I: pbuilder: network access will be disabled during build
I: Current time: Sat May 18 02:01:59 +14 2024
I: pbuilder-time-stamp: 1715947319
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [biojava-live_1.9.7+dfsg-1.dsc]
I: copying [./biojava-live_1.9.7+dfsg.orig.tar.xz]
I: copying [./biojava-live_1.9.7+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Nov 29 07:46:53 2023
gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./biojava-live_1.9.7+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting biojava-live in biojava-live-1.9.7+dfsg
dpkg-source: info: unpacking biojava-live_1.9.7+dfsg.orig.tar.xz
dpkg-source: info: unpacking biojava-live_1.9.7+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying omit_tests_with_problematic_data.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 May 17 12:02 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.21(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=02cdc4b695fe4873ae8d6ca192816aee
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=519350
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5Um3qsL4/pbuilderrc_UU2o --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5Um3qsL4/b2 --logfile b2/build.log biojava-live_1.9.7+dfsg-1.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://46.16.76.132:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 May 17 07:43 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), maven-debian-helper, default-jdk, junit4, libcommons-dbcp-java, libjaxb-api-java, libjgrapht0.8-java, libjgrapht0.8-java-doc, libmaven-javadoc-plugin-java, libxerces2-java
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19719 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on maven-debian-helper; however:
Package maven-debian-helper is not installed.
pbuilder-satisfydepends-dummy depends on default-jdk; however:
Package default-jdk is not installed.
pbuilder-satisfydepends-dummy depends on junit4; however:
Package junit4 is not installed.
pbuilder-satisfydepends-dummy depends on libcommons-dbcp-java; however:
Package libcommons-dbcp-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 libjgrapht0.8-java; however:
Package libjgrapht0.8-java is not installed.
pbuilder-satisfydepends-dummy depends on libjgrapht0.8-java-doc; however:
Package libjgrapht0.8-java-doc is not installed.
pbuilder-satisfydepends-dummy depends on libmaven-javadoc-plugin-java; however:
Package libmaven-javadoc-plugin-java is not installed.
pbuilder-satisfydepends-dummy depends on libxerces2-java; however:
Package libxerces2-java 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:
adwaita-icon-theme{a} ant{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} java-wrappers{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatinject-jsr330-api-java{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbatik-java{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libcairo2{a} libcdi-api-java{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-dbcp-java{a} libcommons-digester-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcommons-pool-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libel-api-java{a} libelf1t64{a} liberror-prone-java{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{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} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libitext1-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjetty9-java{a} libjgraph-java{a} libjgrapht0.8-java{a} libjgrapht0.8-java-doc{a} libjpeg62-turbo{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libnspr4{a} libnss3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libpng16-16t64{a} libproc2-0{a} libqdox-java{a} libqdox2-java{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsub-override-perl{a} libsurefire-java{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunivocity-parsers-java{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebp7{a} libwebsocket-api-java{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxalan2-java{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} po-debconf{a} procps{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} unzip{a} velocity{a} x11-common{a}
The following packages are RECOMMENDED but will NOT be installed:
alsa-topology-conf alsa-ucm-conf ant-optional curl dbus fonts-dejavu-extra icc-profiles-free krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgtk2.0-bin libltdl-dev libmail-sendmail-perl librsvg2-common libsaxon-java libxt-dev lynx mesa-vulkan-drivers psmisc wget xdg-user-dirs
0 packages upgraded, 279 newly installed, 0 to remove and 0 not upgraded.
Need to get 257 MB of archives. After unpacking 720 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-4 [759 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [139 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 46.0-1 [614 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 java-common all 0.75 [6640 B]
Get: 35 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.100-1 [1406 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.2.1-1 [54.8 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B]
Get: 41 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.14-1 [2162 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.52.0-1 [166 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.7-1 [36.4 kB]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-1 [106 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-1 [106 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-1 [122 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-1 [105 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-1 [116 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-1 [108 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-1 [109 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.7-1 [8277 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.7-1 [151 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.11-1 [20.9 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.17-75 [1056 B]
Get: 147 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB]
Get: 148 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B]
Get: 149 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk amd64 17.0.11+9-1 [10.4 kB]
Get: 150 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.17-75 [1068 B]
Get: 151 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 152 http://deb.debian.org/debian unstable/main amd64 java-wrappers all 0.4 [8916 B]
Get: 153 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB]
Get: 154 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-4 [349 kB]
Get: 155 http://deb.debian.org/debian unstable/main amd64 libapiguardian-java all 1.1.2-1 [4656 B]
Get: 156 http://deb.debian.org/debian unstable/main amd64 libopentest4j-java all 1.2.0-4 [9516 B]
Get: 157 http://deb.debian.org/debian unstable/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get: 158 http://deb.debian.org/debian unstable/main amd64 libpicocli-java all 4.6.2-2 [390 kB]
Get: 159 http://deb.debian.org/debian unstable/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get: 160 http://deb.debian.org/debian unstable/main amd64 junit5 all 5.10.1-1 [2458 kB]
Get: 161 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 162 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get: 163 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B]
Get: 164 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7-1 [394 kB]
Get: 165 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get: 166 http://deb.debian.org/debian unstable/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB]
Get: 167 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get: 168 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 169 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.16.1-1 [480 kB]
Get: 170 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 171 http://deb.debian.org/debian unstable/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB]
Get: 172 http://deb.debian.org/debian unstable/main amd64 libbatik-java all 1.17+dfsg-1 [3923 kB]
Get: 173 http://deb.debian.org/debian unstable/main amd64 libbsh-java all 2.0b4-20 [291 kB]
Get: 174 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B]
Get: 175 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-3 [54.3 kB]
Get: 176 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB]
Get: 177 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB]
Get: 178 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB]
Get: 179 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB]
Get: 180 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB]
Get: 181 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 182 http://deb.debian.org/debian unstable/main amd64 libcommons-configuration-java all 1.10-6 [347 kB]
Get: 183 http://deb.debian.org/debian unstable/main amd64 libcommons-pool-java all 1.6-5 [109 kB]
Get: 184 http://deb.debian.org/debian unstable/main amd64 libcommons-dbcp-java all 1.4-8 [157 kB]
Get: 185 http://deb.debian.org/debian unstable/main amd64 libcommons-digester-java all 1.8.1-6 [137 kB]
Get: 186 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB]
Get: 187 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 188 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 189 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 190 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.0-2 [29.0 kB]
Get: 191 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B]
Get: 192 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB]
Get: 193 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.9-1 [143 kB]
Get: 194 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 195 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB]
Get: 196 http://deb.debian.org/debian unstable/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB]
Get: 197 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB]
Get: 198 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get: 201 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB]
Get: 202 http://deb.debian.org/debian unstable/main amd64 libguice-java all 4.2.3-2 [1435 kB]
Get: 203 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 35-1 [6140 B]
Get: 204 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 205 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB]
Get: 206 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 207 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 208 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 209 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 210 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB]
Get: 211 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB]
Get: 212 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB]
Get: 213 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 214 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB]
Get: 215 http://deb.debian.org/debian unstable/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get: 216 http://deb.debian.org/debian unstable/main amd64 libcommons-text-java all 1.11.0-1 [217 kB]
Get: 217 http://deb.debian.org/debian unstable/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB]
Get: 218 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-4 [214 kB]
Get: 219 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.4-1 [312 kB]
Get: 220 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 221 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 222 http://deb.debian.org/debian unstable/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB]
Get: 223 http://deb.debian.org/debian unstable/main amd64 libfontbox2-java all 2.0.29-1 [1510 kB]
Get: 224 http://deb.debian.org/debian unstable/main amd64 libqdox-java all 1.12.1-3 [172 kB]
Get: 225 http://deb.debian.org/debian unstable/main amd64 libfop-java all 1:2.8-3 [10.1 MB]
Get: 226 http://deb.debian.org/debian unstable/main amd64 libitext1-java all 1.4-7 [1257 kB]
Get: 227 http://deb.debian.org/debian unstable/main amd64 libxbean-reflect-java all 4.5-8 [133 kB]
Get: 228 http://deb.debian.org/debian unstable/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 229 http://deb.debian.org/debian unstable/main amd64 libdoxia-java all 1.12.0-1 [459 kB]
Get: 230 http://deb.debian.org/debian unstable/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B]
Get: 231 http://deb.debian.org/debian unstable/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB]
Get: 232 http://deb.debian.org/debian unstable/main amd64 velocity all 1.7-7 [431 kB]
Get: 233 http://deb.debian.org/debian unstable/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB]
Get: 234 http://deb.debian.org/debian unstable/main amd64 liboro-java all 2.0.8a-14 [70.5 kB]
Get: 235 http://deb.debian.org/debian unstable/main amd64 libvelocity-tools-java all 2.0-9 [311 kB]
Get: 236 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 237 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 238 http://deb.debian.org/debian unstable/main amd64 libxalan2-java all 2.7.2-4 [3419 kB]
Get: 239 http://deb.debian.org/debian unstable/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB]
Get: 240 http://deb.debian.org/debian unstable/main amd64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 241 http://deb.debian.org/debian unstable/main amd64 libjansi-java all 2.4.1-2 [100 kB]
Get: 242 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 243 http://deb.debian.org/debian unstable/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 244 http://deb.debian.org/debian unstable/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 245 http://deb.debian.org/debian unstable/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 246 http://deb.debian.org/debian unstable/main amd64 libjetty9-java all 9.4.54-1 [2980 kB]
Get: 247 http://deb.debian.org/debian unstable/main amd64 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB]
Get: 248 http://deb.debian.org/debian unstable/main amd64 libjgrapht0.8-java all 0.8.3-6 [214 kB]
Get: 249 http://deb.debian.org/debian unstable/main amd64 libjgrapht0.8-java-doc all 0.8.3-6 [379 kB]
Get: 250 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 251 http://deb.debian.org/debian unstable/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB]
Get: 252 http://deb.debian.org/debian unstable/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB]
Get: 253 http://deb.debian.org/debian unstable/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB]
Get: 254 http://deb.debian.org/debian unstable/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB]
Get: 255 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-incremental-java all 1.1-4 [9924 B]
Get: 256 http://deb.debian.org/debian unstable/main amd64 libplexus-compiler-java all 2.12.1-2 [99.0 kB]
Get: 257 http://deb.debian.org/debian unstable/main amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get: 258 http://deb.debian.org/debian unstable/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
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Get: 274 http://deb.debian.org/debian unstable/main amd64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 275 http://deb.debian.org/debian unstable/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB]
Get: 276 http://deb.debian.org/debian unstable/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.3+b3 [99.0 kB]
Get: 277 http://deb.debian.org/debian unstable/main amd64 maven all 3.8.7-2 [19.3 kB]
Get: 278 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB]
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Setting up libsnappy-java (1.1.10.5-2) ...
Setting up libfontconfig1:amd64 (2.15.0-1.1) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libcommons-configuration-java (1.10-6) ...
Setting up libwagon-file-java (3.5.3-1) ...
Setting up libxml2-utils (2.9.14+dfsg-1.3+b3) ...
Setting up libcommons-codec-java (1.16.0-1) ...
Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ...
Setting up libavahi-client3:amd64 (0.8-13+b2) ...
Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ...
Setting up libxcb-dri3-0:amd64 (1.17.0-1) ...
Setting up gtk-update-icon-cache (3.24.41-4) ...
Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ...
Setting up velocity (1.7-7) ...
Setting up fontconfig (2.15.0-1.1) ...
Regenerating fonts cache... done.
Setting up libdrm-nouveau2:amd64 (2.4.120-2) ...
Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ...
Setting up libcommons-compress-java (1.25.0-1) ...
Setting up libcommons-io-java (2.16.1-1) ...
Setting up libdrm-radeon1:amd64 (2.4.120-2) ...
Setting up libcommons-digester-java (1.8.1-6) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ...
Setting up libdrm-intel1:amd64 (2.4.120-2) ...
Setting up libgl1-mesa-dri:amd64 (24.0.7-1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b1) ...
Setting up libxmlgraphics-commons-java (2.8-2) ...
Setting up man-db (2.12.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:amd64 (1.18.0-3+b1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up libmaven-filtering-java (3.3.0-1) ...
Setting up libmaven-resolver-java (1.6.3-1) ...
Setting up adwaita-icon-theme (46.0-1) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ...
Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ...
Setting up libxrandr2:amd64 (2:1.5.4-1) ...
Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libmaven-shared-utils-java (3.3.4-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ...
Setting up libmaven-resources-plugin-java (3.3.0-1) ...
Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ...
Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libglx-mesa0:amd64 (24.0.7-1) ...
Setting up libxi6:amd64 (2:1.8.1-1) ...
Setting up libglx0:amd64 (1.7.0-1+b1) ...
Setting up libcommons-validator-java (1:1.7-1) ...
Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ...
Setting up libbatik-java (1.17+dfsg-1) ...
Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ...
Setting up libmaven-invoker-java (3.2.0-1) ...
Setting up debhelper (13.15.3) ...
Setting up libgl1:amd64 (1.7.0-1+b1) ...
Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ...
Setting up libmaven-clean-plugin-java (3.2.0-2) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libfop-java (1:2.8-3) ...
Setting up libmaven-archiver-java (3.6.0-1) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libguava-java (32.0.1-1) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up libguice-java (4.2.3-2) ...
Setting up libplexus-i18n-java (1.0-beta-10-6) ...
Setting up libplexus-container-default1.5-java (2.1.1-1) ...
Setting up libplexus-interactivity-api-java (1.1-2) ...
Setting up libplexus-velocity-java (1.2-3.1) ...
Setting up libmaven3-core-java (3.8.7-2) ...
Setting up libmaven-shared-incremental-java (1.1-4) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ...
Setting up libplexus-compiler-java (2.12.1-2) ...
Setting up libmaven-compiler-plugin-java (3.10.1-2) ...
Setting up libmaven-artifact-transfer-java (0.13.1-2) ...
Setting up libmaven-file-management-java (3.0.0-1) ...
Setting up libmaven-jar-plugin-java (3.3.0-2) ...
Setting up libcommons-text-java (1.11.0-1) ...
Setting up libdoxia-core-java (1.12.0-1) ...
Setting up libdoxia-java (1.12.0-1) ...
Setting up libmaven-reporting-api-java (3.1.1-1) ...
Setting up libmaven-reporting-exec-java (1.6.0-1) ...
Processing triggers for libc-bin (2.38-11) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_FÅ‘tanúsÃtvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up maven-repo-helper (1.11) ...
Setting up maven (3.8.7-2) ...
update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode
Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up ant (1.10.14-1) ...
Setting up junit4 (4.13.2-4) ...
Setting up default-jre-headless (2:1.17-75) ...
Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ...
Setting up default-jre (2:1.17-75) ...
Setting up openjdk-17-jdk:amd64 (17.0.11+9-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ...
Setting up default-jdk-headless (2:1.17-75) ...
Setting up junit5 (5.10.1-1) ...
Setting up default-jdk (2:1.17-75) ...
Processing triggers for sgml-base (1.31) ...
Setting up libvelocity-tools-java (2.0-9) ...
Setting up libdoxia-sitetools-java (1.11.1-1) ...
Setting up libmaven-site-plugin-java (3.12.1-2) ...
Setting up libmaven-javadoc-plugin-java (3.4.1-3) ...
Setting up libmaven-reporting-impl-java (3.2.0-2) ...
Setting up libmaven-plugin-tools-java (3.7.1-1) ...
Setting up libsurefire-java (2.22.3-2) ...
Setting up maven-debian-helper (2.6.4) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20240118) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/biojava-live-1.9.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava-live_1.9.7+dfsg-1_source.changes
dpkg-buildpackage: info: source package biojava-live
dpkg-buildpackage: info: source version 1:1.9.7+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Pierre Gruet
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_auto_clean
bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
mh_unpatchpoms -plibbiojava1.9-java
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
mh_patchpoms -plibbiojava1.9-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo
dh_auto_build
/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.7\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] biojava-legacy [pom]
[INFO] bytecode [jar]
[INFO] core [jar]
[INFO] alignment [jar]
[INFO] biosql [jar]
[INFO] blast [jar]
[INFO] sequencing [jar]
[INFO] gui [jar]
[INFO] phylo [jar]
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] ---------------------< org.biojava:biojava-legacy >---------------------
[INFO] Building biojava-legacy 1.9.7 [1/9]
[INFO] --------------------------------[ pom ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-legacy ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO]
[INFO] ------------------------< org.biojava:bytecode >------------------------
[INFO] Building bytecode 1.9.7 [2/9]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bytecode ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ bytecode ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 44 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Some input files use or override a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bytecode ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ bytecode ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ bytecode ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ bytecode ---
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/bytecode-1.9.7.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ bytecode ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1347: warning: @param argument "lockVar" is not a parameter name.
[WARNING] * @param lockVar Label for the local variable to lock on
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/package.html:146: warning: invalid input: '<'
[WARNING] This will need a constructor. Remember, constructors have the name >init<:,
[WARNING] ^
[WARNING] 3 warnings
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/target/bytecode-1.9.7-javadoc.jar
[INFO]
[INFO] --------------------------< org.biojava:core >--------------------------
[INFO] Building core 1.9.7 [3/9]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ core ---
[INFO] Copying 29 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ core ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1063 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/dist/DistributionTools.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SuffixTree.java: Some input files use or override a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/SuffixTree.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/regex/Search.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/regex/Search.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ core ---
[INFO] Copying 53 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ core ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 148 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/test-classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/seq/io/SeqIOToolsTest.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ontology/SimpleComparableTermTest.java: Some input files use or override a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojavax/ontology/SimpleComparableTermTest.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/test/java/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ core ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ core ---
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/core-1.9.7.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ core ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/proteomics/aaindex/AAindexStreamReader.java:55: warning: invalid input: '<'
[WARNING] * for (int i = 1; i <= symbols.length(); i++) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/AbstractAlphabet.java:51: warning: invalid input: '<'
[WARNING] * This provides the frame-work for maintaining the SymbolParser <-> name
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/AlphabetIndex.java:60: warning: invalid input: '&'
[WARNING] * The previous & changed fields should be arrays of symbols in the order they
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bibliography/BibRefQuery.java:625: warning: invalid input: '&'
[WARNING] * @param properties FIXME: docs & params out of sync
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&'
[WARNING] * An extention of JComponent that contains the points & encapsulates the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&'
[WARNING] * An extention of JComponent that contains the points & encapsulates the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:331: warning: invalid input: '&'
[WARNING] * Hooks up the mouse listener & cursor.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:332: warning: invalid input: '&'
[WARNING] * Chooses default colors & Shapes.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:255: warning: invalid input: '&'
[WARNING] * The index for a symbol is stable accross virtual machines &
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:284: warning: invalid input: '&'
[WARNING] * The index for a symbol is stable accross virtual machines &
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<'
[WARNING] * <123 or >123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<'
[WARNING] * @param sb a StringBuffer
123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:47: warning: invalid input: '<'
[WARNING] * <123 or >123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<'
[WARNING] * SimilarityPairFeature and its score is <= filter's minimum
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<'
[WARNING] * SimilarityPairFeature and its score is <= filter's minimum
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/FuzzyPointLocation.java:34: warning: invalid input: '<'
[WARNING] * the '<123' or '>123' type, which represent an unbounded location,
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<'
[WARNING] * <123 or >123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<'
[WARNING] * @param sb a StringBuffer
delete transitions allowed
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/blast2html/HTMLRenderer.java:116: warning: invalid input: '<'
[WARNING] * formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/NucleotideTools.java:380: warning: invalid input: '&'
[WARNING] * The index for a symbol is stable accross virtual machines &
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/NucleotideTools.java:442: warning: invalid input: '&'
[WARNING] * The index for a symbol is stable accross virtual machines &
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/ontology/obo/OboFileParser.java:49: warning: invalid input: '&view'
[WARNING] * http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/process/OutputHandler.java:33: warning: invalid usage of tag {@linkplain java.lang.Process#getOutputStream()()
[WARNING] * {@linkplain java.lang.Process#getOutputStream()() STDOUT} output and/or the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<'
[WARNING] * <123 or >123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] 100 warnings
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/target/core-1.9.7-javadoc.jar
[INFO]
[INFO] -----------------------< org.biojava:alignment >------------------------
[INFO] Building alignment 1.9.7 [4/9]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ alignment ---
[INFO] Copying 89 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ alignment ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 14 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java uses or overrides a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java: Recompile with -Xlint:removal for details.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ alignment ---
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ alignment ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 5 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/test-classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java uses unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/test/java/org/biojava/bio/alignment/FlexibleAlignmentTest.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ alignment ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ alignment ---
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/alignment-1.9.7.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ alignment ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/AlignmentAlgorithm.java:39: warning: invalid input: '<'
[WARNING] * @author Andreas Dräger
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:217: warning: @param argument "queryLength" is not a parameter name.
[WARNING] * @param queryLength
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/EditableAlignment.java:35: warning: invalid input: '<'
[WARNING] * shifted to the right with offset > 1 to the left with offset <
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/SubstitutionMatrix.java:65: warning: invalid input: '<'
[WARNING] * @author Andreas Dräger
[WARNING] ^
[WARNING] 5 warnings
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/target/alignment-1.9.7-javadoc.jar
[INFO]
[INFO] -------------------------< org.biojava:biosql >-------------------------
[INFO] Building biosql 1.9.7 [5/9]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biosql ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biosql ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 35 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java: Some input files use or override a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDB.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/BioSQLSequence.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biosql ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biosql ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 2 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/test-classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java uses or overrides a deprecated API.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/java/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: Recompile with -Xlint:deprecation for details.
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biosql ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biosql ---
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/biosql-1.9.7.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biosql ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] 1 warning
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/target/biosql-1.9.7-javadoc.jar
[INFO]
[INFO] -------------------------< org.biojava:blast >--------------------------
[INFO] Building blast 1.9.7 [6/9]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ blast ---
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ blast ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 56 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java uses or overrides a deprecated API.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ blast ---
[INFO] Copying 22 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ blast ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 19 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/test-classes
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ blast ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ blast ---
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/blast-1.9.7.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ blast ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/src/main/java/org/biojava/bio/program/BlastLikeToXMLConverter.java:61: warning: invalid input: '<'
[WARNING] * * looks something like then,
[WARNING] ^
[WARNING] 2 warnings
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/target/blast-1.9.7-javadoc.jar
[INFO]
[INFO] -----------------------< org.biojava:sequencing >-----------------------
[INFO] Building sequencing 1.9.7 [7/9]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ sequencing ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ sequencing ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 33 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/AbstractChromatogram.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java: Some input files use or override a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/abi/ABIFParser.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/abi/ABIFParser.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ sequencing ---
[INFO] Copying 77 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ sequencing ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 15 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/test-classes
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ sequencing ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ sequencing ---
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/sequencing-1.9.7.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ sequencing ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:1074: warning: invalid input: '&'
[WARNING] * Default value: {@link BasicStroke} with width 1.0, default cap & join.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/ChromatogramTools.java:67: warning: invalid input: '<'
[WARNING] * for (int i = m ; i < n ; i++)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java:169: warning: invalid input: '&returned'
[WARNING] * PROB_UNDERCALL
are just reversed &returned.
[WARNING] ^
[WARNING] 4 warnings
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/target/sequencing-1.9.7-javadoc.jar
[INFO]
[INFO] --------------------------< org.biojava:gui >---------------------------
[INFO] Building gui 1.9.7 [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.4 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:2.4: Plugin org.apache.maven.plugins:maven-install-plugin:2.4 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-install-plugin:jar:2.4 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:2.7: Plugin org.apache.maven.plugins:maven-deploy-plugin:2.7 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-deploy-plugin:jar:2.7 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:1.3: Plugin org.apache.maven.plugins:maven-antrun-plugin:1.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5: Plugin org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:2.8: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.8 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-dependency-plugin:jar:2.8 has not been downloaded from it before.
[WARNING] The POM for org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 is missing, no dependency information available
[WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:2.5.3: Plugin org.apache.maven.plugins:maven-release-plugin:2.5.3 or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.apache.maven.plugins:maven-release-plugin:jar:2.5.3 has not been downloaded from it before.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ gui ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ gui ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 99 source files to /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/target/classes
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequenceRendererWrapper.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/SequenceRendererWrapper.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Some input files use or override a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java: Recompile with -Xlint:unchecked for details.
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ gui ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ gui ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ gui ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ gui ---
[INFO] Building jar: /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/target/gui-1.9.7.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ gui ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/LogoPainter.java:30: warning: invalid input: '&'
[WARNING] * calculations for sizes & information and the like. The LogoPainter renders
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/glyph/RectangleGlyph.java:32: warning: invalid input: '<'
[WARNING] * @author then,
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1347: warning: @param argument "lockVar" is not a parameter name.
[WARNING] * @param lockVar Label for the local variable to lock on
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:1074: warning: invalid input: '&'
[WARNING] * Default value: {@link BasicStroke} with width 1.0, default cap & join.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/java/org/biojava/bio/chromatogram/ChromatogramTools.java:67: warning: invalid input: '<'
[WARNING] * for (int i = m ; i < n ; i++)
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&'
[WARNING] * An extention of JComponent that contains the points & encapsulates the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:150: warning: invalid input: '&'
[WARNING] * An extention of JComponent that contains the points & encapsulates the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:331: warning: invalid input: '&'
[WARNING] * Hooks up the mouse listener & cursor.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/stats/svm/tools/ClassifierExample.java:332: warning: invalid input: '&'
[WARNING] * Chooses default colors & Shapes.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:255: warning: invalid input: '&'
[WARNING] * The index for a symbol is stable accross virtual machines &
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/DNATools.java:284: warning: invalid input: '&'
[WARNING] * The index for a symbol is stable accross virtual machines &
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/src/main/java/org/biojava/bio/alignment/EditableAlignment.java:35: warning: invalid input: '<'
[WARNING] * shifted to the right with offset > 1 to the left with offset <
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<'
[WARNING] * <123 or >123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<'
[WARNING] * @param sb a StringBuffer
123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblLikeLocationParser.java:55: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:47: warning: invalid input: '<'
[WARNING] * <123 or >123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/EmblProcessor.java:53: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<'
[WARNING] * SimilarityPairFeature and its score is <= filter's minimum
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/FeatureFilter.java:1657: warning: invalid input: '<'
[WARNING] * SimilarityPairFeature and its score is <= filter's minimum
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:86: warning: invalid input: '&'
[WARNING] * be transient and lazily instantiated. Be sure to register & unregister the
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/FuzzyPointLocation.java:34: warning: invalid input: '<'
[WARNING] * the '<123' or '>123' type, which represent an unbounded location,
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:486: warning: invalid input: '<'
[WARNING] * <123 or >123
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:492: warning: invalid input: '<'
[WARNING] * <123..567 or 123..>567 or <123..>567
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/seq/io/AbstractGenEmblFileFormer.java:503: warning: invalid input: '<'
[WARNING] * @param sb a StringBuffer
delete transitions allowed
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/blast2html/HTMLRenderer.java:116: warning: invalid input: '<'
[WARNING] * formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&cvsroot'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/program/formats/Format.java:68: warning: invalid input: '&content'
[WARNING] * the odda formats specification.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/bio/symbol/Location.java:146: warning: invalid input: '&'
[WARNING] * a.contains(b) && b.contains(a). You should call LocationTools.areEqual
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/LogoPainter.java:30: warning: invalid input: '&'
[WARNING] * calculations for sizes & information and the like. The LogoPainter renders
[WARNING] ^
[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/core/src/main/java/org/biojava/utils/AbstractChangeable.java:76: warning: invalid input: '&'
[WARNING] * if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
[WARNING] ^
[WARNING] 100 warnings
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava-legacy 1.9.7:
[INFO]
[INFO] biojava-legacy ..................................... SUCCESS [01:51 min]
[INFO] bytecode ........................................... SUCCESS [ 13.830 s]
[INFO] core ............................................... SUCCESS [01:40 min]
[INFO] alignment .......................................... SUCCESS [ 34.971 s]
[INFO] biosql ............................................. SUCCESS [ 34.377 s]
[INFO] blast .............................................. SUCCESS [ 17.994 s]
[INFO] sequencing ......................................... SUCCESS [ 27.872 s]
[INFO] gui ................................................ SUCCESS [ 42.808 s]
[INFO] phylo .............................................. SUCCESS [ 21.692 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 06:47 min
[INFO] Finished at: 2024-05-17T12:11:29Z
[INFO] ------------------------------------------------------------------------
dh_auto_test
/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.7\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode test
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] biojava-legacy [pom]
[INFO] bytecode [jar]
[INFO] core [jar]
[INFO] alignment [jar]
[INFO] biosql [jar]
[INFO] blast [jar]
[INFO] sequencing [jar]
[INFO] gui [jar]
[INFO] phylo [jar]
[INFO]
[INFO] ---------------------< org.biojava:biojava-legacy >---------------------
[INFO] Building biojava-legacy 1.9.7 [1/9]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO]
[INFO] ------------------------< org.biojava:bytecode >------------------------
[INFO] Building bytecode 1.9.7 [2/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bytecode ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ bytecode ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bytecode ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ bytecode ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ bytecode ---
[INFO] No tests to run.
[INFO]
[INFO] --------------------------< org.biojava:core >--------------------------
[INFO] Building core 1.9.7 [3/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ core ---
[INFO] Copying 29 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ core ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ core ---
[INFO] Copying 53 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ core ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ core ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojavax.SimpleDocRefTest
testGetTitle
testToString
testGetLocation
testSetCrossref
testGetCrossref
testCompareTo
testGetAuthors
testGetAuthorList
testHashCode
testSetRemark
testEquals
testGetCRC
testGetRemark
[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 s - in org.biojavax.SimpleDocRefTest
[INFO] Running org.biojavax.SimpleCrossRefTest
testGetNoteSet
testGetAccession
testToString
testCompareTo
testGetAnnotation
testSetNoteSet
testGetVersion
testHashCode
testGetDbname
testEquals
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojavax.SimpleCrossRefTest
[INFO] Running org.biojavax.SimpleRankedDocRefTest
testGetStart
testSetLocation
testToString
testGetDocumentReference
testCompareTo
testGetRank
testHashCode
testEquals
testGetEnd
testSetRank
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojavax.SimpleRankedDocRefTest
[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojavax.ga.functions.ProportionalSelectionTest
[INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.9 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest
[INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest
[INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest
[INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest
[INFO] Running org.biojavax.ga.impl.SimpleOrganismTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.impl.SimpleOrganismTest
[INFO] Running org.biojavax.ga.impl.SimplePopulationTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.ga.impl.SimplePopulationTest
[INFO] Running org.biojavax.ga.util.WeightedSetTest
[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.ga.util.WeightedSetTest
[INFO] Running org.biojavax.ga.util.GAToolsTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojavax.ga.util.GAToolsTest
[INFO] Running org.biojavax.EmptyRichAnnotationTest
testGetNoteSet
testAddNote
testAsMap
testClear
testKeys
testGetNote
testSetNoteSet
testContains
testSetProperty
testRemoveNote
testGetProperty
testRemoveProperty
testEquals
testContainsProperty
[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.EmptyRichAnnotationTest
[INFO] Running org.biojavax.ontology.SimpleComparableTermTest
testSetDescription
testGetRankedCrossRefs
testToString
testGetSynonyms
testCompareTo
testAddSynonym
testGetName
testGetOntology
testSetRankedCrossRefs
testGetIdentifier
testGetAnnotation
testRemoveRankedCrossRef
testGetDescription
testSetIdentifier
testHashCode
testEquals
testAddRankedCrossRef
testRemoveSynonym
testSetObsolete
testGetObsolete
[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojavax.ontology.SimpleComparableTermTest
[INFO] Running org.biojavax.ontology.SimpleComparableTripleTest
testGetSubject
testSetDescriptors
testToString
testGetSynonyms
testRemoveDescriptor
testCompareTo
testAddSynonym
testGetName
testGetOntology
testGetPredicate
testGetAnnotation
testGetDescription
testGetDescriptors
testHashCode
testAddDescriptor
testEquals
testGetObject
testRemoveSynonym
[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojavax.ontology.SimpleComparableTripleTest
[INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest
testSetTripleSet
testCreateTriple
testContainsTriple
testGetTerms
testCreateVariable
testContainsTerm
testGetTermSet
testSetDescription
testToString
testGetOrCreateTerm
testCompareTo
testGetTriples
testGetName
testGetTerm
testGetOrImportTerm
testGetTripleSet
testCreateTerm
testGetDescription
testSetTermSet
testHashCode
testDeleteTerm
testEquals
testGetOps
testImportTerm
[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojavax.ontology.SimpleComparableOntologyTest
[INFO] Running org.biojavax.bio.SimpleBioEntryTest
testGetNamespace
testGetNoteSet
testGetRankedDocRefs
testGetRelationships
testGetTaxon
testSetDescription
testGetAccession
testGetRankedCrossRefs
testToString
testCompareTo
testGetName
testRemoveComment
testSetRankedCrossRefs
testGetIdentifier
testGetAnnotation
testSetNoteSet
testRemoveRankedCrossRef
testRemoveRankedDocRef
testRemoveRelationship
testGetVersion
testGetDescription
testSetIdentifier
testGetComments
testHashCode
testEquals
testAddRankedCrossRef
testAddRankedDocRef
testAddRelationship
testSetDivision
testGetDivision
testSetTaxon
testAddComment
[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojavax.bio.SimpleBioEntryTest
[INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest
Location 467: 467
Location 340..565: 340..565
Location <345..500: <345..500
Location <1..888: <1..888
Location (102.110): (102.110)
Location (23.45)..600: (23.45)..600
Location (122.133)..(204.221): (122.133)..(204.221)
Location 123^124: 123^124
Location 145^177: 145^177
Location join(12..78,134..202): join(12..78,134..202)
Location complement(1..23): complement(1..23)
Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163))
Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163))
Location complement(34..(122.126)): complement(34..(122.126))
Location complement((122.126)..34): complement((122.126)..34)
Location J00194:100..202: J00194:100..202
Location (8298.8300)..10206: (8298.8300)..10206
Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855)
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest
[INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojavax.bio.seq.io.EMBLFormatTest
[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.263 s - in org.biojavax.bio.seq.io.GenbankFormatTest
[INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojavax.bio.seq.io.UniProtFormatTest
[INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojavax.bio.seq.io.Bug2249_2248Test
[INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.399 s - in org.biojavax.bio.seq.io.Bug2250_2256Test
[INFO] Running org.biojavax.bio.seq.io.Bug2255Test
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.seq.io.Bug2255Test
[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 s - in org.biojavax.bio.seq.io.INSDseqFormatTest
[INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest
testEquals
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest
[INFO] Running org.biojavax.bio.seq.RichLocationToolsTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojavax.bio.seq.RichLocationToolsTest
[INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest
testEquals
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.CompoundRichLocationTest
[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojavax.bio.seq.SimpleRichFeatureTest
[INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest
testEquals
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.seq.SimpleRichLocationTest
[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest
testGetNameClass
testToString
testCompareTo
testSetNameClass
testGetName
testHashCode
testEquals
testSetName
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest
[INFO] Running org.biojavax.SimpleNoteTest
testGetValue
testToString
testCompareTo
testGetRank
testGetTerm
testHashCode
testEquals
testSetRank
testSetTerm
testSetValue
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojavax.SimpleNoteTest
[INFO] Running org.biojavax.DummyCrossReferenceResolverTest
testGetRemoteBioEntry
testGetRemoteSymbolList
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojavax.DummyCrossReferenceResolverTest
[INFO] Running org.biojavax.SimpleNamespaceTest
testGetAuthority
testSetDescription
testToString
testGetAcronym
testCompareTo
testGetName
testSetAuthority
testGetDescription
testHashCode
testSetAcronym
testEquals
testGetURI
testSetURI
[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojavax.SimpleNamespaceTest
[INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.CrossReferenceResolutionExceptionTest
[INFO] Running org.biojavax.SimpleRankedCrossRefTest
testToString
testGetCrossRef
testCompareTo
testGetRank
testHashCode
testEquals
testSetRank
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.SimpleRankedCrossRefTest
[INFO] Running org.biojavax.SimpleDocRefAuthorTest
testIsConsortium
testToString
testCompareTo
testGetName
testHashCode
testEquals
testGetExtendedName
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.SimpleDocRefAuthorTest
[INFO] Running org.biojavax.SimpleRichAnnotationTest
testGetNoteSet
testAddNote
testAsMap
testClear
testKeys
testToString
testGetNote
testSetNoteSet
testContains
testGetPropertys
testSetProperty
testRemoveNote
testGetProperty
testRemoveProperty
testRemoveProperty2
testContainsProperty
[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojavax.SimpleRichAnnotationTest
[INFO] Running org.biojavax.SimpleCommentTest
testSetComment
testToString
testCompareTo
testGetRank
testHashCode
testGetComment
testEquals
testSetRank
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleCommentTest
[INFO] Running org.biojava.utils.process.ExternalProcessTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.418 s - in org.biojava.utils.process.ExternalProcessTest
[INFO] Running org.biojava.utils.process.AllTests
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.157 s - in org.biojava.utils.process.AllTests
[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest
[INFO] Running org.biojava.utils.walker.WalkerFactoryTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 s - in org.biojava.utils.walker.WalkerFactoryTest
[INFO] Running org.biojava.utils.walker.WalkerTest
Increasing counter: Overlaps([20,50])
Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)
Increasing counter: Overlaps([20,50])
Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature))
Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature)
Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature)
Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))
Increasing counter: Overlaps([20,50])
Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))
OverlapsLocation: Overlaps([20,50])
Feature: ByClass(org.biojava.bio.seq.StrandedFeature)
Feature: ByClass(org.biojava.bio.seq.ComponentFeature)
Feature: ByClass(org.biojava.bio.seq.StrandedFeature)
Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))
OverlapsLocation: Overlaps([20,50])
Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)))
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.393 s - in org.biojava.utils.walker.WalkerTest
[INFO] Running org.biojava.utils.RepeatedCharSequenceTest
JAM
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.utils.RepeatedCharSequenceTest
[INFO] Running org.biojava.utils.regex.PatternCheckerTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.regex.PatternCheckerTest
[INFO] Running org.biojava.utils.regex.RegexTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.utils.regex.RegexTest
[INFO] Running org.biojava.utils.SmallMapTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.SmallMapTest
[INFO] Running org.biojava.utils.automata.NfaTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.utils.automata.NfaTest
[INFO] Running org.biojava.utils.ListToolsTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.ListToolsTest
[INFO] Running org.biojava.ontology.OntologyTest
[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.ontology.OntologyTest
[INFO] Running org.biojava.ontology.TermImplTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TermImplTest
[INFO] Running org.biojava.ontology.ParseOBOFileTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 s - in org.biojava.ontology.ParseOBOFileTest
[INFO] Running org.biojava.ontology.TripleImplTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest
[INFO] Running org.biojava.bio.search.SeqContentPatternTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SeqContentPatternTest
[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest
[INFO] Running org.biojava.bio.search.MaxMismatchPatternTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.MaxMismatchPatternTest
[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest
[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest
[INFO] Running org.biojava.bio.proteomics.MassCalcTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.proteomics.MassCalcTest
[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest
[INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest
java.lang.NullPointerException: name is null.
at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172)
at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at junit.framework.TestCase.runTest(TestCase.java:177)
at junit.framework.TestCase.runBare(TestCase.java:142)
at junit.framework.TestResult$1.protect(TestResult.java:122)
at junit.framework.TestResult.runProtected(TestResult.java:142)
at junit.framework.TestResult.run(TestResult.java:125)
at junit.framework.TestCase.run(TestCase.java:130)
at junit.framework.TestSuite.runTest(TestSuite.java:241)
at junit.framework.TestSuite.run(TestSuite.java:236)
at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159)
at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418)
org.biojava.bio.seq.db.IllegalIDException: No table found with name test.
at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175)
at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at junit.framework.TestCase.runTest(TestCase.java:177)
at junit.framework.TestCase.runBare(TestCase.java:142)
at junit.framework.TestResult$1.protect(TestResult.java:122)
at junit.framework.TestResult.runProtected(TestResult.java:142)
at junit.framework.TestResult.run(TestResult.java:125)
at junit.framework.TestCase.run(TestCase.java:130)
at junit.framework.TestSuite.runTest(TestSuite.java:241)
at junit.framework.TestSuite.run(TestSuite.java:236)
at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159)
at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418)
java.lang.NullPointerException: table is null.
at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145)
at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at junit.framework.TestCase.runTest(TestCase.java:177)
at junit.framework.TestCase.runBare(TestCase.java:142)
at junit.framework.TestResult$1.protect(TestResult.java:122)
at junit.framework.TestResult.runProtected(TestResult.java:142)
at junit.framework.TestResult.run(TestResult.java:125)
at junit.framework.TestCase.run(TestCase.java:130)
at junit.framework.TestSuite.runTest(TestSuite.java:241)
at junit.framework.TestSuite.run(TestSuite.java:236)
at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159)
at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418)
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest
[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest
[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest
org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN
at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327)
at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601)
at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67)
at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at junit.framework.TestCase.runTest(TestCase.java:177)
at junit.framework.TestCase.runBare(TestCase.java:142)
at junit.framework.TestResult$1.protect(TestResult.java:122)
at junit.framework.TestResult.runProtected(TestResult.java:142)
at junit.framework.TestResult.run(TestResult.java:125)
at junit.framework.TestCase.run(TestCase.java:130)
at junit.framework.TestSuite.runTest(TestSuite.java:241)
at junit.framework.TestSuite.run(TestSuite.java:236)
at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159)
at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418)
[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.proteomics.aaindex.AAindexTest
[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest
[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.molbio.RestrictionEnzymeTest
[INFO] Running org.biojava.bio.dp.MarkovModelEventTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.dp.MarkovModelEventTest
[INFO] Running org.biojava.bio.dp.DPSerializationTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.347 s - in org.biojava.bio.dp.DPSerializationTest
[INFO] Running org.biojava.bio.dp.EmissionStateEventTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dp.EmissionStateEventTest
[INFO] Running org.biojava.bio.MergeAnnotationTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.MergeAnnotationTest
[INFO] Running org.biojava.bio.dist.DistSerTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.bio.dist.DistSerTest
[INFO] Running org.biojava.bio.dist.DistributionTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dist.DistributionTest
[INFO] Running org.biojava.bio.dist.DistributionToolsTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.bio.dist.DistributionToolsTest
[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dist.TranslatedDistributionTest
[INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.944 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest
[INFO] Running org.biojava.bio.symbol.MergeLocationTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest
[INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest
[INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet
[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet
[INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.212 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest
[INFO] Running org.biojava.bio.symbol.AlphabetManagerTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.AlphabetManagerTest
[INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest
Adding symbol list taccaccagga$
Adding symbol list taccaccagga$
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest
[INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CodonPrefToolsTest
[INFO] Running org.biojava.bio.symbol.SymbolListTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.14 s - in org.biojava.bio.symbol.SymbolListTest
[INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.SimpleSymbolEventTest
[INFO] Running org.biojava.bio.symbol.CircularLocationTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.symbol.CircularLocationTest
[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.symbol.GappedSymbolListTest
[INFO] Running org.biojava.bio.symbol.CompoundLocationTest
[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.bio.symbol.CompoundLocationTest
[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest
[INFO] Running org.biojava.bio.symbol.RangeLocationTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest
[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.symbol.SymbolSerializationTest
[INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest
symbolForIndex
getAlphabet
indexForSymbol
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest
[INFO] Running org.biojava.bio.symbol.NameTokenizationTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.symbol.NameTokenizationTest
[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IntegerAlphabetTest
[INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CrossProductTokenizationTest
[INFO] Running org.biojava.bio.symbol.TranslationTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TranslationTest
[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.bio.symbol.AlphabetSerializationTest
[INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest
[INFO] Running org.biojava.bio.symbol.BetweenLocationTest
[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.BetweenLocationTest
[INFO] Running org.biojava.bio.symbol.PointLocationTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.PointLocationTest
[INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.DoubleAlphabetTest
[INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest
[INFO] Running org.biojava.bio.symbol.MotifToolsTest
[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.MotifToolsTest
[INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolListTest
[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleCodonPrefTest
[INFO] Running org.biojava.bio.AnnotationTypeTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.AnnotationTypeTest
[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.bio.seq.NewSimpleAssemblyTest
[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.275 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest
[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest
[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest
idb length: 79
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.709 s - in org.biojava.bio.seq.io.SeqIOToolsTest
[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest
[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.seq.io.LocationFormatterTest
[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest
[INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest
[INFO] Running org.biojava.bio.seq.RNAToolsTest
[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.seq.RNAToolsTest
[INFO] Running org.biojava.bio.seq.ProteinToolsTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.ProteinToolsTest
[INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest
[INFO] Running org.biojava.bio.seq.DNAToolsTest
[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.DNAToolsTest
[INFO] Running org.biojava.bio.seq.FeatureFilterTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.FeatureFilterTest
[INFO] Running org.biojava.bio.seq.SimpleAssemblyTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.seq.SimpleAssemblyTest
[INFO] Running org.biojava.bio.seq.CircularSequenceTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.CircularSequenceTest
[INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest
[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.MergeFeatureHolderTest
[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest
[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest
[INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest
[INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.seq.db.TestHashSequenceDB
[INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest
[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest
[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.HashSequenceDBTest
[INFO] Running org.biojava.bio.seq.FilterUtilsTest
[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.bio.seq.FilterUtilsTest
[INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.FeatureHolderUtilsTest
[INFO] Running org.biojava.bio.seq.impl.SubSequenceTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.bio.seq.impl.SubSequenceTest
[INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.impl.GappedSequenceTest
[INFO] Running org.biojava.bio.seq.impl.ViewSequenceTest
template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1}
orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1}
copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1}
template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1}
orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1}
copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1}
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.seq.impl.ViewSequenceTest
[INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest
[INFO] Running org.biojava.bio.seq.SeqSerializationTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.bio.seq.SeqSerializationTest
[INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.filter.FilterTransformerTest
[INFO] Running org.biojava.bio.program.phred.PhredToolsTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.phred.PhredToolsTest
[INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.bio.program.indexdb.IndexToolsTest
[INFO] Running org.biojava.directory.RegistryConfigurationTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.directory.RegistryConfigurationTest
[INFO] Running org.biojava.directory.OBDARegistryParserTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.directory.OBDARegistryParserTest
[INFO] Running org.biojava.directory.SystemRegistryTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.directory.SystemRegistryTest
[INFO] Running org.biojava.naming.ObdaUriParserTest
urn:obda.org:format:embl/ac
:trail
oneName
lead:
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.naming.ObdaUriParserTest
[INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest
Reached
Attributes: No attributes
Binding: urn -> org.biojava.naming.ObdaContext@2b441e56
Reached urn
Attributes: No attributes
Binding: open-bio.org -> org.biojava.naming.ObdaContext@267891bf
Reached urn:open-bio.org
Attributes: {description=description:
This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed
by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the
module obda-specs in the cvs repository located at
pub.open-bio.org:/home/repository/obf-common.
}
Binding: type -> org.biojava.naming.ObdaContext@111a7973
Reached urn:open-bio.org:type
Attributes: {description=description:
The namespace for URNs that identify data types. It is expected that the types
that are given IDs will be very general in nature, such as Sequence and
File Format. All types are of type urn:open-bio.org:type:type. Any URN in the
type namespace that is not of this type is not conforming to the OBDA
specification for this namespace.
}
Binding: type -> org.biojava.naming.ObdaContext@1a2773a8
Reached urn:open-bio.org:type:type
Attributes: {description=description:
The OBDA URN that identifies the concept of 'type'. In a given language, this
may map to the types of data structures, or objects. Alternativel, it may
map to a particular set of keys being present in a map, or a term in an
ontology. This is not important. The important thing is that we have unique
identifiers for common types that all projects use and interact with.
}
Binding: format -> org.biojava.naming.ObdaContext@78b0ec3a
Reached urn:open-bio.org:type:format
Attributes: {description=description:
A file format. Many file formats are used in bioinformatics. Entities of this
type identify a format. The format can be used to choose how to treat a file.
The format is not expected to be resolvable to a formal deffinition of the
file structure using OBDA-supplied functionality. Different applications may
chose to process a stream with the same format URN in different ways. This
type of URN is purely there to identify the format of the stream, not the
manner in which it should be processed.
}
Binding: alphabet -> org.biojava.naming.ObdaContext@46612bfc
Reached urn:open-bio.org:type:alphabet
Attributes: {description=description:
A biological sequence alphabet. Biological sequences are often represented as
strings of characters. However, in differnt circumstances, the same characters
can represent different things. For example, in DNA, the 't' character
represents tyrosine. In Protein, this same character represents tryptophan.
Associating alphabets with these sequences disambiguates their interpretation.
Alphabets do not define a mapping to or from strings, but should be used
wherever the type of the content of a sequence needs to be stated.
}
Binding: format -> org.biojava.naming.ObdaContext@4f213a2
Reached urn:open-bio.org:format
Attributes: {description=description:
A namespace for OBDA URNs that define formats. All URNs within this namespace
must be of the type urn:open-bio.org:type:format. Any URN in this namespace that
is not of that type is not a valid OBDA URN.
}
Binding: enzyme -> org.biojava.naming.ObdaContext@25699aa7
Reached urn:open-bio.org:format:enzyme
Attributes: {description=description:
The Enzyme database entry format. The enzyme database can be downloaded from
the ebi at:
ftp://ftp.ebi.ac.uk/pub/databases/enzyme/
For an example of a file in this format, see:
ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat
The format is described more fully in
ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt
}
Binding: genbank -> org.biojava.naming.ObdaContext@5a47730c
Reached urn:open-bio.org:format:genbank
Attributes: {description=description:
The GENBANK file format associated with the GENBANK sequence database.
}
Binding: swissprot -> org.biojava.naming.ObdaContext@15369d73
Reached urn:open-bio.org:format:swissprot
Attributes: {description=description:
The SWISSPROT file format as used in the SWISSPROT sequence database.
}
Binding: embl -> org.biojava.naming.ObdaContext@1cde374
Reached urn:open-bio.org:format:embl
Attributes: {description=description:
The EMBL file format associated with entries in the EMBL sequence database.
}
Binding: alphabet -> org.biojava.naming.ObdaContext@6818fd48
Reached urn:open-bio.org:alphabet
Attributes: {description=description:
A namespace within which to store alphabet identifiers. Alphabets should
represent URNs that represent objects of the type identified by
urn:open-bio.org:type:alphabet, and any useage outside of this is not supported.
}
Binding: rna -> org.biojava.naming.ObdaContext@9263c54
Reached urn:open-bio.org:alphabet:rna
Attributes: {description=description:
The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry
or genetics introductory textbook to find out more. Commonly, the nucleotides
are reprsented by the four letters a, g, c and u. However, this is not a
formal requirement for a resource to declare this alphabet as its type.
}
Binding: protein -> org.biojava.naming.ObdaContext@28daf506
Reached urn:open-bio.org:alphabet:protein
Attributes: {description=description:
The protein alphabet. Proteins are composed from amino-acids. To find out more,
read a biochemistry or genetics text book. It is common for protein sequences
to be represented by characters, but this is not a formal requirement for
a resource to publish an alphabet equal to this identifier.
}
Binding: dna -> org.biojava.naming.ObdaContext@4662752a
Reached urn:open-bio.org:alphabet:dna
Attributes: {description=description:
The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry
or genetics introductory textbook to find out more. Commonly, the nucleotides
are reprsented by the four letters a, g, c and t. However, this is not a
formal requirement for a resource to declare this alphabet as its type.
}
lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@33bdd01}
My component is urn:open-bio.org:format:embl
lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@7ac48f05}
My component is open-bio.org:format:embl
lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@7af1d072, format=org.biojava.naming.ObdaContext@27ffd9f8, alphabet=org.biojava.naming.ObdaContext@642c6461}
My component is format:embl
lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@3ace6346, genbank=org.biojava.naming.ObdaContext@4e48462d, swissprot=org.biojava.naming.ObdaContext@17216605, embl=org.biojava.naming.ObdaContext@10a907ec}
My component is embl
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.naming.ObdaInitialContextFactoryTest
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 890, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO]
[INFO] -----------------------< org.biojava:alignment >------------------------
[INFO] Building alignment 1.9.7 [4/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ alignment ---
[INFO] Copying 89 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ alignment ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ alignment ---
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ alignment ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ alignment ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.624 s - in org.biojava.bio.alignment.FlexibleAlignmentTest
[INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest
[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.161 s - in org.biojava.bio.alignment.SubstitutionMatrixTest
[INFO] Running org.biojava.bio.alignment.AlignmentPairTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.bio.alignment.AlignmentPairTest
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 102, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO]
[INFO] -------------------------< org.biojava:biosql >-------------------------
[INFO] Building biosql 1.9.7 [5/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biosql ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biosql ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biosql ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biosql ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biosql ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest
No hsqldb driver found.
[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO]
[INFO] -------------------------< org.biojava:blast >--------------------------
[INFO] Building blast 1.9.7 [6/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ blast ---
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ blast ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ blast ---
[INFO] Copying 22 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ blast ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ blast ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.bio.program.sax.BlastTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.84 s - in org.biojava.bio.program.sax.BlastTest
[INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.328 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.412 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.074 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.677 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.641 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.486 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.428 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.368 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.488 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.983 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.582 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.623 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.526 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.735 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test
[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 118, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO]
[INFO] -----------------------< org.biojava:sequencing >-----------------------
[INFO] Building sequencing 1.9.7 [7/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ sequencing ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ sequencing ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ sequencing ---
[INFO] Copying 77 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ sequencing ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ sequencing ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.bio.program.scf.SCFTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.708 s - in org.biojava.bio.program.scf.SCFTest
[INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest
[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest
[INFO] Running org.biojava.bio.program.fastq.FastqVariantTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.program.fastq.FastqVariantTest
[INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest
[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.bio.program.fastq.FastqBuilderTest
[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest
[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.211 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest
[INFO] Running org.biojava.bio.program.fastq.FastqTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.FastqTest
[INFO] Running org.biojava.bio.program.fastq.FastqToolsTest
[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 s - in org.biojava.bio.program.fastq.FastqToolsTest
[INFO] Running org.biojava.bio.program.fastq.ConvertTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.bio.program.fastq.ConvertTest
[INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest
[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest
[INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest
[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest
[INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 192, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO]
[INFO] --------------------------< org.biojava:gui >---------------------------
[INFO] Building gui 1.9.7 [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ gui ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ gui ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ gui ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ gui ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ gui ---
[INFO] No tests to run.
[INFO]
[INFO] -------------------------< org.biojava:phylo >--------------------------
[INFO] Building phylo 1.9.7 [9/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ phylo ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ phylo ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ phylo ---
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ phylo ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ phylo ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.884 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava-legacy 1.9.7:
[INFO]
[INFO] biojava-legacy ..................................... SUCCESS [ 0.010 s]
[INFO] bytecode ........................................... SUCCESS [ 2.631 s]
[INFO] core ............................................... SUCCESS [ 32.200 s]
[INFO] alignment .......................................... SUCCESS [ 10.720 s]
[INFO] biosql ............................................. SUCCESS [ 10.439 s]
[INFO] blast .............................................. SUCCESS [ 40.474 s]
[INFO] sequencing ......................................... SUCCESS [ 10.432 s]
[INFO] gui ................................................ SUCCESS [ 0.221 s]
[INFO] phylo .............................................. SUCCESS [ 10.361 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:58 min
[INFO] Finished at: 2024-05-17T12:13:30Z
[INFO] ------------------------------------------------------------------------
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.7\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Ddebian.package=libbiojava1.9-java -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] biojava-legacy [pom]
[INFO] bytecode [jar]
[INFO] core [jar]
[INFO] alignment [jar]
[INFO] biosql [jar]
[INFO] blast [jar]
[INFO] sequencing [jar]
[INFO] gui [jar]
[INFO] phylo [jar]
[INFO]
[INFO] ---------------------< org.biojava:biojava-legacy >---------------------
[INFO] Building biojava-legacy 1.9.7 [1/9]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-legacy ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] --no-parent
[INFO]
[INFO] ------------------------< org.biojava:bytecode >------------------------
[INFO] Building bytecode 1.9.7 [2/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ bytecode ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for bytecode into /usr/share/java
[INFO]
[INFO] --------------------------< org.biojava:core >--------------------------
[INFO] Building core 1.9.7 [3/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ core ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/core/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for core into /usr/share/java
[INFO]
[INFO] -----------------------< org.biojava:alignment >------------------------
[INFO] Building alignment 1.9.7 [4/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ alignment ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/alignment/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for alignment into /usr/share/java
[INFO]
[INFO] -------------------------< org.biojava:biosql >-------------------------
[INFO] Building biosql 1.9.7 [5/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biosql ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for biosql into /usr/share/java
[INFO]
[INFO] -------------------------< org.biojava:blast >--------------------------
[INFO] Building blast 1.9.7 [6/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ blast ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/blast/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for blast into /usr/share/java
[INFO]
[INFO] -----------------------< org.biojava:sequencing >-----------------------
[INFO] Building sequencing 1.9.7 [7/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ sequencing ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/sequencing/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for sequencing into /usr/share/java
[INFO]
[INFO] --------------------------< org.biojava:gui >---------------------------
[INFO] Building gui 1.9.7 [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ gui ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for gui into /usr/share/java
[INFO]
[INFO] -------------------------< org.biojava:phylo >--------------------------
[INFO] Building phylo 1.9.7 [9/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ phylo ---
[INFO] Cleaning pom file: /build/reproducible-path/biojava-live-1.9.7+dfsg/phylo/pom.xml.save with options:
[INFO] --keep-pom-version --package=libbiojava1.9-java
[INFO] --rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.rules
[INFO] --ignore-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.ignoreRules
[INFO] --published-rules=/build/reproducible-path/biojava-live-1.9.7+dfsg/debian/maven.publishedRules
[INFO] Install jar for phylo into /usr/share/java
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava-legacy 1.9.7:
[INFO]
[INFO] biojava-legacy ..................................... SUCCESS [ 2.463 s]
[INFO] bytecode ........................................... SUCCESS [ 0.418 s]
[INFO] core ............................................... SUCCESS [ 0.288 s]
[INFO] alignment .......................................... SUCCESS [ 0.212 s]
[INFO] biosql ............................................. SUCCESS [ 0.238 s]
[INFO] blast .............................................. SUCCESS [ 0.213 s]
[INFO] sequencing ......................................... SUCCESS [ 0.284 s]
[INFO] gui ................................................ SUCCESS [ 0.276 s]
[INFO] phylo .............................................. SUCCESS [ 0.252 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5.548 s
[INFO] Finished at: 2024-05-17T12:13:43Z
[INFO] ------------------------------------------------------------------------
mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --javadoc --base-directory=/build/reproducible-path/biojava-live-1.9.7\+dfsg --non-explore
Analysing pom.xml...
Analysing alignment/pom.xml...
Checking the parent dependency in the sub project alignment/pom.xml
Analysing biosql/pom.xml...
Checking the parent dependency in the sub project biosql/pom.xml
Analysing blast/pom.xml...
Checking the parent dependency in the sub project blast/pom.xml
Analysing bytecode/pom.xml...
Checking the parent dependency in the sub project bytecode/pom.xml
Analysing core/pom.xml...
Checking the parent dependency in the sub project core/pom.xml
Analysing gui/pom.xml...
Checking the parent dependency in the sub project gui/pom.xml
Analysing phylo/pom.xml...
Checking the parent dependency in the sub project phylo/pom.xml
Analysing sequencing/pom.xml...
Checking the parent dependency in the sub project sequencing/pom.xml
Checking dependencies for documentation packages...
> dpkg --search /usr/share/doc/libcommons-dbcp-java/api/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java/api/index.html
> dpkg --search /usr/share/doc/libcommons-dbcp-java-doc/api/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java-doc/api/index.html
> dpkg --search /usr/share/doc/libcommons-dbcp-java/apidocs/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java/apidocs/index.html
> dpkg --search /usr/share/doc/libcommons-dbcp-java-doc/apidocs/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libcommons-dbcp-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libguava-java/api/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/api/index.html
> dpkg --search /usr/share/doc/libguava-java-doc/api/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/api/index.html
> dpkg --search /usr/share/doc/libguava-java/apidocs/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java/apidocs/index.html
> dpkg --search /usr/share/doc/libguava-java-doc/apidocs/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libguava-java-doc/apidocs/index.html
> dpkg --search /usr/share/doc/libjgrapht0.8-java/api/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java/api/index.html
> dpkg --search /usr/share/doc/libjgrapht0.8-java-doc/api/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java-doc/api/index.html
> dpkg --search /usr/share/doc/libjgrapht0.8-java/apidocs/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java/apidocs/index.html
> dpkg --search /usr/share/doc/libjgrapht0.8-java-doc/apidocs/index.html
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht0.8-java-doc/apidocs/index.html
bash -c "rm -f target/apidocs/*.sh target/apidocs/options"
mh_unpatchpoms -plibbiojava1.9-java
dh_install
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/reproducible-path/biojava-live-1.9.7+dfsg'
dh_installdocs
# Deleting calls to urchinTracker to enhance privacy.
for F in $(find . -name "*.html"); do \
sed -i 's/^$//' $F; \
done
make[1]: Leaving directory '/build/reproducible-path/biojava-live-1.9.7+dfsg'
dh_installchangelogs
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package libbiojava1.9-java: substitution variable ${maven:CompileDepends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava1.9-java: substitution variable ${maven:DocDepends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined
dpkg-gencontrol: warning: package libbiojava-java-doc: substitution variable ${maven:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.7+dfsg-1_all.deb'.
dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.7+dfsg-1_all.deb'.
dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.7+dfsg-1_all.deb'.
dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.7+dfsg-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../biojava-live_1.9.7+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/519350/tmp/hooks/B01_cleanup finished
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/519350 and its subdirectories
I: Current time: Sat May 18 02:19:10 +14 2024
I: pbuilder-time-stamp: 1715948350