query chr18_random:2936640-6667223 ... Testing query chr21_random:6212251-8673018 ... Testing query chr1_random:1062720-2585432 ... Testing query chr21_random:5965453-7655829 ... Testing query chrX_random:2147524-2773583 ... Testing query chr13_random:368974-2821747 ... Testing query chr5_random:1943780-5626512 ... Testing query chr20:30472-8431478 ... Testing query chr10_random:1574710-2300026 ... Testing query chr16_random:5290469-9294719 ... Testing query chr22:2213818-3185623 ... Testing query chr18:2186838-5554932 ... Testing query chr1_random:4416515-6829118 ... Testing query chr17_random:4168349-9033195 ... Testing query chr4_random:7231065-9006087 ... Testing query chr3:6627861-7098084 ... Testing query chr21:4791386-7462661 ... Testing query chr6:5486440-6497547 ... Testing query chr7:7583780-8490132 ... Testing query chr15:4167629-9516050 ... Testing query chr13:412129-3106131 ... Testing query chr6:2242528-3392002 ... Testing query chr13:4573366-8565166 ... Testing query chr14:1012727-4265512 ... Testing query chrX:8331093-8914945 ... Testing query chr19:3587675-9174187 ... Testing query chr7:296443-1800051 ... Testing query chr3:5277077-9767087 ... Testing query chr21:7692109-7739057 ... Testing query chr11:3448455-8411453 ... Testing query chr1_random:2275881-3676442 ... Testing query chr4_random:6322956-7587151 ... Testing query chr22_random:4609088-7067795 ... Testing query chr11:1103974-5115622 ... Testing query chr17:8733322-9618772 ... Testing query chr5_random:1779768-6935553 ... Testing query chr8_random:2538535-9879832 ... Testing query chr22:768294-3209930 ... Testing query chr22:943981-2330158 ... Testing query chr12:4987241-7314877 ... Testing query chr2:3120747-6311500 ... Testing query chrX:1829150-5592634 ... Testing query chr7:795351-9692074 ... Testing query chr9:5469158-7108447 ... Testing query chr18:1967306-6204810 ... Testing query chr4_random:8969152-9598463 ... Testing query chr4_random:1579186-2839628 ... Testing query chr15:5974419-7281533 ... Testing query chr8_random:3609626-6631230 ... Testing query chr17:3094989-6618173 ... Testing query chr15:1799279-6576530 ... Testing query chr3:5157964-8423765 ... Testing query chr22_random:2813926-5797993 ... Testing query chr2:2248206-3931961 ... Testing query chr7:3205910-9801772 ... Testing query chr21_random:623490-6775587 ... Testing query chrM:8166786-8509161 ... Testing query chr17:1804940-2950404 ... Testing query chr10_random:2511464-6816559 ... Testing query chr21_random:153036-5827934 ... Testing query chr2_random:8263243-9685626 ... Testing query chr21:1111482-5812333 ... Testing query chr8:4290604-9166817 ... Testing query chr13:3398929-7913910 ... Testing query chr10:4553797-9072246 ... Testing query chr20:7207944-7471721 ... Testing query chrY:1982521-2897985 ... Testing query chr10_random:5100074-7818426 ... Testing query chr15:4365944-8388476 ... Testing query chr13:50044-8373169 ... Testing query chr12:5115399-7648840 ... Testing query chr4:2962742-8829366 ... Testing query chr6_random:1322565-9235978 ... Testing query chr12:6057343-7930326 ... Testing query chr3:1612029-2982153 ... Testing query chr15:6582900-8591795 ... Testing query chr21:5009971-6424414 ... Testing query chr6:706279-8162934 ... Testing query chr16:3267535-9670332 ... Testing query chr16:2694606-3346697 ... Testing query chrY:9108749-9339860 ... Testing query chr18:1265164-5476362 ... Testing query chr8_random:1135765-3131623 ... Testing query chr1_random:4068577-5850392 ... Testing query chr10_random:8086436-9515610 ... Testing query chr12:786080-9272524 ... Testing query chr2_random:3529918-9107547 ... Testing query chrX:33039-720704 ... Testing query chrY:7759964-8753893 ... Testing query chr18_random:9023306-9399435 ... Testing query chr6:5281117-9258674 ... Testing query chr2_random:3737881-7335740 ... Testing query chr18_random:486302-3415910 ... Testing query chr9_random:4036001-4224366 ... Testing query chr1_random:676459-981484 ... Testing query chr21:213055-9194219 ... Testing query chr3:5273397-7935759 ... Testing query chr7:5844019-5928029 ... Testing query chr22:4400032-4947008 ... Testing query chr1_random:6368632-9050986 ... Testing query chr6_random:3521181-8577335 ... Testing query chr11_random:4864475-5742060 ... Testing query chr9:691952-3618418 ... Testing query chr16:5899296-6778697 ... Testing query chr16:865613-6607475 ... Testing query chr17_random:4739682-6923211 ... Testing query chrY:2356621-4914419 ... Testing query chr3_random:1842297-6259766 ... Testing query chr3_random:5126637-7321281 ... Testing query chrX:4209013-9761426 ... Testing query chr5_random:4596157-5675945 ... Testing query chr21_random:3696079-6024271 ... Testing query chr3_random:5067064-8876286 ... Testing query chr21_random:5565110-6689301 ... Testing query chr21_random:15781-4584722 ... Testing query chr1:3346110-7059075 ... Testing query chrX:5966696-6933232 ... Testing query chr17:5021510-8070334 ... Testing query chr6:1149206-6788407 ... Testing query chr3_random:3744515-8291994 ... Testing query chr2:22996-4588290 ... Testing query chr17_random:5326761-6699939 ... Testing query chr11_random:2696057-3080563 ... Testing query chr9:6885746-7594235 ... Testing query chr2:4534733-7295296 ... Testing query chr13_random:3998213-9469962 ... Testing query chr1_random:5426791-6149949 ... Testing query chr9_random:530950-725978 ... Testing query chr11:4184033-9403368 ... Testing query chr15_random:1456012-6938955 ... Testing query chr4:527074-2332486 ... Testing query chr15:6231961-6744661 ... Testing query chr4_random:1429017-4799661 ... Testing query chrX_random:1288951-8906564 ... Testing query chr5:203973-5396390 ... Testing query chr22_random:6924137-9556382 ... Testing query chr13:3692768-5792536 ... Testing query chr7_random:4736121-7190035 ... Testing query chr19_random:1067060-5424230 ... Testing query chr5:4645403-9655346 ... Testing query chr21:6194788-9692460 ... Testing query chr3_random:6249249-8849610 ... Testing query chr1_random:116005-4931104 ... Testing query chr9_random:2264542-9177908 ... Testing query chr5:1920701-3940100 ... Testing query chr19:3510626-6120416 ... Testing query chr8_random:1385330-9139475 ... Testing query chr5_random:4560385-9932819 ... Testing query chr10_random:1546770-4255829 ... Testing query chrY:1634712-6195051 ... Testing query chr21:1934284-3805640 ... Testing query chr10:1098075-1222293 ... Testing query chrX:3147440-5915627 ... Testing query chr12:644340-9578661 ... Testing query chr7:3815107-7552297 ... Testing query chr7_random:979254-6592345 ... Testing query chr15_random:4031375-9529529 ... Testing query chr20:809453-6417655 ... Testing query chr3_random:1311668-6592135 ... Testing query chr16_random:4796848-9917504 ... Testing query chr2:2316239-8809758 ... Testing query chr22_random:3700813-7193581 ... Testing query chr2_random:5629881-8301170 ... Testing query chr2:4292815-5793077 ... Testing query chr16:4963697-5732378 ... Testing query chr20:1818167-2602981 ... Testing query chr13_random:857910-3186701 ... Testing query chr8:7828099-7863231 ... Testing query chr2:3039751-5869790 ... Testing query chr7_random:948462-2258714 ... Testing query chr12:2176474-8835346 ... Testing query chr4_random:4818082-9335116 ... Testing query chr9_random:949590-4937462 ... Testing query chr3_random:139177-2147902 ... Testing query chr15_random:4086655-7110200 ... Testing query chr7:1707937-7031178 ... Testing query chr15:6704897-7523233 ... Testing query chr8_random:3261310-3388805 ... Testing query chr11:4627964-9758513 ... Testing query chr3_random:1269243-5807226 ... Testing query chr9_random:564250-7036410 ... Testing query chr8_random:5129373-5437488 ... Testing query chr18:2171501-3304941 ... Testing query chr17_random:5747642-6505556 ... Testing query chrY:3819311-5517038 ... Testing query chr11_random:4980823-9419145 ... Testing query chrX:3246258-6297440 ... Testing query chr1_random:810216-9835846 ... Testing query chr9_random:227030-6294798 ... Testing query chr1_random:301295-1576363 ... Testing query chr21:4560202-9527465 ... Testing query chr11:3926303-4702504 ... Testing query chr13_random:4053954-7799426 ... Testing query chr8_random:1615788-4228091 ... Testing query chrX:5354321-7998054 ... Testing query chr5:428791-7222158 ... Testing query chrY:5600982-5656729 ... Testing query chr4_random:3857931-8313241 ... Testing query chr15:1925774-5199208 ... Testing query chr11_random:1107850-6997032 ... Testing query chr14:2769511-5526141 ... Testing query chr22:1129798-7717631 ... Testing query chr22_random:2940332-5279177 ... Testing query chr9:1067427-1150594 ... Testing query chr8:5146545-9541542 ... Testing query chr15:7089597-8473958 ... Testing query chr12:5527737-5802706 ... Testing query chr7:1551097-6396733 ... Testing query chr2_random:3022570-3558123 ... Testing query chr5_random:385945-6563916 ... Testing query chr19_random:3546106-9160937 ... Testing query chr15_random:3701260-8137083 ... Testing query chr5:1805515-5128679 ... Testing query chr10_random:748486-5680503 ... Testing query chr18:1342370-7881611 ... Testing query chr18_random:770908-6308398 ... Testing query chr19:7484581-8473209 ... Testing query chr7:4518548-7588072 ... Testing query chr9_random:7255308-8443827 ... Testing query chrX:5799987-8117438 ... Testing query chr14:7540848-8413963 ... Testing query chr19_random:2328053-2556284 ... Testing query chr16_random:7230921-7518347 ... Testing query chr19_random:276347-1547597 ... Testing query chr13:765679-7048818 ... Testing query chrM:2605992-5897739 ... Testing query chrX:7913839-8348655 ... Testing query chr2_random:7115229-7577760 ... Testing query chr21:7618516-8976664 ... Testing query chr10_random:5113402-9511617 ... Testing query chr3_random:2749825-6235208 ... Testing query chr7_random:4542464-5736534 ... Testing query chr22:3287391-8684233 ... Testing query chr1:6551268-8138439 ... Testing query chr18_random:7072081-7642659 ... Testing query chr1_random:375703-2560467 ... Testing query chr21:5140483-9431223 ... Testing query chr19:320517-7295855 ... Testing query chr12:585392-5511186 ... Testing query chr18_random:8083366-8235379 ... Testing query chr10:126713-1547118 ... Testing query chr10:5632955-8746379 ... Testing query chr10_random:3676138-6848091 ... Testing query chr9:4589897-9207905 ... Testing query chr6_random:7846883-9764185 ... Testing query chr18_random:4290690-8214747 ... Testing query chr13_random:2540819-4559633 ... Testing query chr11_random:3861379-5778337 ... Testing query chr16_random:1701866-3678380 ... Testing query chr15:6359944-8126244 ... Testing query chr9_random:3748170-8007098 ... Testing query chr9:7943740-9455802 ... Testing query chr19_random:1042691-5523628 ... Testing query chr1_random:1492517-5228447 ... Testing query chr6:5705000-6113711 ... Testing query chr20:323999-8013692 ... Testing query chr10_random:2403788-4666817 ... Testing query chr12:809220-4859122 ... Testing query chr7:4626441-6767688 ... Testing query chr9:1227373-9861818 ... Testing query chr9_random:1646320-4830906 ... Testing query chr5:1816686-8010796 ... Testing query chr18_random:2978620-4099625 ... Testing query chr2:2092284-6363784 ... Testing query chr11:6697928-8978854 ... Testing query chr15:4328362-7736553 ... Testing query chr19:2684370-4694361 ... Testing query chr8_random:1549783-2052889 ... Testing query chr10_random:343773-5114298 ... Testing query chr22:239978-7311092 ... Testing query chr10:59830-4498628 ... Testing query chr6_random:4394006-8726576 ... Testing query chr2:2521493-6006376 ... Testing query chrY:174190-248602 ... Testing query chr5_random:3175374-3810594 ... Testing query chr21:458207-4328406 ... Testing query chr7:746735-8755260 ... Testing query chr1:8376346-9926832 ... Testing query chrX:1558302-6671795 ... Testing query chr3:90115-6523026 ... Testing query chr17_random:1954593-2055586 ... Testing query chr9:2137572-9471850 ... Testing query chr18_random:7412031-7927783 ... Testing query chr7:2153207-4745373 ... Testing query chrX:4532293-8914932 ... Testing query chr11:2910609-3421044 ... Testing query chr9:6096367-7279687 ... Testing query chr3:2070513-7395995 ... Testing query chr8_random:835918-1827839 ... Testing query chr18:248820-4981110 ... Testing query chr11_random:4573607-7438971 ... Testing query chrX:4061785-7455437 ... Testing query chr3:5179852-5811856 ... Testing query chr7_random:3320586-3880101 ... Testing query chr22:1201575-8615117 ... Testing query chr4:6832003-9027563 ... Testing query chr5_random:2075108-2231968 ... Testing query chrX_random:59800-714902 ... Testing query chrX_random:2828941-5491980 ... Testing query chr8:1038109-7255118 ... Testing query chr19:564478-5162536 ... Testing query chr21:6696589-7247970 ... Testing query chr6:918960-1474816 ... Testing query chrM:5636321-9968137 ... Testing query chr7_random:5485027-5682623 ... Testing query chrY:4149126-7271874 ... Testing query chrX_random:2119447-7981903 ... Testing query chr8:392266-4278110 ... Testing query chr15:126791-8741531 ... Testing query chrY:1970354-3699838 ... Testing query chr16:4070891-8181737 ... Testing query chr18_random:1308317-5408953 ... Testing query chr9:1486842-2579174 ... Testing query chr9_random:3614823-8021197 ... Testing query chr19_random:4100590-7401362 ... Testing query chr13:9198949-9562213 ... Testing query chr13_random:3477250-5979150 ... Testing query chr8:702816-7724269 ... Testing query chrX:1173848-9916277 ... Testing query chr19_random:1528939-7213477 ... Testing query chrY:4055178-8006125 ... Testing query chr21_random:5600720-8897721 ... Testing query chr13:5754292-7802376 ... Testing query chr6_random:2337681-6172508 ... Testing query chr2:5799739-7134812 ... Testing query chrX_random:3353632-6262401 ... Testing query chr21:945894-5132876 ... Testing query chr18_random:2350673-9531784 ... Testing query chr22_random:5048930-8474866 ... Testing query chr19:6352226-8501858 ... Testing query chr20:3392059-9830746 ... Testing query chr16_random:4090981-7752074 ... Testing query chr11_random:5905570-6251642 ... Testing query chr13:360298-9358487 ... Testing query chr6_random:882947-4758560 ... Testing query chr11:2340078-2932391 ... Testing query chr22_random:2213551-2534609 ... Testing query chr21:5841676-5846763 ... Testing query chr11_random:4038782-7000307 ... Testing query chr6_random:25409-5762752 ... Testing query chr16:5928354-8501435 ... Testing query chrY:694230-6280406 ... Testing query chr11:7243231-8376959 ... Testing query chr16_random:7306380-8046651 ... Testing query chr16:1271045-7843225 ... Testing query chr15:3261152-4143715 ... Testing query chr16:3643483-7977448 ... Testing query chrM:2682115-4251696 ... Testing query chrM:8447185-9660353 ... Testing query chr17_random:4662108-9040099 ... Testing query chr15:2717869-3422290 ... Testing query chr9_random:2276674-4258729 ... Testing query chrX_random:975097-5521164 ... Testing query chr11:2146529-8617542 ... Testing query chr10_random:1180053-8007684 ... Testing query chr3_random:3693000-4565796 ... Testing query chr11:145445-2682401 ... Testing query chr8_random:6750591-7945127 ... Testing query chr1:8320362-9511438 ... Testing query chr8:7013549-9472948 ... Testing query chr13_random:3536637-5003209 ... Testing query chr9:6558793-7284938 ... Testing query chr21_random:2580219-9412760 ... Testing query chr10:406321-2977770 ... Testing query chr21:492284-7994828 ... Testing query chr8:2657319-7983432 ... Testing query chrX:4732048-8043746 ... Testing query chr20:3307597-9305376 ... Testing query chr2_random:755380-8957174 ... Testing query chrY:2933069-9880634 ... Testing query chr6:774738-5674081 ... Testing query chr22_random:715809-9050909 ... Testing query chr4:1349527-3344979 ... Testing query chr6:8028105-9684178 ... Testing query chr5_random:4787471-8881473 ... Testing query chr10_random:2634703-3696440 ... Testing query chr11_random:829085-1727870 ... Testing query chr15_random:592933-9165180 ... Testing query chr4_random:4418610-8898086 ... Testing query chrX_random:2431444-6884713 ... Testing query chr8_random:6475456-8480814 ... Testing query chr7:3815530-7026545 ... Testing query chr19:7331585-7602899 ... Testing query chr1_random:874465-3320587 ... Testing query chr13_random:733794-6825035 ... Testing query chr15_random:9014536-9668872 ... Testing query chr17_random:6591609-9129777 ... Testing query chrM:656068-4356620 ... Testing query chr8:405654-9125605 ... Testing query chrX:2091850-6675177 ... Testing query chr17_random:7703315-8296743 ... Testing query chr5:6509082-7915180 ... Testing query chr22:2553656-7681295 ... Testing query chr14:3268086-7514168 ... Testing query chr8:4422671-6192314 ... Testing query chr1:65591-912831 ... Testing query chr3_random:5754696-6365576 ... Testing query chr19:3761804-6226235 ... Testing query chr15_random:437782-2343429 ... Testing query chr21_random:6464723-8352688 ... Testing query chr2:2429164-5768260 ... Testing query chr4:470318-7002218 ... Testing query chr4:3690943-5461445 ... Testing query chr22_random:5183905-6703677 ... Testing query chr6:956010-4837181 ... Testing query chr22_random:4644999-6726863 ... Testing query chr3:461910-2847795 ... Testing query chrM:1898841-4804510 ... Testing query chr17_random:4508018-9521979 ... Testing query chr5_random:324986-2917264 ... Testing query chr21_random:5399136-5748620 ... Testing query chr22:2778077-4812793 ... Testing query chr10:4969555-6126688 ... Testing query chr18:1713300-5060476 ... Testing query chr13_random:3333348-5290509 ... Testing query chr11_random:4081564-5917103 ... Testing query chr4_random:5054748-8642850 ... Testing query chr1:2326146-4227874 ... Testing query chr18:1537257-7925976 ... Testing query chr22_random:8252153-8805544 ... Testing query chr3_random:1198809-9011283 ... Testing query chr17_random:6967406-8885184 ... Testing query chr13:1386877-2947412 ... Testing query chrM:6757870-7928951 ... Testing query chr21:4074861-7649457 ... Testing query chrX_random:1019101-6500619 ... Testing query chrX:1825987-5504513 ... Testing query chr21_random:3186073-5713305 ... Testing query chr4:6259611-8028235 ... Testing query chr4:1743818-8599191 ... Testing query chr17:1858282-6524491 ... Testing query chr15_random:4438074-7157093 ... Testing query chr3_random:397131-735889 ... Testing query chr8:6928096-9944821 ... Testing query chr4_random:1300717-4919221 ... Testing query chr5_random:338852-4544685 ... Testing query chr7_random:9056136-9688355 ... Testing query chr13:2503131-3346435 ... Testing query chr15_random:4163332-8152391 ... Testing query chr11_random:3309623-7440495 ... Testing query chr5_random:9256148-9879716 ... Testing query chr17_random:1285404-9731324 ... Testing query chr11:8839451-9081378 ... Testing query chr13:8871343-9845159 ... Testing query chr22:4961912-7272246 ... Testing query chr7_random:1546612-1704922 ... Testing query chr4_random:3988885-5892099 ... Testing query chr16:3240803-6856154 ... Testing query chr16:217614-7256181 ... Testing query chr8_random:9247976-9386452 ... Testing query chr3_random:6627763-9791298 ... Testing query chr2:2529288-4212123 ... Testing query chrX_random:2988973-8007994 ... Testing query chr15:7917609-9330719 ... Testing query chr11_random:3494062-5554433 ... Testing query chr10_random:550231-9169795 ... Testing query chrM:2348914-4789264 ... Testing query chr10_random:1774094-2022615 ... Testing query chrY:1233622-1787356 ... Testing query chr16:1423379-2759956 ... Testing query chr15_random:2179216-5955676 ... Testing query chr13_random:4485355-8258869 ... Testing query chr16:1540718-7599890 ... Testing query chr16:3470124-5210468 ... Testing query chr5_random:2480219-3389498 ... Testing query chrX_random:2150354-9183393 ... Testing query chr4_random:7326066-8687796 ... Testing query chr9_random:778644-7335950 ... Testing query chr3_random:117405-711777 ... Testing query chr3_random:1627027-5946622 ... Testing query chr14:1896619-3058485 ... Testing query chr4:361451-8469991 ... Testing query chr13:8016007-9409673 ... Testing query chr15_random:4902505-9345392 ... Testing query chr11_random:7321862-9499733 ... Testing query chr4:1033220-5712150 ... Testing query chr8:3549734-9090035 ... Testing query chrM:5081509-5962772 ... Testing query chrX_random:97240-6137606 ... Testing query chr8_random:4271059-4291635 ... Testing query chrX_random:530035-1682825 ... Testing query chr15:2788773-5483281 ... Testing query chrX_random:4759178-9377757 ... Testing query chrM:3245025-4297984 ... Testing query chr19_random:3021529-4576251 ... Testing query chr4_random:1397040-5761345 ... Testing query chrM:561371-7187972 ... Testing query chr22:5413646-8736775 ... Testing query chr17_random:1425366-7019792 ... Testing query chr3_random:572179-7205526 ... Testing query chr5:4328737-9239750 ... Testing query chr22:5069432-6659616 ... Testing query chr13:48249-7303858 ... Testing query chr3:305799-6869287 ... Testing query chr21:3873459-5093561 ... Testing query chr19:5939843-9027189 ... Testing query chr2:5873453-6683127 ... Testing query chr22_random:3713598-5598641 ... Testing query chr20:179927-8450235 ... Testing query chr13_random:8308459-9668938 ... Testing query chr11:1199780-7649669 ... Testing query chr19:4137076-6447341 ... Testing query chrM:78280-8559488 ... Testing query chr4:623887-7069138 ... Testing query chr16:3039657-4345359 ... Testing query chr17:3391405-4744719 ... Testing query chr20:2910861-7899348 ... Testing query chr19_random:913985-2128081 ... Testing query chr22:1426695-8605324 ... Testing query chr12:1887213-4358077 ... Testing query chrX:5563613-8375913 ... Testing query chr7_random:136737-595720 ... Testing query chr22:3649338-3715557 ... Testing query chr22_random:1857324-2876705 ... Testing query chr3_random:1299041-9034999 ... Testing query chr15:978485-8350193 ... Testing query chr19_random:4068601-6523086 ... Testing query chr2:201488-4273604 ... Testing query chr19_random:5966187-9871009 ... Testing query chrM:1330413-9761840 ... Testing query chr7:4263424-8956444 ... Testing query chr5:710131-1481160 ... Testing query chr22_random:3228001-4696776 ... Testing query chr3:64585-1673488 ... Testing query chr16:8045346-8459636 ... Testing query chr13_random:1741393-4393228 ... Testing query chr22_random:2624571-7878001 ... Testing query chr20:4312366-7263897 ... Testing query chr2_random:792986-9926045 ... Testing query chr4:876557-8032416 ... Testing query chr7_random:9474728-9775529 ... Testing query chrY:196281-2297210 ... Testing query chr11_random:1815604-1988691 ... Testing query chr17:327462-9941596 ... Testing query chr4:1225057-5716342 ... Testing query chrX_random:5518830-9291836 ... Testing query chr19_random:8850582-9837888 ... Testing query chr10_random:906079-4133872 ... Testing query chrX:1487717-2363048 ... Testing query chrX:315413-7567516 ... Testing query chr8_random:6478215-9426080 ... Testing query chr20:2999407-4776774 ... Testing query chr5_random:1309090-5902755 ... Testing query chr4_random:4737388-7952008 ... Testing query chr21_random:3092337-5111212 ... Testing query chr12:4888197-9051400 ... Testing query chr13_random:4483564-5744770 ... Testing query chr22_random:54755-6638497 ... Testing query chr13_random:5891419-7679795 ... Testing query chr12:1730038-8775120 ... Testing query chr10:3971454-8725046 ... Testing query chr13_random:2420218-3946730 ... Testing query chr16_random:6268326-9602951 ... Testing query chr15_random:6201359-7624324 ... Testing query chr8_random:1897294-5156982 ... Testing query chr1:2597385-4514890 ... Testing query chrX_random:338730-7953560 ... Testing query chr7:5484367-7925032 ... Testing query chr5_random:6298235-7470139 ... Testing query chr21_random:3834366-4459713 ... Testing query chr5:2361767-8905807 ... Testing query chrM:3162105-9086123 ... Testing query chrX_random:4940689-6482079 ... Testing query chr4:4948264-5128137 ... Testing query chr3:4207686-7342748 ... Testing query chr19_random:2021389-9994958 ... Testing query chr18:3680011-9706840 ... Testing query chr17_random:5951397-8238603 ... Testing query chr15_random:4175461-7481270 ... Testing query chr4:498362-9165782 ... Testing query chr21:4179687-5159563 ... Testing query chr1:5178637-7992880 ... Testing query chr15_random:6053128-8149868 ... Testing query chr5:4008322-7971530 ... Testing query chr19_random:1097409-1939223 ... Testing query chr15:7469377-8821183 ... Testing query chr11_random:1627957-5387469 ... Testing query chr9:5855393-7238773 ... Testing query chr22:3055704-4751301 ... Testing query chr18_random:2752026-7569770 ... Testing query chr6:2659325-3383321 ... Testing query chr19_random:6031799-9193165 ... Testing query chr10:2867928-7456748 ... Testing query chr17:803521-2016747 ... Testing query chr11_random:2756837-9309974 ... Testing query chr9_random:4932323-6215308 ... Testing query chr19_random:1738738-9429398 ... Testing query chr4_random:162435-8328176 ... Testing query chr17:138893-2694455 ... Testing query chrX_random:4137996-9339319 ... Testing query chr19:2497402-8914940 ... Testing query chr13_random:3513964-5910759 ... Testing query chrX:1099583-2639169 ... Testing query chr11_random:6266637-8387131 ... Testing query chr8_random:3059827-5229064 ... Testing query chr6:380960-2560436 ... Testing query chr15_random:5618328-6876961 ... Testing query chr2_random:3878460-5680854 ... Testing query chr8_random:2477614-4148075 ... Testing query chr18_random:5415785-8338387 ... Testing query chr10_random:8209397-8355863 ... Testing query chr11_random:4475489-6604223 ... Testing query chr1_random:754948-7226484 ... Testing query chr9:2946100-8357028 ... Testing query chr15:7199317-8245905 ... Testing query chr7_random:7269507-8820498 ... Testing query chr16:1621267-2368637 ... Testing query chr7_random:2996833-9854987 ... Testing query chrM:6484003-6911983 ... Testing query chr13:1771424-4738191 ... Testing query chr13_random:1828228-4302873 ... Testing query chrM:2962858-5957962 ... Testing query chr6_random:4242794-9824359 ... Testing query chr13:415874-9331256 ... Testing query chr8:7417568-9299672 ... Testing query chr5_random:6880184-8188312 ... Testing query chr10_random:1892176-5188920 ... Testing query chr21_random:4076206-6101050 ... Testing query chr20:5126731-9990106 ... Testing query chr4:3133535-3261569 ... Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.4583200393580885374.bai #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.17698151869763701092.bai #BAMIndexWriterTest diff /tmp/javaBai.4583200393580885374.bai /tmp/cBai.17698151869763701092.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.11995423072522769296.bai.txt #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.180506444818905342java.bai #BAMIndexWriterTest diff /tmp/javaBai.180506444818905342java.bai.txt /tmp/cBai.11995423072522769296.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 1ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT 0ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT Creating file /tmp/BCOST.12342687605734593673.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT Creating file /tmp/testCustomDeflater.7416811330150690641.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT Creating file /tmp/BCOST.479254824423457784.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMSliceMD5Test.testExceptionWhileReadingWithWrongReference STANDARD_ERROR ERROR 2021-06-20 03:23:16 Slice Reference MD5 mismatch for slice 0:1-31, .aAbBcCdDgGhHkKmMnNrRsStTvVwWyY Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 Adding chunk: 10 - 20 Adding chunk: 100 - 200 Adding chunk: 1048575 - 1048576 Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_first_3_bytes STANDARD_ERROR Adding chunk: 0 - 1 Adding chunk: 1 - 2 Adding chunk: 2 - 3 Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_range_read STANDARD_ERROR Adding chunk: 0 - 100 Adding chunk: 10 - 20 Adding chunk: 100 - 200 Adding chunk: 1048575 - 1048576 Adding chunk: 0 - 100 Adding chunk: 10 - 20 Adding chunk: 100 - 200 Adding chunk: 1048575 - 1048576 Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest STANDARD_ERROR Resetting tmpdir Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.testPositive[2](no ram records, 10, 0) STANDARD_ERROR Could not delete file tmp Could not delete file pbuilder1 Could not delete file DiskBackedQueueTest Could not delete file diskbackedqueue.13576980183707611374.tmp Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.testPositive[5](greater than threshold, 550, 100) STANDARD_ERROR Could not delete file tmp Could not delete file pbuilder1 Could not delete file DiskBackedQueueTest Could not delete file diskbackedqueue.8526443767336674932.tmp Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.testPositive[6](threshold multiple, 600, 100) STANDARD_ERROR Could not delete file tmp Could not delete file pbuilder1 Could not delete file DiskBackedQueueTest Could not delete file diskbackedqueue.10591736445144609955.tmp Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.testPositive[7](threshold multiple plus one, 101, 100) STANDARD_ERROR Could not delete file tmp Could not delete file pbuilder1 Could not delete file DiskBackedQueueTest Could not delete file diskbackedqueue.9464704884846552555.tmp Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.testReadOnlyQueueJustBeforeReadingFromDisk STANDARD_ERROR Could not delete file tmp Could not delete file pbuilder1 Could not delete file DiskBackedQueueTest Could not delete file diskbackedqueue.5384045213918729387.tmp Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.spillToDiskTest STANDARD_ERROR Could not delete file tmp Could not delete file pbuilder1 Could not delete file DiskBackedQueueTest Gradle suite > Gradle test STANDARD_ERROR Could not delete file diskbackedqueue.4837077572525631048.tmp Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT Time to construct a tree with 50000 nodes: 84 milliseconds Queried for the same 100-length mapping 72559922 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters[0](unsorted.sam, samFilter01.js, 8) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters[1](unsorted.sam, samFilter02.js, 10) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) chr3:50911035-50911051 + null intersection null (len 17)=>chr3:50936014-50936030 + .(+) using chain 3 ; pct matched 0.9411765 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[1](chr2:111013693-111013832 + .) STANDARD_OUT Diagnosing chr2:111013693-111013832 + . (len 140) chr2:111013693-111013832 + null intersection null (len 140)=>null using chain 1 chr2:111013693-111013832 + null intersection null (len 140)=>chr2:108482693-108482783 - .(-) using chain 53 ; pct matched 0.65 chr2:111013693-111013832 + null intersection null (len 140)=>chr2:113152284-113152332 + .(+) using chain 310 ; pct matched 0.35 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[2](chr3:14174511-14175398 + .) STANDARD_OUT Diagnosing chr3:14174511-14175398 + . (len 888) chr3:14174511-14175398 + null intersection null (len 888)=>chr3:14199509-14200394 + .(+) using chain 3 ; pct matched 0.9166667 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[3](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) chr3:50911035-50911051 + null intersection null (len 17)=>chr3:50936014-50936030 + .(+) using chain 3 ; pct matched 0.9411765 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[4](chr6:32071709-32071869 + .) STANDARD_OUT Diagnosing chr6:32071709-32071869 + . (len 161) chr6:32071709-32071869 + null intersection null (len 161)=>chr6:31963730-31963890 + .(+) using chain 6 ; pct matched 0.89440995 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[5](chr6:32072183-32072358 + .) STANDARD_OUT Diagnosing chr6:32072183-32072358 + . (len 176) chr6:32072183-32072358 + null intersection null (len 176)=>chr6:31964204-31964379 + .(+) using chain 6 ; pct matched 0.90909094 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[6](chr6:32104446-32104606 + .) STANDARD_OUT Diagnosing chr6:32104446-32104606 + . (len 161) chr6:32104446-32104606 + null intersection null (len 161)=>chr6:31996468-31996628 + .(+) using chain 6 ; pct matched 0.89440995 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[7](chr6:32104920-32105095 + .) STANDARD_OUT Diagnosing chr6:32104920-32105095 + . (len 176) chr6:32104920-32105095 + null intersection null (len 176)=>chr6:31996942-31997117 + .(+) using chain 6 ; pct matched 0.90909094 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[8](chr7:101995561-101995739 + .) STANDARD_OUT Diagnosing chr7:101995561-101995739 + . (len 179) chr7:101995561-101995739 + null intersection null (len 179)=>chr7:102208488-102208633 + .(+) using chain 7 ; pct matched 0.8156425 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[9](chr7:142178782-142178825 + .) STANDARD_OUT Diagnosing chr7:142178782-142178825 + . (len 44) chr7:142178782-142178825 + null intersection null (len 44)=>null using chain 7 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[10](chr7:142179850-142180013 + .) STANDARD_OUT Diagnosing chr7:142179850-142180013 + . (len 164) chr7:142179850-142179857 + null intersection null (len 8)=>chr7:142479907-142479914 + .(+) using chain 31548103 ; pct matched 0.048780486 chr7:142179946-142180009 + null intersection null (len 64)=>chr7:142480003-142480066 + .(+) using chain 30171758 ; pct matched 0.3902439 chr7:142179850-142180013 + null intersection null (len 164)=>null using chain 7 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[11](chr7:142181067-142181324 + .) STANDARD_OUT Diagnosing chr7:142181067-142181324 + . (len 258) chr7:142181067-142181324 + null intersection null (len 258)=>null using chain 7 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[12](chr7:142181720-142181860 + .) STANDARD_OUT Diagnosing chr7:142181720-142181860 + . (len 141) chr7:142181720-142181860 + null intersection null (len 141)=>null using chain 7 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[13](chr7:142182157-142182313 + .) STANDARD_OUT Diagnosing chr7:142182157-142182313 + . (len 157) chr7:142182157-142182313 + null intersection null (len 157)=>null using chain 7 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[14](chr15:19335778-19336302 + .) STANDARD_OUT Diagnosing chr15:19335778-19336302 + . (len 525) chr15:19335778-19336302 + null intersection null (len 525)=>chr15:21071199-21071612 + .(+) using chain 16 ; pct matched 0.7885714 chr15:19335778-19336302 + null intersection null (len 525)=>null using chain 110 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[15](chr17:33364376-33364428 + .) STANDARD_OUT Diagnosing chr17:33364376-33364428 + . (len 53) chr17:33364376-33364428 + null intersection null (len 53)=>chr17:36289992-36290044 + .(+) using chain 18 ; pct matched 0.3207547 chr17:33364385-33364428 + null intersection null (len 44)=>chr17:36342590-36342625 - .(-) using chain 363 ; pct matched 0.6792453 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[16](chr17:33546162-33546214 + .) STANDARD_OUT Diagnosing chr17:33546162-33546214 + . (len 53) chr17:33546162-33546214 + null intersection null (len 53)=>null using chain 18 chr17:33546162-33546214 + null intersection null (len 53)=>null using chain 1564 chr17:33546162-33546214 + null intersection null (len 53)=>chr17:36289992-36290044 - .(-) using chain 363 ; pct matched 0.3207547 chr17:33546162-33546214 + null intersection null (len 53)=>chr17:36342590-36342625 + .(+) using chain 1571 ; pct matched 0.6792453 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[17](chr17:33706667-33706736 + .) STANDARD_OUT Diagnosing chr17:33706667-33706736 + . (len 70) chr17:33706667-33706736 + null intersection null (len 70)=>chr17:36453148-36453217 + .(+) using chain 18 ; pct matched 0.75714284 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[18](chr17:59772721-59772781 + .) STANDARD_OUT Diagnosing chr17:59772721-59772781 + . (len 61) chr17:59772721-59772781 + null intersection null (len 61)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[19](chr17:59779355-59779421 + .) STANDARD_OUT Diagnosing chr17:59779355-59779421 + . (len 67) chr17:59779355-59779421 + null intersection null (len 67)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[20](chr17:59781483-59781540 + .) STANDARD_OUT Diagnosing chr17:59781483-59781540 + . (len 58) chr17:59781483-59781540 + null intersection null (len 58)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[21](chr17:59783488-59783565 + .) STANDARD_OUT Diagnosing chr17:59783488-59783565 + . (len 78) chr17:59783488-59783565 + null intersection null (len 78)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[22](chr17:59784584-59784615 + .) STANDARD_OUT Diagnosing chr17:59784584-59784615 + . (len 32) chr17:59784584-59784615 + null intersection null (len 32)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[23](chr17:59786025-59786136 + .) STANDARD_OUT Diagnosing chr17:59786025-59786136 + . (len 112) chr17:59786025-59786136 + null intersection null (len 112)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[24](chr17:59787203-59787494 + .) STANDARD_OUT Diagnosing chr17:59787203-59787494 + . (len 292) chr17:59787203-59787494 + null intersection null (len 292)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[25](chr17:59791235-59791514 + .) STANDARD_OUT Diagnosing chr17:59791235-59791514 + . (len 280) chr17:59791235-59791514 + null intersection null (len 280)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[26](chr17:59794247-59794502 + .) STANDARD_OUT Diagnosing chr17:59794247-59794502 + . (len 256) chr17:59794247-59794502 + null intersection null (len 256)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[27](chr17:59801884-59802193 + .) STANDARD_OUT Diagnosing chr17:59801884-59802193 + . (len 310) chr17:59801884-59802193 + null intersection null (len 310)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[28](chr17:59804685-59804982 + .) STANDARD_OUT Diagnosing chr17:59804685-59804982 + . (len 298) chr17:59804685-59804982 + null intersection null (len 298)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[29](chr17:59817352-59817382 + .) STANDARD_OUT Diagnosing chr17:59817352-59817382 + . (len 31) chr17:59817352-59817382 + null intersection null (len 31)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[30](chr17:59817465-59817532 + .) STANDARD_OUT Diagnosing chr17:59817465-59817532 + . (len 68) chr17:59817465-59817532 + null intersection null (len 68)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[31](chr17:59875754-59875812 + .) STANDARD_OUT Diagnosing chr17:59875754-59875812 + . (len 59) chr17:59875754-59875812 + null intersection null (len 59)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[32](chr17:59875899-59875944 + .) STANDARD_OUT Diagnosing chr17:59875899-59875944 + . (len 46) chr17:59875899-59875944 + null intersection null (len 46)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[33](chr17:59879183-59879456 + .) STANDARD_OUT Diagnosing chr17:59879183-59879456 + . (len 274) chr17:59879183-59879456 + null intersection null (len 274)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[34](chr17:59883988-59884276 + .) STANDARD_OUT Diagnosing chr17:59883988-59884276 + . (len 289) chr17:59883988-59884276 + null intersection null (len 289)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[35](chr17:59887398-59887512 + .) STANDARD_OUT Diagnosing chr17:59887398-59887512 + . (len 115) chr17:59887398-59887512 + null intersection null (len 115)=>null using chain 18 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058 + .) STANDARD_OUT Diagnosing chrX:48774611-48775058 + . (len 448) chrX:48774611-48775058 + null intersection null (len 448)=>null using chain 8 Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT read_28833_29006_6945 0 chr21 28833 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 read_28833_29006_6945 0 chr21 30000 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 read_28701_28881_323b 0 chrX 28834 255 36M * 0 0 GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG $>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O RG:Z:1 read_28701_28881_323b 0 chrX 28835 255 36M * 0 0 GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG $>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O RG:Z:1 read_28701_28881_323c 0 chrX 28835 255 36M * 0 0 CTCAACGTATTCATACAGGCCCTTTTCGAATAGCTG %$=LPJ?D6&@R!"KJCOI+05?>>J9CJ)'@-O>K RG:Z:1 Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaReadOrderMultiIterator STANDARD_OUT a b c d e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT d b e c a Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](.bam) STANDARD_ERROR Ignoring SAM validation error: ERROR: File /tmp/tmp.10743433084342252335.bam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](.bam) STANDARD_ERROR Ignoring SAM validation error: ERROR: File /work/testMakeWriterPath.bam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](.bam) STANDARD_ERROR Ignoring SAM validation error: ERROR: File /work/testMakeWriterPath.bam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null), false) STANDARD_ERROR ERROR 2021-06-20 03:24:06 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.seekablestream.SeekableStreamFactoryTest.testGetStreamFor SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testFailsMD5Check STANDARD_ERROR ERROR 2021-06-20 03:24:09 Slice Reference MD5 mismatch for slice 0:1-20, CTAGCTCAGAAAAAAAAAA Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR Resetting tmpdir Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Resetting tmpdir Gradle Test Executor 1 finished executing tests. Finished generating test XML results (0.339 secs) into: /build/htsjdk-2.18.2+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (0.31 secs) into: /build/htsjdk-2.18.2+dfsg/build/reports/tests/test :test (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 5 mins 9.83 secs. BUILD SUCCESSFUL in 5m 29s 5 actionable tasks: 4 executed, 1 up-to-date make[1]: Leaving directory '/build/htsjdk-2.18.2+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_testroot -O--buildsystem=gradle dh_prep -O--buildsystem=gradle rm -f -- debian/libhtsjdk-java.substvars debian/libhtsjdk-java-doc.substvars rm -fr -- debian/.debhelper/generated/libhtsjdk-java/ debian/libhtsjdk-java/ debian/tmp/ debian/.debhelper/generated/libhtsjdk-java-doc/ debian/libhtsjdk-java-doc/ dh_auto_install -O--buildsystem=gradle install -d /build/htsjdk-2.18.2\+dfsg/debian/tmp dh_install -O--buildsystem=gradle install -d debian/libhtsjdk-java/usr/share/libhtsjdk-java cp --reflink=auto -a ./scripts/explain_sam_flags.py debian/libhtsjdk-java/usr/share/libhtsjdk-java/ install -d debian/.debhelper/generated/libhtsjdk-java install -d debian/.debhelper/generated/libhtsjdk-java-doc jh_installjavadoc -O--buildsystem=gradle Installing javadoc from build/docs/javadoc into package libhtsjdk-java-doc install -d debian/libhtsjdk-java-doc//usr/share/doc/libhtsjdk-java cp -r build/docs/javadoc debian/libhtsjdk-java-doc//usr/share/doc/libhtsjdk-java/api/ cat > debian/libhtsjdk-java-doc.doc-base.javadoc dh_installdocs -O--buildsystem=gradle install -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java install -p -m0644 debian/libhtsjdk-java.README.Debian debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/README.Debian install -p -m0644 debian/copyright debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/copyright install -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc install -p -m0644 debian/copyright debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/copyright install -d debian/libhtsjdk-java-doc/usr/share/doc-base/ install -p -m0644 debian/libhtsjdk-java-doc.doc-base.javadoc debian/libhtsjdk-java-doc/usr/share/doc-base/libhtsjdk-java-doc dh_installchangelogs -O--buildsystem=gradle install -p -m0644 debian/changelog debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian install -p -m0644 debian/changelog debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian dh_installinit -O--buildsystem=gradle dh_installsystemduser -O--buildsystem=gradle dh_perl -O--buildsystem=gradle dh_link -O--buildsystem=gradle rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log debian/rules override_jh_installlibs make[1]: Entering directory '/build/htsjdk-2.18.2+dfsg' jh_installlibs --version-strip='[+]dfsg[.0-9]*' install -d debian/libhtsjdk-java/usr/share/java install -p -m0644 ./build/libs/htsjdk-2.18.2.jar debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-2.18.2.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar make[1]: Leaving directory '/build/htsjdk-2.18.2+dfsg' jh_classpath -O--buildsystem=gradle jh_manifest -plibhtsjdk-java "--classpath=/usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/snappy-java.jar /usr/share/java/commons-compress.jar /usr/share/java/xz.jar /usr/share/java/ngs-java.jar /usr/share/java/libjaxb-api.jar /usr/share/java/jaxb-impl.jar" debian/libhtsjdk-java/usr/share/java/htsjdk.jar Updating symlinked /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar) Reading manifest from /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar Updating manifest in /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar jh_manifest -O--buildsystem=gradle find debian/libhtsjdk-java -name '*.jar' Found usr/share/java/htsjdk-2.18.2.jar Found symlink usr/share/java/htsjdk.jar Reading manifest from debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar No update of debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar required. find debian/libhtsjdk-java-doc -name '*.jar' jh_exec -O--buildsystem=gradle jh_depends -O--buildsystem=gradle Searching /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java for libhtsjdk-java Searching /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar Found Jars: /usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/jaxb-impl.jar /usr/share/java/libjaxb-api.jar /usr/share/java/ngs-java.jar /usr/share/java/snappy-java.jar /usr/share/java/xz.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/commons-compress.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-compress.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/commons-jexl2.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-jexl2.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/commons-logging-1.2.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-logging-1.2.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/jaxb-runtime.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/jaxb-runtime.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/libjaxb-api.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/libjaxb-api.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/ngs-java-2.9.3.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/ngs-java-2.9.3.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/snappy-java.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/snappy-java.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java/usr/share/java/xz-1.8.jar Checking: /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc/usr/share/java/xz-1.8.jar Found Debs: libcommons-compress-java libcommons-jexl2-java libcommons-logging-java libjaxb-java libngs-java libsnappy-java libxz-java Adding substvars: java:Depends=libcommons-compress-java, libcommons-jexl2-java, libcommons-logging-java, libjaxb-java, libngs-java, libsnappy-java, libxz-java java:Recommends= Searching /build/htsjdk-2.18.2+dfsg/debian/libhtsjdk-java-doc for libhtsjdk-java-doc Searching Found Jars: Found Debs: Adding substvars: java:Depends= java:Recommends= mh_installpoms -O--buildsystem=gradle mh_installpom --package=libhtsjdk-java --has-package-version --usj-name=htsjdk debian/htsjdk.pom mh_cleanpom --package=libhtsjdk-java --has-package-version --rules=debian/maven.rules debian/htsjdk.pom debian/.mh/pom.xml debian/.mh/pom.properties mv debian/.mh/pom.xml debian/.mh/htsjdk-debian.pom install -m 644 -D debian/.mh/htsjdk-2.14.3.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.pom install -m 644 -D debian/.mh/htsjdk-debian.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.pom mh_linkjars --skip-clean-poms -O--buildsystem=gradle mh_linkjar --has-package-version --package=libhtsjdk-java --skip-clean-pom debian/htsjdk.pom /usr/share/java/htsjdk.jar dh_link -plibhtsjdk-java /usr/share/javahtsjdk.jar usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-2.18.2.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar dh_link -plibhtsjdk-java /usr/share/javahtsjdk.jar usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-2.18.2.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar dh_strip_nondeterminism -O--buildsystem=gradle Using 1551477897 as canonical time Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-2.18.2.jar using File::StripNondeterminism::handlers::jar Using 1551477897 as canonical time Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanTree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html using File::StripNondeterminism::handlers::javadoc Normalizing 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/Version.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/li Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCFVersion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Decoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-tree.html using 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CountingInputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc jdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc rmalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc hare/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLoggerInterface.html using File::StripNondeterminism::handlers::javadoc nism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html using File::StripNondeterminism::handlers::javadoc ng File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc s::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NameAwareCodec.html using File::StripNondeterminism::handlers::javadoc ::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/MultiRefSliceAlignmentSpanReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc s/cram/lossy/ReadCategoryType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/lossy/ReadCategory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/lossy/QualityScoreTreatmentType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/lossy/QualityScoreTreatment.html using File::StripNondeterminism::handlers::javadoc tsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc hare/doc/libhtsjdk-java/api/htsjdk/samtools/filter/WholeReadClippedFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/TagFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SolexaNoiseFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.html using File::StripNondeterminism::handlers::javadoc bhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/IntHashMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersionPolicies.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Sam2CramRecordFactory.html using File::StripNondeterminism::handlers::javadoc til/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DelegatingIterator.html using File::StripNondeterminism::handlers::javadoc dh_compress -O--buildsystem=gradle cd debian/libhtsjdk-java-doc cd debian/libhtsjdk-java chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian cd '/build/htsjdk-2.18.2+dfsg' chmod a-x usr/share/doc/libhtsjdk-java-doc/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian cd '/build/htsjdk-2.18.2+dfsg' dh_fixperms -O--buildsystem=gradle find debian/libhtsjdk-java-doc -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libhtsjdk-java -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libhtsjdk-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--buildsystem=gradle dh_installdeb -O--buildsystem=gradle install -d debian/libhtsjdk-java/DEBIAN install -d debian/libhtsjdk-java-doc/DEBIAN dh_gencontrol -O--buildsystem=gradle echo misc:Depends= >> debian/libhtsjdk-java.substvars echo misc:Pre-Depends= >> debian/libhtsjdk-java.substvars dpkg-gencontrol -plibhtsjdk-java -ldebian/changelog -Tdebian/libhtsjdk-java.substvars -Pdebian/libhtsjdk-java -UMulti-Arch echo misc:Depends= >> debian/libhtsjdk-java-doc.substvars echo misc:Pre-Depends= >> debian/libhtsjdk-java-doc.substvars dpkg-gencontrol -plibhtsjdk-java-doc -ldebian/changelog -Tdebian/libhtsjdk-java-doc.substvars -Pdebian/libhtsjdk-java-doc -UMulti-Arch chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control chown 0:0 -- debian/libhtsjdk-java/DEBIAN/control chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/control chown 0:0 -- debian/libhtsjdk-java-doc/DEBIAN/control dh_md5sums -O--buildsystem=gradle cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhtsjdk-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java/DEBIAN/md5sums chown 0:0 -- debian/libhtsjdk-java/DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums chown 0:0 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums dh_builddeb -O--buildsystem=gradle dpkg-deb --build debian/libhtsjdk-java .. dpkg-deb --build debian/libhtsjdk-java-doc .. dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_2.18.2+dfsg-2_all.deb'. dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_2.18.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../htsjdk_2.18.2+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) 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/13073 and its subdirectories I: Current time: Sun Jun 20 03:25:01 -12 2021 I: pbuilder-time-stamp: 1624202701 Sun Jun 20 15:25:01 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sun Jun 20 15:25:01 UTC 2021 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sun Jun 20 15:36:35 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sun Jun 20 15:36:35 UTC 2021 I: htsjdk_2.18.2+dfsg-2_amd64.changes: Format: 1.8 Date: Fri, 01 Mar 2019 23:04:57 +0100 Source: htsjdk Binary: libhtsjdk-java libhtsjdk-java-doc Architecture: all Version: 2.18.2+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libhtsjdk-java - Java API for high-throughput sequencing data (HTS) formats libhtsjdk-java-doc - Documentation for the java HTSJDK library Closes: 923539 Changes: htsjdk (2.18.2+dfsg-2) unstable; urgency=medium . [ Matthias Klose ] * Disabled the java/htsjdk/samtools/util/HttpUtilsTest test, requires network access. Closes: #923539 Checksums-Sha1: 44c9fdab3fb1f9f456ce27180f140e5cb6e65930 14914 htsjdk_2.18.2+dfsg-2_amd64.buildinfo f48bed8228fd0de0f8b312b4ea8aaca591b1217c 1080108 libhtsjdk-java-doc_2.18.2+dfsg-2_all.deb f7d6fb2462fb1963f83f8c3999d83c8567d24e63 1499276 libhtsjdk-java_2.18.2+dfsg-2_all.deb Checksums-Sha256: a3e128889825beffaefbe3ded928e8eaef1507cd4c9ee233bd90d00974092cf0 14914 htsjdk_2.18.2+dfsg-2_amd64.buildinfo 4cabef2ab127ed71c3cba9b586ec7ee6c207e4c9e4b26d80777d094f5b393aaf 1080108 libhtsjdk-java-doc_2.18.2+dfsg-2_all.deb 380253ce79b3441324f0dba65151d9af50f6acf9ec70d10fa4abcc9bff175b6c 1499276 libhtsjdk-java_2.18.2+dfsg-2_all.deb Files: 1e010036ed3898eb5442d24e4d3393c8 14914 science optional htsjdk_2.18.2+dfsg-2_amd64.buildinfo 247bb313121f561d946d109a61c4a570 1080108 doc optional libhtsjdk-java-doc_2.18.2+dfsg-2_all.deb 562a270f62e930e6f5acc80d1aa5b539 1499276 java optional libhtsjdk-java_2.18.2+dfsg-2_all.deb Sun Jun 20 15:36:36 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.LASAkCP8BM/htsjdk_2.18.2+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.LASAkCP8BM/htsjdk_2.18.2+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.LASAkCP8BM/htsjdk_2.18.2+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.LASAkCP8BM/b1/htsjdk_2.18.2+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.LASAkCP8BM/b2/htsjdk_2.18.2+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.372s) 0.372s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.121s) 0.120s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jun 20 15:36:38 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Jun 20 15:36:38 UTC 2021 I: htsjdk from buster built successfully and reproducibly on amd64. Sun Jun 20 15:36:50 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Jun 20 15:36:50 UTC 2021 I: Submitting 16K b1/htsjdk_2.18.2+dfsg-2_amd64.buildinfo.asc Sun Jun 20 15:36:51 UTC 2021 I: Submitting 16K b2/htsjdk_2.18.2+dfsg-2_amd64.buildinfo.asc Sun Jun 20 15:36:52 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jun 20 15:36:52 UTC 2021 I: Done submitting .buildinfo files. Sun Jun 20 15:36:52 UTC 2021 I: Removing signed htsjdk_2.18.2+dfsg-2_amd64.buildinfo.asc files: removed './b1/htsjdk_2.18.2+dfsg-2_amd64.buildinfo.asc' removed './b2/htsjdk_2.18.2+dfsg-2_amd64.buildinfo.asc'