Tue Jan 23 21:52:04 UTC 2024 I: starting to build biojava6-live/bookworm/i386 on jenkins on '2024-01-23 21:51' Tue Jan 23 21:52:04 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/10512/console.log Tue Jan 23 21:52:04 UTC 2024 I: Downloading source for bookworm/biojava6-live=6.1.0+dfsg-4 --2024-01-23 21:52:04-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/biojava6-live/biojava6-live_6.1.0%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3360 (3.3K) [text/prs.lines.tag] Saving to: ‘biojava6-live_6.1.0+dfsg-4.dsc’ 0K ... 100% 11.7M=0s 2024-01-23 21:52:05 (11.7 MB/s) - ‘biojava6-live_6.1.0+dfsg-4.dsc’ saved [3360/3360] Tue Jan 23 21:52:05 UTC 2024 I: biojava6-live_6.1.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: biojava6-live Binary: libbiojava6-java, libbiojava6-java-doc Architecture: all Version: 6.1.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet Homepage: https://www.biojava.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/biojava6-live Vcs-Git: https://salsa.debian.org/med-team/biojava6-live.git Build-Depends: debhelper-compat (= 13), javahelper, maven-debian-helper Build-Depends-Indep: default-jdk, default-jdk-doc, junit4 , libactivation-java, libciftools-java, libcommons-codec-java, libcommons-math-java, libguava-java, libitext5-java, libjackson2-databind-java, libjaxb-api-java, libjaxb-java, libjgrapht-java, libjmol-java (>= 14.32.77+dfsg-1~), libjson-simple-java, liblog4j2-java, libmaven-antrun-plugin-java, libmaven-assembly-plugin-java, libmaven-dependency-plugin-java, libmaven-deploy-plugin-java, libmaven-enforcer-plugin-java, libmaven-install-plugin-java, libmaven-javadoc-plugin-java, libmaven-jaxb2-plugin-java, libmmtf-java, libslf4j-java, libvecmath-java, libxmlunit-java Package-List: libbiojava6-java deb java optional arch=all libbiojava6-java-doc deb doc optional arch=all Checksums-Sha1: 7016114b4e93972f0011b051033c52b88f47dfa4 716817 biojava6-live_6.1.0+dfsg.orig-forester.tar.gz 8c9e87252aa79ae087f053f04169ccc519d78553 12099 biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz 3ef1b57421b0bf55e9fb18bffe0297decd30eec4 17827888 biojava6-live_6.1.0+dfsg.orig.tar.gz 26e5b5f670f1867589b21d39d1ee63279a9ed612 27320 biojava6-live_6.1.0+dfsg-4.debian.tar.xz Checksums-Sha256: c62105605104c93848056ea2726220552ac7460b5024eb98e163afe20d8247d6 716817 biojava6-live_6.1.0+dfsg.orig-forester.tar.gz d6548c423ad6202bc8f75eaa8b5839654a34591dfde51c129829ea14b3feeb8a 12099 biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz 0e544639aa1f0b7b8c265fae902c7653a5a03f379bcf8ebbc3201abb94c574e0 17827888 biojava6-live_6.1.0+dfsg.orig.tar.gz 28b5c564b2f7c9e36828f8ac1d3a2dc0567d96085f761aae5eb747922a0334e8 27320 biojava6-live_6.1.0+dfsg-4.debian.tar.xz Files: 1e9f85109426e43845585480f703addb 716817 biojava6-live_6.1.0+dfsg.orig-forester.tar.gz df2215c3446dd89de728b19bbbb02ec8 12099 biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz 57fdf02efb490c3966af01ccc9bb586b 17827888 biojava6-live_6.1.0+dfsg.orig.tar.gz 899aba4c2d3906f2570e8d8ce9eae369 27320 biojava6-live_6.1.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIyBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmPiKYoACgkQYAMWptwn dHa/rw/40XHhwYAhfd8K+xxNvJe8j2NEALFG+Xk2zl2uwNLWmCvwtvvXH3OjoZgK jegIK1JR2tR3pzYsR+zBnCT/q89ohGk82ldiMMXtwVWPuKzxVUoHWA03rXBsz+qy z06xX8dgIAQ7gSi/QExKAjkYuMw6rjn4EytA6vx5rck7Lba+ILYY+Rj/alpB/QRR y0wD39odzUhGveq0vMPV3ulw3D0rWPPZiTKRXtYSPjPv2VpRp2UPSwtoo4+WqBRE zzPD1Q8UPmSzwdD4QtZe2ek8Sxb5fsCMhEeGnWqmiqZEVgwOhSSosmx0F1PKsIlt KBwv6VNuGn+1r43a3zmSvyQ4D71Ebs4KQJdngpWdKHamfsCXF8GdouiMXh2QvwnH 9FrpKVbiqtj6erSdFvU/ila+5NH27E3tdRi4oJmXDmOYOFoPj5SFHhVdrOYr2Z6l v09RQvpJKR7C3AfT7ESaImp3KiqHCF/qWqNdADfbbutmX0h7ezH23EqE1jf6eZWy FmQMT3oDRA3u5pv87JAIzaqWh9vb2vCKf026VrhDR+1MRDu/4eev99ujzPJFjlrb 0BPdrU1gU1SHkeGoirMy7fhlxGGLuoQ9QIuePMLWVJCdqKlX2LXwIF3GFmBsabtT hITkMnM393bBqeqKdtRBIWH4ypJpKxRCYXPTSzgb5M3spmtkuQ== =OMCH -----END PGP SIGNATURE----- Tue Jan 23 21:52:05 UTC 2024 I: Checking whether the package is not for us Tue Jan 23 21:52:05 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Tue Jan 23 21:52:05 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Tue Jan 23 22:36:35 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 24 16:15:08 -12 2025 I: pbuilder-time-stamp: 1740456908 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [biojava6-live_6.1.0+dfsg-4.dsc] I: copying [./biojava6-live_6.1.0+dfsg.orig-forester.tar.gz] I: copying [./biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz] I: copying [./biojava6-live_6.1.0+dfsg.orig.tar.gz] I: copying [./biojava6-live_6.1.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Feb 7 10:35:54 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava6-live_6.1.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting biojava6-live in biojava6-live-6.1.0+dfsg dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig.tar.gz dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig-forester.tar.gz dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg.orig-jcolorbrewer.tar.gz dpkg-source: info: unpacking biojava6-live_6.1.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_itext_class_updates.patch dpkg-source: info: applying use_simple_json.patch dpkg-source: info: applying fix_import.patch dpkg-source: info: applying fix_ascii_characters_mapping.patch dpkg-source: info: applying skip_network_related_tests.patch dpkg-source: info: applying remove_openchart_use.patch dpkg-source: info: applying ignore_fake_tests.patch dpkg-source: info: applying poms.patch dpkg-source: info: applying jmol_path_in_pom.patch dpkg-source: info: applying remove_tests_needing_junitx.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25528/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='acd136b92a65462499bcd7dae4c23fb4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='25528' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/pbuilderrc_YPTv --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 23 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 23 2023 more -rwsr-xr-x 1 root root 58912 Mar 23 2023 mount -rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 23 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/25528/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: i386 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), javahelper, maven-debian-helper, default-jdk, default-jdk-doc, junit4, libactivation-java, libciftools-java, libcommons-codec-java, libcommons-math-java, libguava-java, libitext5-java, libjackson2-databind-java, libjaxb-api-java, libjaxb-java, libjgrapht-java, libjmol-java (>= 14.32.77+dfsg-1~), libjson-simple-java, liblog4j2-java, libmaven-antrun-plugin-java, libmaven-assembly-plugin-java, libmaven-dependency-plugin-java, libmaven-deploy-plugin-java, libmaven-enforcer-plugin-java, libmaven-install-plugin-java, libmaven-javadoc-plugin-java, libmaven-jaxb2-plugin-java, libmmtf-java, libslf4j-java, libvecmath-java, libxmlunit-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 ... 18156 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 javahelper; however: Package javahelper 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 default-jdk-doc; however: Package default-jdk-doc is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 is not installed. pbuilder-satisfydepends-dummy depends on libactivation-java; however: Package libactivation-java is not installed. pbuilder-satisfydepends-dummy depends on libciftools-java; however: Package libciftools-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-codec-java; however: Package libcommons-codec-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math-java; however: Package libcommons-math-java is not installed. pbuilder-satisfydepends-dummy depends on libguava-java; however: Package libguava-java is not installed. pbuilder-satisfydepends-dummy depends on libitext5-java; however: Package libitext5-java is not installed. pbuilder-satisfydepends-dummy depends on libjackson2-databind-java; however: Package libjackson2-databind-java is not installed. pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however: Package libjaxb-api-java is not installed. pbuilder-satisfydepends-dummy depends on libjaxb-java; however: Package libjaxb-java is not installed. pbuilder-satisfydepends-dummy depends on libjgrapht-java; however: Package libjgrapht-java is not installed. pbuilder-satisfydepends-dummy depends on libjmol-java (>= 14.32.77+dfsg-1~); however: Package libjmol-java is not installed. pbuilder-satisfydepends-dummy depends on libjson-simple-java; however: Package libjson-simple-java is not installed. pbuilder-satisfydepends-dummy depends on liblog4j2-java; however: Package liblog4j2-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-antrun-plugin-java; however: Package libmaven-antrun-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-assembly-plugin-java; however: Package libmaven-assembly-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-dependency-plugin-java; however: Package libmaven-dependency-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-deploy-plugin-java; however: Package libmaven-deploy-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-enforcer-plugin-java; however: Package libmaven-enforcer-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-install-plugin-java; however: Package libmaven-install-plugin-java 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 libmaven-jaxb2-plugin-java; however: Package libmaven-jaxb2-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libmmtf-java; however: Package libmmtf-java is not installed. pbuilder-satisfydepends-dummy depends on libslf4j-java; however: Package libslf4j-java is not installed. pbuilder-satisfydepends-dummy depends on libvecmath-java; however: Package libvecmath-java is not installed. pbuilder-satisfydepends-dummy depends on libxmlunit-java; however: Package libxmlunit-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} ant-optional{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} java-wrappers{a} javahelper{a} junit{a} junit4{a} junit5{a} libactivation-java{a} libantlr4-runtime-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbatik-java{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libcairo2{a} libcdi-api-java{a} libciftools-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcodemodel-java{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{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} libdtd-parser-java{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-java{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-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} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libimport-into-perl{a} libinchi1{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libitext1-java{a} libitext5-java{a} libjackson2-annotations-java{a} libjackson2-core-java{a} libjackson2-databind-java{a} libjakarta-activation-java{a} libjansi-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjetty9-java{a} libjgrapht-java{a} libjgraphx-java{a} libjheaps-java{a} libjmol-java{a} libjni-inchi-java{a} libjni-inchi-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjson-simple-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm15{a} liblog4j1.2-java{a} liblog4j2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-deploy-plugin-java{a} libmaven-enforcer-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-install-plugin-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-jaxb2-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} libmmtf-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libmsgpack-java{a} libnaga-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0{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} libparams-classify-perl{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} libpng16-16{a} libproc2-0{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8{a} libregexp-ipv6-perl{a} librelaxng-datatype-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-override-perl{a} libsub-quote-perl{a} libsurefire-java{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvecmath-java{a} libvelocity-tools-java{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{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} libxmlunit-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{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} media-types{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} unzip{a} velocity{a} wdiff{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra icc-profiles-free javascript-common libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx pristine-tar psmisc python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget xdg-user-dirs 0 packages upgraded, 397 newly installed, 0 to remove and 0 not upgraded. Need to get 348 MB of archives. After unpacking 1118 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.11-1~deb12u2 [1423 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 shared-mime-info i386 2.2-1 [730 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.2+deb12u1 [294 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-6+deb12u1 [332 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libgdk-pixbuf-2.0-0 i386 2.42.10+dfsg-1+b1 [147 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 gtk-update-icon-cache i386 3.24.38-2~deb12u1 [44.6 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 adwaita-icon-theme all 43-1 [5124 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 ca-certificates-java all 20230710~deb12u1 [11.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 java-common all 0.74 [6388 B] Get: 46 http://deb.debian.org/debian bookworm/main i386 libavahi-common-data i386 0.8-10 [107 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libavahi-common3 i386 0.8-10 [43.5 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libdbus-1-3 i386 1.14.10-1~deb12u1 [215 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libavahi-client3 i386 0.8-10 [47.6 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libcups2 i386 2.4.2-3+deb12u5 [262 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libnspr4 i386 2:4.35-1 [123 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libnss3 i386 2:3.87.1-1 [1439 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libasound2-data all 1.2.8-1 [20.5 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libasound2 i386 1.2.8-1+b1 [388 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libpcsclite1 i386 1.9.9-2 [50.9 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 openjdk-17-jre-headless i386 17.0.9+9-1~deb12u1 [42.6 MB] Get: 65 http://deb.debian.org/debian bookworm/main i386 default-jre-headless i386 2:1.17-74 [2932 B] Get: 66 http://deb.debian.org/debian bookworm/main i386 ant all 1.10.13-1 [2161 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 ant-optional all 1.10.13-1 [449 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 at-spi2-common all 2.46.0-5 [162 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 dctrl-tools i386 2.24-3 [105 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 80 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 82 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libatk1.0-0 i386 2.46.0-5 [49.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2+deb12u2 [782 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 fontconfig i386 2.14.1-4 [450 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libthai-data all 0.1.29-1 [176 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 libdatrie1 i386 0.2.13-2+b1 [45.0 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libthai0 i386 0.1.29-1 [58.6 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 libpango-1.0-0 i386 1.50.12+ds-1 [220 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 libpangoft2-1.0-0 i386 1.50.12+ds-1 [50.5 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 libpangocairo-1.0-0 i386 1.50.12+ds-1 [35.4 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 libxcomposite1 i386 1:0.4.5-1 [16.9 kB] Get: 111 http://deb.debian.org/debian bookworm/main i386 libxfixes3 i386 1:6.0.0-2 [23.0 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 libxcursor1 i386 1:1.2.1-1 [42.4 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 libxdamage1 i386 1:1.1.6-1 [15.3 kB] Get: 114 http://deb.debian.org/debian bookworm/main i386 libxi6 i386 2:1.8-1+b1 [86.2 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 libxinerama1 i386 2:1.1.4-3 [18.1 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 libxrandr2 i386 2:1.5.2-2+b1 [40.8 kB] Get: 117 http://deb.debian.org/debian bookworm/main i386 libgtk2.0-0 i386 2.24.33-2 [1970 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 libglvnd0 i386 1.6.0-1 [42.7 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 libdrm-common all 2.4.114-1 [7112 B] Get: 120 http://deb.debian.org/debian bookworm/main i386 libdrm2 i386 2.4.114-1+b1 [40.8 kB] Get: 121 http://deb.debian.org/debian bookworm/main i386 libglapi-mesa i386 22.3.6-1+deb12u1 [35.6 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 libx11-xcb1 i386 2:1.8.4-2+deb12u2 [192 kB] Get: 123 http://deb.debian.org/debian bookworm/main i386 libxcb-dri2-0 i386 1.15-1 [107 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 libxcb-dri3-0 i386 1.15-1 [107 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 libxcb-glx0 i386 1.15-1 [124 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 libxcb-present0 i386 1.15-1 [106 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 libxcb-randr0 i386 1.15-1 [118 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 libxcb-sync1 i386 1.15-1 [109 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 libxcb-xfixes0 i386 1.15-1 [110 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 libxshmfence1 i386 1.3-1 [8976 B] Get: 131 http://deb.debian.org/debian bookworm/main i386 libxxf86vm1 i386 1:1.1.4-1+b2 [21.7 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 libdrm-amdgpu1 i386 2.4.114-1+b1 [24.1 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 libpciaccess0 i386 0.17-2 [53.4 kB] Get: 134 http://deb.debian.org/debian bookworm/main i386 libdrm-intel1 i386 2.4.114-1+b1 [67.9 kB] Get: 135 http://deb.debian.org/debian bookworm/main i386 libdrm-nouveau2 i386 2.4.114-1+b1 [20.7 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 libdrm-radeon1 i386 2.4.114-1+b1 [22.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 138 http://deb.debian.org/debian bookworm/main i386 libz3-4 i386 4.8.12-3.1 [7853 kB] Get: 139 http://deb.debian.org/debian bookworm/main i386 libllvm15 i386 1:15.0.6-4+b1 [26.5 MB] Get: 140 http://deb.debian.org/debian bookworm/main i386 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 libsensors5 i386 1:3.6.0-7.1 [35.1 kB] Get: 142 http://deb.debian.org/debian bookworm/main i386 libgl1-mesa-dri i386 22.3.6-1+deb12u1 [7417 kB] Get: 143 http://deb.debian.org/debian bookworm/main i386 libglx-mesa0 i386 22.3.6-1+deb12u1 [156 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 libglx0 i386 1.6.0-1 [36.6 kB] Get: 145 http://deb.debian.org/debian bookworm/main i386 libgl1 i386 1.6.0-1 [82.1 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 libgif7 i386 5.2.1-2.5 [48.3 kB] Get: 147 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 148 http://deb.debian.org/debian bookworm/main i386 libxtst6 i386 2:1.2.3-1.1 [28.6 kB] Get: 149 http://deb.debian.org/debian bookworm/main i386 openjdk-17-jre i386 17.0.9+9-1~deb12u1 [184 kB] Get: 150 http://deb.debian.org/debian bookworm/main i386 default-jre i386 2:1.17-74 [1056 B] Get: 151 http://deb.debian.org/debian bookworm/main i386 openjdk-17-jdk-headless i386 17.0.9+9-1~deb12u1 [73.9 MB] Get: 152 http://deb.debian.org/debian bookworm/main i386 default-jdk-headless i386 2:1.17-74 [1108 B] Get: 153 http://deb.debian.org/debian bookworm/main i386 openjdk-17-jdk i386 17.0.9+9-1~deb12u1 [2797 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 default-jdk i386 2:1.17-74 [1068 B] Get: 155 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 156 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 157 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 158 http://deb.debian.org/debian bookworm/main i386 openjdk-17-doc all 17.0.9+9-1~deb12u1 [12.8 MB] Get: 159 http://deb.debian.org/debian bookworm/main i386 default-jdk-doc i386 2:1.17-74 [3020 B] Get: 160 http://deb.debian.org/debian bookworm/main i386 libassuan0 i386 2.5.5-5 [50.3 kB] Get: 161 http://deb.debian.org/debian bookworm/main i386 gpgconf i386 2.2.40-1.1 [572 kB] Get: 162 http://deb.debian.org/debian bookworm/main i386 libksba8 i386 1.6.3-2 [135 kB] Get: 163 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 164 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 165 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 166 http://deb.debian.org/debian bookworm/main i386 libnpth0 i386 1.6-3 [19.1 kB] Get: 167 http://deb.debian.org/debian bookworm/main i386 dirmngr i386 2.2.40-1.1 [819 kB] Get: 168 http://deb.debian.org/debian bookworm/main i386 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 169 http://deb.debian.org/debian bookworm/main i386 gnupg-utils i386 2.2.40-1.1 [973 kB] Get: 170 http://deb.debian.org/debian bookworm/main i386 gpg i386 2.2.40-1.1 [991 kB] Get: 171 http://deb.debian.org/debian bookworm/main i386 pinentry-curses i386 1.2.1-1 [79.0 kB] Get: 172 http://deb.debian.org/debian bookworm/main i386 gpg-agent i386 2.2.40-1.1 [715 kB] Get: 173 http://deb.debian.org/debian bookworm/main i386 gpg-wks-client i386 2.2.40-1.1 [551 kB] Get: 174 http://deb.debian.org/debian bookworm/main i386 gpg-wks-server i386 2.2.40-1.1 [541 kB] Get: 175 http://deb.debian.org/debian bookworm/main i386 gpgsm i386 2.2.40-1.1 [691 kB] Get: 176 http://deb.debian.org/debian bookworm/main i386 gnupg all 2.2.40-1.1 [846 kB] Get: 177 http://deb.debian.org/debian bookworm/main i386 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 178 http://deb.debian.org/debian bookworm/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 179 http://deb.debian.org/debian bookworm/main i386 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 180 http://deb.debian.org/debian bookworm/main i386 libfile-touch-perl all 0.12-2 [8816 B] Get: 181 http://deb.debian.org/debian bookworm/main i386 libio-pty-perl i386 1:1.17-1 [36.5 kB] Get: 182 http://deb.debian.org/debian bookworm/main i386 libipc-run-perl all 20220807.0-1 [104 kB] Get: 183 http://deb.debian.org/debian bookworm/main i386 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 184 http://deb.debian.org/debian bookworm/main i386 libclass-xsaccessor-perl i386 1.19-4+b1 [38.0 kB] Get: 185 http://deb.debian.org/debian bookworm/main i386 libb-hooks-op-check-perl i386 0.22-2+b1 [10.6 kB] Get: 186 http://deb.debian.org/debian bookworm/main i386 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 187 http://deb.debian.org/debian bookworm/main i386 libdevel-callchecker-perl i386 0.008-2 [15.8 kB] Get: 188 http://deb.debian.org/debian bookworm/main i386 libparams-classify-perl i386 0.015-2+b1 [23.7 kB] Get: 189 http://deb.debian.org/debian bookworm/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 190 http://deb.debian.org/debian bookworm/main i386 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 191 http://deb.debian.org/debian bookworm/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 192 http://deb.debian.org/debian bookworm/main i386 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 193 http://deb.debian.org/debian bookworm/main i386 libmoo-perl all 2.005005-1 [58.0 kB] Get: 194 http://deb.debian.org/debian bookworm/main i386 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 195 http://deb.debian.org/debian bookworm/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 196 http://deb.debian.org/debian bookworm/main i386 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 197 http://deb.debian.org/debian bookworm/main i386 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 198 http://deb.debian.org/debian bookworm/main i386 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 199 http://deb.debian.org/debian bookworm/main i386 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 200 http://deb.debian.org/debian bookworm/main i386 liburi-perl all 5.17-1 [90.4 kB] Get: 201 http://deb.debian.org/debian bookworm/main i386 libhtml-parser-perl i386 3.81-1 [102 kB] Get: 202 http://deb.debian.org/debian bookworm/main i386 libhtml-tree-perl all 5.07-3 [211 kB] Get: 203 http://deb.debian.org/debian bookworm/main i386 libclone-perl i386 0.46-1 [13.8 kB] Get: 204 http://deb.debian.org/debian bookworm/main i386 libio-html-perl all 1.004-3 [16.2 kB] Get: 205 http://deb.debian.org/debian bookworm/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 206 http://deb.debian.org/debian bookworm/main i386 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 207 http://deb.debian.org/debian bookworm/main i386 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 208 http://deb.debian.org/debian bookworm/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 209 http://deb.debian.org/debian bookworm/main i386 perl-openssl-defaults i386 7+b1 [7920 B] Get: 210 http://deb.debian.org/debian bookworm/main i386 libnet-ssleay-perl i386 1.92-2+b1 [318 kB] Get: 211 http://deb.debian.org/debian bookworm/main i386 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 212 http://deb.debian.org/debian bookworm/main i386 libnet-http-perl all 6.22-1 [25.3 kB] Get: 213 http://deb.debian.org/debian bookworm/main i386 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 214 http://deb.debian.org/debian bookworm/main i386 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 215 http://deb.debian.org/debian bookworm/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 216 http://deb.debian.org/debian bookworm/main i386 libwww-perl all 6.68-1 [186 kB] Get: 217 http://deb.debian.org/debian bookworm/main i386 patchutils i386 0.4.2-1 [79.6 kB] Get: 218 http://deb.debian.org/debian bookworm/main i386 wdiff i386 1.2.2-5 [120 kB] Get: 219 http://deb.debian.org/debian bookworm/main i386 devscripts i386 2.23.4+deb12u1 [1073 kB] Get: 220 http://deb.debian.org/debian bookworm/main i386 unzip i386 6.0-28 [166 kB] Get: 221 http://deb.debian.org/debian bookworm/main i386 java-wrappers all 0.4 [8916 B] Get: 222 http://deb.debian.org/debian bookworm/main i386 javahelper all 0.78 [97.2 kB] Get: 223 http://deb.debian.org/debian bookworm/main i386 junit all 3.8.2-9 [110 kB] Get: 224 http://deb.debian.org/debian bookworm/main i386 libhamcrest-java all 2.2-1 [121 kB] Get: 225 http://deb.debian.org/debian bookworm/main i386 junit4 all 4.13.2-3 [348 kB] Get: 226 http://deb.debian.org/debian bookworm/main i386 libapiguardian-java all 1.1.2-1 [4656 B] Get: 227 http://deb.debian.org/debian bookworm/main i386 libopentest4j-java all 1.2.0-4 [9516 B] Get: 228 http://deb.debian.org/debian bookworm/main i386 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 229 http://deb.debian.org/debian bookworm/main i386 libpicocli-java all 4.6.2-2 [390 kB] Get: 230 http://deb.debian.org/debian bookworm/main i386 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 231 http://deb.debian.org/debian bookworm/main i386 junit5 all 5.9.2-1 [2398 kB] Get: 232 http://deb.debian.org/debian bookworm/main i386 libactivation-java all 1.2.0-2 [84.7 kB] Get: 233 http://deb.debian.org/debian bookworm/main i386 libantlr4-runtime-java all 4.7.2-5 [315 kB] Get: 234 http://deb.debian.org/debian bookworm/main i386 libaopalliance-java all 20070526-7 [8572 B] Get: 235 http://deb.debian.org/debian bookworm/main i386 libapache-pom-java all 29-2 [5276 B] Get: 236 http://deb.debian.org/debian bookworm/main i386 libargs4j-java all 2.33-2 [138 kB] Get: 237 http://deb.debian.org/debian bookworm/main i386 libasm-java all 9.4-1 [389 kB] Get: 238 http://deb.debian.org/debian bookworm/main i386 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 239 http://deb.debian.org/debian bookworm/main i386 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 240 http://deb.debian.org/debian bookworm/main i386 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 241 http://deb.debian.org/debian bookworm/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 242 http://deb.debian.org/debian bookworm/main i386 libcommons-io-java all 2.11.0-2 [319 kB] Get: 243 http://deb.debian.org/debian bookworm/main i386 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 244 http://deb.debian.org/debian bookworm/main i386 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 245 http://deb.debian.org/debian bookworm/main i386 libbatik-java all 1.16+dfsg-1+deb12u1 [3949 kB] Get: 246 http://deb.debian.org/debian bookworm/main i386 libbsh-java all 2.0b4-20 [291 kB] Get: 247 http://deb.debian.org/debian bookworm/main i386 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 248 http://deb.debian.org/debian bookworm/main i386 libcdi-api-java all 1.2-3 [54.3 kB] Get: 249 http://deb.debian.org/debian bookworm/main i386 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 250 http://deb.debian.org/debian bookworm/main i386 libgoogle-gson-java all 2.10-1 [261 kB] Get: 251 http://deb.debian.org/debian bookworm/main i386 libciftools-java all 4.0.5-1 [2139 kB] Get: 252 http://deb.debian.org/debian bookworm/main i386 libjaxen-java all 1.1.6-4 [214 kB] Get: 253 http://deb.debian.org/debian bookworm/main i386 libdom4j-java all 2.1.3-2 [310 kB] Get: 254 http://deb.debian.org/debian bookworm/main i386 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 255 http://deb.debian.org/debian bookworm/main i386 libcommons-cli-java all 1.5.0-1 [60.0 kB] Get: 256 http://deb.debian.org/debian bookworm/main i386 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 257 http://deb.debian.org/debian bookworm/main i386 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 258 http://deb.debian.org/debian bookworm/main i386 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 259 http://deb.debian.org/debian bookworm/main i386 libguava-java all 31.1-1 [2613 kB] Get: 260 http://deb.debian.org/debian bookworm/main i386 libguice-java all 4.2.3-2 [1435 kB] Get: 261 http://deb.debian.org/debian bookworm/main i386 libmaven-parent-java all 35-1 [6140 B] Get: 262 http://deb.debian.org/debian bookworm/main i386 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 263 http://deb.debian.org/debian bookworm/main i386 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 264 http://deb.debian.org/debian bookworm/main i386 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 265 http://deb.debian.org/debian bookworm/main i386 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 266 http://deb.debian.org/debian bookworm/main i386 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 267 http://deb.debian.org/debian bookworm/main i386 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 268 http://deb.debian.org/debian bookworm/main i386 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 269 http://deb.debian.org/debian bookworm/main i386 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 270 http://deb.debian.org/debian bookworm/main i386 libslf4j-java all 1.7.32-1 [144 kB] Get: 271 http://deb.debian.org/debian bookworm/main i386 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 272 http://deb.debian.org/debian bookworm/main i386 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 273 http://deb.debian.org/debian bookworm/main i386 libmaven3-core-java all 3.8.7-1 [1572 kB] Get: 274 http://deb.debian.org/debian bookworm/main i386 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 275 http://deb.debian.org/debian bookworm/main i386 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 276 http://deb.debian.org/debian bookworm/main i386 libcommons-compress-java all 1.22-1 [615 kB] Get: 277 http://deb.debian.org/debian bookworm/main i386 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 278 http://deb.debian.org/debian bookworm/main i386 libsnappy1v5 i386 1.1.9-3 [27.7 kB] Get: 279 http://deb.debian.org/debian bookworm/main i386 libsnappy-jni i386 1.1.8.3-1 [7384 B] Get: 280 http://deb.debian.org/debian bookworm/main i386 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 281 http://deb.debian.org/debian bookworm/main i386 libxz-java all 1.9-1 [143 kB] Get: 282 http://deb.debian.org/debian bookworm/main i386 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 283 http://deb.debian.org/debian bookworm/main i386 libhttpcore-java all 4.4.16-1 [636 kB] Get: 284 http://deb.debian.org/debian bookworm/main i386 libcommons-codec-java all 1.15-1 [292 kB] Get: 285 http://deb.debian.org/debian bookworm/main i386 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 286 http://deb.debian.org/debian bookworm/main i386 libjsoup-java all 1.15.3-1 [431 kB] Get: 287 http://deb.debian.org/debian bookworm/main i386 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 288 http://deb.debian.org/debian bookworm/main i386 libistack-commons-java all 3.0.6-5 [145 kB] Get: 289 http://deb.debian.org/debian bookworm/main i386 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 290 http://deb.debian.org/debian bookworm/main i386 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 291 http://deb.debian.org/debian bookworm/main i386 libcommons-beanutils-java all 1.9.4-1 [232 kB] Get: 292 http://deb.debian.org/debian bookworm/main i386 libcommons-collections4-java all 4.2-1 [662 kB] Get: 293 http://deb.debian.org/debian bookworm/main i386 libcommons-lang-java all 2.6-10 [273 kB] Get: 294 http://deb.debian.org/debian bookworm/main i386 libcommons-configuration-java all 1.10-6 [347 kB] Get: 295 http://deb.debian.org/debian bookworm/main i386 libcommons-digester-java all 1.8.1-5 [168 kB] Get: 296 http://deb.debian.org/debian bookworm/main i386 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 297 http://deb.debian.org/debian bookworm/main i386 libcommons-math-java all 2.2-8 [926 kB] Get: 298 http://deb.debian.org/debian bookworm/main i386 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 299 http://deb.debian.org/debian bookworm/main i386 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 300 http://deb.debian.org/debian bookworm/main i386 libcommons-text-java all 1.10.0-1 [211 kB] Get: 301 http://deb.debian.org/debian bookworm/main i386 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 302 http://deb.debian.org/debian bookworm/main i386 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 303 http://deb.debian.org/debian bookworm/main i386 libfontbox2-java all 2.0.27-2 [1510 kB] Get: 304 http://deb.debian.org/debian bookworm/main i386 libqdox-java all 1.12.1-3 [172 kB] Get: 305 http://deb.debian.org/debian bookworm/main i386 libfop-java all 1:2.8-2 [10.1 MB] Get: 306 http://deb.debian.org/debian bookworm/main i386 libitext1-java all 1.4-7 [1257 kB] Get: 307 http://deb.debian.org/debian bookworm/main i386 libxbean-reflect-java all 4.5-8 [133 kB] Get: 308 http://deb.debian.org/debian bookworm/main i386 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 309 http://deb.debian.org/debian bookworm/main i386 libdoxia-java all 1.12.0-1 [459 kB] Get: 310 http://deb.debian.org/debian bookworm/main i386 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 311 http://deb.debian.org/debian bookworm/main i386 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 312 http://deb.debian.org/debian bookworm/main i386 velocity all 1.7-6 [429 kB] Get: 313 http://deb.debian.org/debian bookworm/main i386 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 314 http://deb.debian.org/debian bookworm/main i386 liboro-java all 2.0.8a-14 [70.5 kB] Get: 315 http://deb.debian.org/debian bookworm/main i386 libvelocity-tools-java all 2.0-8 [308 kB] Get: 316 http://deb.debian.org/debian bookworm/main i386 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 317 http://deb.debian.org/debian bookworm/main i386 libxerces2-java all 2.12.2-1 [1440 kB] Get: 318 http://deb.debian.org/debian bookworm/main i386 libxalan2-java all 2.7.2-4 [3419 kB] Get: 319 http://deb.debian.org/debian bookworm/main i386 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 320 http://deb.debian.org/debian bookworm/main i386 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 321 http://deb.debian.org/debian bookworm/main i386 libel-api-java all 3.0.0-3 [64.9 kB] Get: 322 http://deb.debian.org/debian bookworm/main i386 libexec-maven-plugin-java all 3.1.0-1 [66.2 kB] Get: 323 http://deb.debian.org/debian bookworm/main i386 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 324 http://deb.debian.org/debian bookworm/main i386 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 325 http://deb.debian.org/debian bookworm/main i386 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 326 http://deb.debian.org/debian bookworm/main i386 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 327 http://deb.debian.org/debian bookworm/main i386 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 328 http://deb.debian.org/debian bookworm/main i386 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 329 http://deb.debian.org/debian bookworm/main i386 libfastutil-java all 8.5.11+dfsg-1 [19.6 MB] Get: 330 http://deb.debian.org/debian bookworm/main i386 libinchi1 i386 1.03+dfsg-4 [423 kB] Get: 331 http://deb.debian.org/debian bookworm/main i386 libitext5-java all 5.5.13.3-2 [2665 kB] Get: 332 http://deb.debian.org/debian bookworm/main i386 libjackson2-annotations-java all 2.14.0-1 [68.8 kB] Get: 333 http://deb.debian.org/debian bookworm/main i386 libjackson2-core-java all 2.14.1-1 [447 kB] Get: 334 http://deb.debian.org/debian bookworm/main i386 libjackson2-databind-java all 2.14.0-1 [1584 kB] Get: 335 http://deb.debian.org/debian bookworm/main i386 libjakarta-activation-java all 2.0.0-1 [59.8 kB] Get: 336 http://deb.debian.org/debian bookworm/main i386 libjansi-java all 2.4.0-2 [105 kB] Get: 337 http://deb.debian.org/debian bookworm/main i386 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 338 http://deb.debian.org/debian bookworm/main i386 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 339 http://deb.debian.org/debian bookworm/main i386 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 340 http://deb.debian.org/debian bookworm/main i386 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 341 http://deb.debian.org/debian bookworm/main i386 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 342 http://deb.debian.org/debian bookworm/main i386 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 343 http://deb.debian.org/debian bookworm/main i386 libjetty9-java all 9.4.50-4+deb12u2 [2981 kB] Get: 344 http://deb.debian.org/debian bookworm/main i386 libjheaps-java all 0.14-2 [144 kB] Get: 345 http://deb.debian.org/debian bookworm/main i386 libjgraphx-java all 2.1.0.7-3 [807 kB] Get: 346 http://deb.debian.org/debian bookworm/main i386 libjgrapht-java all 1.5.1-3 [1584 kB] Get: 347 http://deb.debian.org/debian bookworm/main i386 libjni-inchi-jni i386 0.8+dfsg-7 [8948 B] Get: 348 http://deb.debian.org/debian bookworm/main i386 libmaven-shared-incremental-java all 1.1-3 [9524 B] Get: 349 http://deb.debian.org/debian bookworm/main i386 libplexus-compiler-java all 2.12.1-1 [99.8 kB] Get: 350 http://deb.debian.org/debian bookworm/main i386 libqdox2-java all 2.0.3-1 [296 kB] Get: 351 http://deb.debian.org/debian bookworm/main i386 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 352 http://deb.debian.org/debian bookworm/main i386 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 353 http://deb.debian.org/debian bookworm/main i386 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 354 http://deb.debian.org/debian bookworm/main i386 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 355 http://deb.debian.org/debian bookworm/main i386 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 356 http://deb.debian.org/debian bookworm/main i386 libjmol-java all 14.32.83+dfsg-2 [8699 kB] Get: 357 http://deb.debian.org/debian bookworm/main i386 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 358 http://deb.debian.org/debian bookworm/main i386 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 359 http://deb.debian.org/debian bookworm/main i386 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 360 http://deb.debian.org/debian bookworm/main i386 libmongodb-java all 3.6.3-2 [1901 kB] Get: 361 http://deb.debian.org/debian bookworm/main i386 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 362 http://deb.debian.org/debian bookworm/main i386 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 363 http://deb.debian.org/debian bookworm/main i386 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 364 http://deb.debian.org/debian bookworm/main i386 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB] Get: 365 http://deb.debian.org/debian bookworm/main i386 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 366 http://deb.debian.org/debian bookworm/main i386 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 367 http://deb.debian.org/debian bookworm/main i386 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB] Get: 368 http://deb.debian.org/debian bookworm/main i386 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 369 http://deb.debian.org/debian bookworm/main i386 libmaven-dependency-analyzer-java all 1.13.0-1 [30.4 kB] Get: 370 http://deb.debian.org/debian bookworm/main i386 libmaven-dependency-tree-java all 3.2.1-1 [34.7 kB] Get: 371 http://deb.debian.org/debian bookworm/main i386 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 372 http://deb.debian.org/debian bookworm/main i386 libmaven-dependency-plugin-java all 3.5.0-1 [173 kB] Get: 373 http://deb.debian.org/debian bookworm/main i386 libmaven-deploy-plugin-java all 3.0.0-1 [34.6 kB] Get: 374 http://deb.debian.org/debian bookworm/main i386 libmaven-enforcer-plugin-java all 3.1.0-1 [135 kB] Get: 375 http://deb.debian.org/debian bookworm/main i386 libmaven-install-plugin-java all 3.1.0-1 [28.1 kB] Get: 376 http://deb.debian.org/debian bookworm/main i386 libmaven-invoker-java all 3.2.0-1 [28.1 kB] Get: 377 http://deb.debian.org/debian bookworm/main i386 libplexus-interactivity-api-java all 1.1-2 [11.0 kB] Get: 378 http://deb.debian.org/debian bookworm/main i386 libmaven-javadoc-plugin-java all 3.4.1-2 [454 kB] Get: 379 http://deb.debian.org/debian bookworm/main i386 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 380 http://deb.debian.org/debian bookworm/main i386 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 381 http://deb.debian.org/debian bookworm/main i386 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 382 http://deb.debian.org/debian bookworm/main i386 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 383 http://deb.debian.org/debian bookworm/main i386 libmaven-jaxb2-plugin-java all 0.15.1-1 [118 kB] Get: 384 http://deb.debian.org/debian bookworm/main i386 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 385 http://deb.debian.org/debian bookworm/main i386 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 386 http://deb.debian.org/debian bookworm/main i386 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 387 http://deb.debian.org/debian bookworm/main i386 libmsgpack-java all 0.9.3-1 [155 kB] Get: 388 http://deb.debian.org/debian bookworm/main i386 libmmtf-java all 1.0.11-1 [187 kB] Get: 389 http://deb.debian.org/debian bookworm/main i386 libsurefire-java all 2.22.3-2 [1169 kB] Get: 390 http://deb.debian.org/debian bookworm/main i386 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 391 http://deb.debian.org/debian bookworm/main i386 libwagon-file-java all 3.5.3-1 [8388 B] Get: 392 http://deb.debian.org/debian bookworm/main i386 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 393 http://deb.debian.org/debian bookworm/main i386 libxml2-utils i386 2.9.14+dfsg-1.3~deb12u1 [99.1 kB] Get: 394 http://deb.debian.org/debian bookworm/main i386 libxmlunit-java all 1.6-2 [100 kB] Get: 395 http://deb.debian.org/debian bookworm/main i386 maven all 3.8.7-1 [18.9 kB] Get: 396 http://deb.debian.org/debian bookworm/main i386 maven-repo-helper all 1.11 [142 kB] Get: 397 http://deb.debian.org/debian bookworm/main i386 maven-debian-helper all 2.6.3 [108 kB] Fetched 348 MB in 6s (56.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18156 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18472 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18906 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... 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Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../015-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../017-hicolor-icon-theme_0.17-2_all.deb ... Unpacking hicolor-icon-theme (0.17-2) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../018-libgdk-pixbuf2.0-common_2.42.10+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../019-libglib2.0-0_2.74.6-2_i386.deb ... Unpacking libglib2.0-0:i386 (2.74.6-2) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../020-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../021-libxml2_2.9.14+dfsg-1.3~deb12u1_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../022-shared-mime-info_2.2-1_i386.deb ... Unpacking shared-mime-info (2.2-1) ... Selecting previously unselected package libjpeg62-turbo:i386. Preparing to unpack .../023-libjpeg62-turbo_1%3a2.1.5-2_i386.deb ... Unpacking libjpeg62-turbo:i386 (1:2.1.5-2) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../024-libpng16-16_1.6.39-2_i386.deb ... Unpacking libpng16-16:i386 (1.6.39-2) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../025-libdeflate0_1.14-1_i386.deb ... Unpacking libdeflate0:i386 (1.14-1) ... Selecting previously unselected package libjbig0:i386. Preparing to unpack .../026-libjbig0_2.1-6.1_i386.deb ... 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Setting up media-types (10.0.0) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libgraphite2-3:i386 (1.3.14-1) ... Setting up liblcms2-2:i386 (2.14-2) ... Setting up libpixman-1-0:i386 (0.42.2-1) ... Setting up libfastutil-java (8.5.11+dfsg-1) ... Setting up libjackson2-annotations-java (2.14.0-1) ... Setting up libdtd-parser-java (1.2-1) ... Setting up wdiff (1.2.2-5) ... Setting up libpciaccess0:i386 (0.17-2) ... Setting up libslf4j-java (1.7.32-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libqdox-java (1.12.1-3) ... Setting up libopentest4j-reporting-java (0.1.0-M1-2) ... Setting up libicu72:i386 (72.1-3) ... Setting up libplexus-build-api-java (0.0.7-4) ... Setting up liblerc4:i386 (4.0.0+ds-2) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.38.1-5+b1) ... 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Setting up openssl (3.0.11-1~deb12u2) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... Setting up liburi-perl (5.17-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3) ... Setting up libinchi1 (1.03+dfsg-4) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libnet-ssleay-perl:i386 (1.92-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-1) ... Setting up libdom4j-java (2.1.3-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libjetty9-java (9.4.50-4+deb12u2) ... Setting up libxcb-xfixes0:i386 (1.15-1) ... Setting up java-wrappers (0.4) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:i386 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:i386 (3.1-20221030-2) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:i386 (0.8-10) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnet-http-perl (6.22-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:i386 (2:3.87.1-1) ... 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Setting up libgdk-pixbuf-2.0-0:i386 (2.42.10+dfsg-1+b1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up ca-certificates-java (20230710~deb12u1) ... 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~deb12u1) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libxcomposite1:i386 (1:0.4.5-1) ... Setting up libavahi-client3:i386 (0.8-10) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up gnupg-utils (2.2.40-1.1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libdrm-amdgpu1:i386 (2.4.114-1+b1) ... Setting up libxcb-dri3-0:i386 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ... Setting up libx11-xcb1:i386 (2:1.8.4-2+deb12u2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-6) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:i386 (2.4.114-1+b1) ... Setting up libxdamage1:i386 (1:1.1.6-1) ... Setting up gpg-agent (2.2.40-1.1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:i386 (2.4.114-1+b1) ... Setting up libcommons-digester-java (1.8.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libparams-classify-perl:i386 (0.015-2+b1) ... Setting up gpgsm (2.2.40-1.1) ... Setting up libpango-1.0-0:i386 (1.50.12+ds-1) ... Setting up libdrm-intel1:i386 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:i386 (22.3.6-1+deb12u1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up default-jdk-doc (2:1.17-74) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.16.0-7) ... Setting up libxxf86vm1:i386 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-1.1) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (43-1) ... 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 libmodule-runtime-perl (0.016-2) ... Setting up libxfixes3:i386 (1:6.0.0-2) ... Setting up libxinerama1:i386 (2:1.1.4-3) ... Setting up libxrandr2:i386 (2:1.5.2-2+b1) ... Setting up gpg-wks-server (2.2.40-1.1) ... Setting up libcups2:i386 (2.4.2-3+deb12u5) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-dependency-tree-java (3.2.1-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libpangoft2-1.0-0:i386 (1.50.12+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libpangocairo-1.0-0:i386 (1.50.12+ds-1) ... Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:i386 (22.3.6-1+deb12u1) ... Setting up libxi6:i386 (2:1.8-1+b1) ... Setting up gpg-wks-client (2.2.40-1.1) ... Setting up libglx0:i386 (1.6.0-1) ... Setting up libmaven-install-plugin-java (3.1.0-1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:i386 (2:1.2.3-1.1) ... Setting up libbatik-java (1.16+dfsg-1+deb12u1) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libxcursor1:i386 (1:1.2.1-1) ... Setting up libmaven-invoker-java (3.2.0-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libmaven-deploy-plugin-java (3.0.0-1) ... Setting up libgl1:i386 (1.6.0-1) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up openjdk-17-jre-headless:i386 (17.0.9+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfop-java (1:2.8-2) ... Setting up libgtk2.0-0:i386 (2.24.33-2) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.68-1) ... Setting up devscripts (2.23.4+deb12u1) ... Setting up libguava-java (31.1-1) ... Setting up javahelper (0.78) ... 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 (3.8.7-1) ... Setting up libmaven-shared-incremental-java (1.1-3) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libmaven-dependency-analyzer-java (1.13.0-1) ... Setting up libplexus-compiler-java (2.12.1-1) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-artifact-transfer-java (0.13.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (14.32.83+dfsg-2) ... Setting up libmaven-enforcer-plugin-java (3.1.0-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libmaven-assembly-plugin-java (3.4.2-1) ... Setting up libcommons-text-java (1.10.0-1) ... Setting up libmsgpack-java (0.9.3-1) ... Setting up libmmtf-java (1.0.11-1) ... Setting up libjgrapht-java (1.5.1-3) ... 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 (2.36-9+deb12u3) ... Processing triggers for ca-certificates-java (20230710~deb12u1) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven-repo-helper (1.11) ... Setting up maven (3.8.7-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk-headless:i386 (17.0.9+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.13-1) ... Setting up junit4 (4.13.2-3) ... Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre:i386 (17.0.9+9-1~deb12u1) ... Setting up default-jre (2:1.17-74) ... Setting up openjdk-17-jdk:i386 (17.0.9+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up ant-optional (1.10.13-1) ... Setting up default-jdk-headless (2:1.17-74) ... Setting up junit5 (5.9.2-1) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up default-jdk (2:1.17-74) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ... Setting up libtxw2-java (2.3.0.1-10.1) ... Setting up libjaxb-java (2.3.0.1-10.1) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-8) ... 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 (3.4.1-2) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-dependency-plugin-java (3.5.0-1) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libmaven-jaxb2-plugin-java (0.15.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.3) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230710~deb12u1) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava6-live_6.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package biojava6-live dpkg-buildpackage: info: source version 6.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dpkg: warning: --compare-versions used with obsolete relation operator '>' dh clean --with javahelper 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 -plibbiojava6-java jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' dh_clean rm -rf target rm -rf biojava-*/target find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print rm -rf biojava-forester rm -rf biojava-jcolorbrewer make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' # Creating the directories for forester and jcolorbrewer, with symlinks. mkdir -p biojava-forester/src/main/java/ cp -a forester/org biojava-forester/src/main/java/ mkdir -p biojava-jcolorbrewer/src/main/java/ cp -a jcolorbrewer/org biojava-jcolorbrewer/src/main/java/ # Putting the pom.xml files of forester and jcolorbrewer into their dirs. sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomForester.xml > biojava-forester/pom.xml sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomJcolorbrewer.xml > biojava-jcolorbrewer/pom.xml dh_auto_configure mh_patchpoms -plibbiojava6-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' # Insert the correct JSON_SIMPLE_PACKAGE in the code. find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ -e 's,@JSON_SIMPLE_PACKAGE@,org.json.simple,' \ {} \; -print ./biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java 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/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 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... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0 [WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava [pom] [INFO] biojava-core [jar] [INFO] biojava-forester [jar] [INFO] biojava-alignment [jar] [INFO] biojava-structure [jar] [INFO] biojava-jcolorbrewer [jar] [INFO] biojava-structure-gui [jar] [INFO] biojava-genome [jar] [INFO] biojava-modfinder [jar] [INFO] biojava-ws [jar] [INFO] biojava-protein-disorder [jar] [INFO] biojava-aa-prop [jar] [INFO] biojava-survival [jar] [INFO] biojava-ontology [jar] [INFO] biojava-protein-comparison-tool [jar] [WARNING] The artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has been relocated to org.apache.maven.plugins:maven-antrun-plugin:jar:3.1.0 [WARNING] The artifact org.apache.maven.plugins:maven-assembly-plugin:jar:2.2-beta-5 has been relocated to org.apache.maven.plugins:maven-assembly-plugin:jar:3.4.2 [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [1/15] [INFO] --------------------------------[ pom ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava --- [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 6.1.0 [2/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-core --- [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 188 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-core --- [INFO] Copying 48 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 60 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-core --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/biojava-core-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-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] Loading source files for package org.biojava.nbio.core.util... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.features... [WARNING] Loading source files for package org.biojava.nbio.core.sequence... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.views... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription... [WARNING] Loading source files for package org.biojava.nbio.core.alignment... [WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices... [WARNING] Loading source files for package org.biojava.nbio.core.alignment.template... [WARNING] Loading source files for package org.biojava.nbio.core.exceptions... [WARNING] Loading source files for package org.biojava.nbio.core.search.io... [WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAindexFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/ABITrace.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/ABITracerCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/AbstractFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/AbstractLocation.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: Tag @link: reference not found: #getAllSubLocations() [WARNING] * {@link #getAllSubLocations()}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/AbstractReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractSequence.AnnotationType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/AccesionedLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Accessioned.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/AccessionID.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner [WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex > [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:133: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner [WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityDNARNAHybridCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityRNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/BasicSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/BitSequenceReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&' [WARNING] * Class is immutable & so this is unsupported [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastHspBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastTabularParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastXMLParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java:524: warning: invalid input: '<' [WARNING] * @exception IllegalArgumentException If readAheadLimit is < 0 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/CDSComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/CDSSequence.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:35: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [WARNING] * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:93: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [WARNING] * {@link http://www.sequenceontology.org/gff3.shtml} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:94: warning: invalid usage of tag {@link http://biowiki.org/~yam/bioe131/GFF.ppt [WARNING] * {@link http://biowiki.org/~yam/bioe131/GFF.ppt} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ChromosomeSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/ClasspathResource.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/CodonCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/ComplementCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/ComplementSequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Compound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/CompoundNotFoundException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/CompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/CompoundTranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/ConcurrencyTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/CRC64Checksum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DataSource.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/DBReferenceInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/DemoSixFrameTranslation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/DNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DNASequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DNASequence.DNAType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/DNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.AbstractEdit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Delete.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Insert.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Substitute.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblId.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblRecord.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/Equals.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ExonComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ExonSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaGeneWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java:127: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Amr ALHOSSARY [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaReaderHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaSequenceParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaWriterHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java:99: warning: @param argument "dnaSequences" is not a parameter name. [WARNING] * @param dnaSequences [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureInterface.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java:72: warning: @return tag cannot be used in method with void return type. [WARNING] public void setDescription(String description); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureRetriever.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/FileDownloadUtils.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:291: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:266: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:171: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Peter Rose [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:220: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author BalusC, [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:256: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Jacek Grzebyta [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:266: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:291: warning: invalid input: '&' [WARNING] * Recursively delete a folder & contents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name. [WARNING] * @param fastaFile [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java:58: warning: @param argument "fastaFile" is not a parameter name. [WARNING] * @param fastaFile [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name. [WARNING] * @param fastaFile [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/FlatFileCache.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java:126: warning: invalid input: '{@' [WARNING] * If the cache is {@}, returns -1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.FourBitArrayWorker.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Frame.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/FuzzyPoint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:36: warning: Tag @param cannot be used in field documentation. It can only be used in the following types of documentation: class/interface, constructor, method. [WARNING] * @param sequence [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:37: warning: Tag @return cannot be used in field documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:45: warning: invalid input: '<' [WARNING] * @author Karl Nicholas [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:46: warning: invalid input: '<' [WARNING] * @author Jacek Grzebyta [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java:142: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Amr ALHOSSARY [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/GenbankReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankWriter.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java:85: warning: @param argument "lineSeparator" is not a parameter name. [WARNING] * @param lineSeparator [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:185: warning: @inheritDoc used but setAccession(String) does not override or implement any method. [WARNING] public void setAccession(String accession) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:219: warning: @inheritDoc used but setComment(String) does not override or implement any method. [WARNING] public void setComment(String comment) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:193: warning: @inheritDoc used but setDescription(String) does not override or implement any method. [WARNING] public void setDescription(String description) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:201: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method. [WARNING] public void setIdentifier(String identifier) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:210: warning: @inheritDoc used but setName(String) does not override or implement any method. [WARNING] public void setName(String name) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:168: warning: @inheritDoc used but setVersion(int) does not override or implement any method. [WARNING] public void setVersion(int version) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:168: warning: @inheritDoc used but setVersion(int) does not override or implement any method. [WARNING] public void setVersion(int version) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:185: warning: @inheritDoc used but setAccession(String) does not override or implement any method. [WARNING] public void setAccession(String accession) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:193: warning: @inheritDoc used but setDescription(String) does not override or implement any method. [WARNING] public void setDescription(String description) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:201: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method. [WARNING] public void setIdentifier(String identifier) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:210: warning: @inheritDoc used but setName(String) does not override or implement any method. [WARNING] public void setName(String name) throws ParserException { [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:219: warning: @inheritDoc used but setComment(String) does not override or implement any method. [WARNING] public void setComment(String comment) throws ParserException { [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/GeneSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/Hashcoder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Hit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Hsp.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/InputStreamProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.BondLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.GroupLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.OneOfLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.OrderLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/IntronSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/IOUtils.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: Tag @link: reference not found: IOUtils#processReader(String) [WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/IOUtils.ReaderProcessor.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: Tag @link: reference not found: IOUtils#processReader(String) [WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/IUPACParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/IUPACParser.IUPACTable.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java:264: warning: @param argument "nucleotides" is not a parameter name. [WARNING] * @param nucleotides The nucleotide set to use when building BioJava [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<' [WARNING] * Allows creation of the store from List>. CompoundSet [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&' [WARNING] * attempting to skip onto the next sequence as & when it is asked to [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<' [WARNING] * Allows creation of the store from List>. CompoundSet [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&' [WARNING] * attempting to skip onto the next sequence as & when it is asked to [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/LightweightProfile.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:55: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:71: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/LightweightProfile.StringFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Location.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: Tag @link: reference not found: #getAllSubLocations() [WARNING] * {@link #getAllSubLocations()}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Location.Tools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:169: warning: @param argument "location" is not a parameter name. [WARNING] * @param location The location which currently expresses the outer [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/LocationHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&' [WARNING] * Assumes that the first element is the start & clones it [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:116: warning: @param argument "location" is not a parameter name. [WARNING] * @param location The location which currently expresses the outer [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&' [WARNING] * Assumes that the first element is the start & clones it [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/Messages.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/NucleotideCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/ParseFastaFileDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/ParserException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/PlainFastaHeaderParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Point.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Point.Resolver.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/PrettyXMLWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/Profile.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:61: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:116: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:125: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:135: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:144: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:160: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:170: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:180: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:239: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/Profile.StringFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/ProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/ProfileView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ProteinSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/ProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/Qualifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/QualityFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/QuantityFeature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/ReferenceInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Result.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/ResultFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/ReversedSequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/RNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/RNASequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/RNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/RnaSequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/SearchIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Sequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SequenceLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceMixin.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: Tag @link: reference not found: SequenceBackingStore [WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: Tag @link: reference not found: Compound#toString() [WARNING] * filled with the results of {@link Compound#toString()}. Does not [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:153: warning: @param argument "writer" is not a parameter name. [WARNING] * @param writer The writer to send data to [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: Tag @link: reference not found: Compound#toString() [WARNING] * filled with the results of {@link Compound#toString()}. Does not [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: Tag @link: reference not found: SequenceBackingStore [WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:288: warning: invalid input: '&' [WARNING] * ATG, TGT & GTA [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:346: warning: invalid input: '&' [WARNING] * length & compound sets used. The code will also bail out the moment [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:362: warning: invalid input: '&' [WARNING] * length & compound sets used. The code will also bail out the moment [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceMixin.SequenceIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceCollection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceUsage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/SequencePair.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:44: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:53: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:62: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:71: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength() [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:80: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:89: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java:35: warning: @param argument "dataInput" is not a parameter name. [WARNING] * @param dataInput [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceProxyView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/SequenceTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SimpleLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SimplePoint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: Tag @link: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) [WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) } [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: Tag @link: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) [WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) } [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/SingleLinkageClusterer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/SoftHashMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/StartCodonSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/StopCodonSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/Strand.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/StringManipulationHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:81: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author andreas [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:207: warning: invalid input: '<' [WARNING] * @throws IllegalArgumentException if n <= 0 [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:219: warning: invalid input: '<' [WARNING] * @throws IllegalArgumentException if n <= 0 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java:106: warning: invalid input: '<' [WARNING] * @throws IllegalArgumentException if scale < 1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:81: warning: invalid input: '&' [WARNING] * Returns Blosum 100 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:89: warning: invalid input: '&' [WARNING] * Returns Blosum 30 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:97: warning: invalid input: '&' [WARNING] * Returns Blosum 35 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:105: warning: invalid input: '&' [WARNING] * Returns Blosum 40 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:113: warning: invalid input: '&' [WARNING] * Returns Blosum 45 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:121: warning: invalid input: '&' [WARNING] * Returns Blosum 50 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:129: warning: invalid input: '&' [WARNING] * Returns Blosum 55 matrix by Henikoff & Henikoff [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Table.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Sequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceProxyView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractNucleotideCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Accessioned.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ComplementCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Substitute.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Insert.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Delete.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.AbstractEdit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/StringProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/SequenceFileProxyLoader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/GenbankProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/UniprotProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/ArrayListProxySequenceReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.CaseInsensitiveTriplet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.Codon.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Frame.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.Builder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/ParserException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/CompoundNotFoundException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/DemoSixFrameTranslation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/ParseFastaFileDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/UncompressFile.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/biojava-core-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 6.1.0 [3/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-forester --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 359 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-forester --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-forester --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-forester --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/biojava-forester-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-forester --- [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. 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[WARNING] 31 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/biojava-forester-6.1.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 6.1.0 [4/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-alignment --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 53 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-alignment --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 24 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-alignment --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/biojava-alignment-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-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] Loading source files for package org.biojava.nbio.phylo... [WARNING] Loading source files for package org.biojava.nbio.alignment... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java:119: warning: invalid usage of tag {@link #pamDistance(MultipleSequenceAlignment [WARNING] * method {@link #pamDistance(MultipleSequenceAlignment}). The gapped [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/DistanceTreeEvaluator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/ForesterWrapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/FractionalIdentityScorer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/FractionalSimilarityScorer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GapPenalty.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GapPenalty.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/GuanUberbacher.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning: invalid input: '<' [WARNING] * space complexity is a modest (a multiple < 2) increase in time. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/GuideTree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/GuideTree.Node.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/GuideTreeNode.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/HierarchicalClusterer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/MatrixAligner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning: Tag @link: reference not found: Profile [WARNING] * @param each element of the alignment {@link Profile} is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/NeedlemanWunsch.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/PairwiseSequenceScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/PartitionRefiner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning: Tag @link: reference not found: Profile [WARNING] * @param each element of the alignment {@link Profile} is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/ProfileProfileAligner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning: Tag @link: reference not found: Profile [WARNING] * @param each {@link Sequence} in the pair of alignment {@link Profile}s is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/ProfileProfileScorer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/RescoreRefiner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning: Tag @link: reference not found: Profile [WARNING] * @param each element of the alignment {@link Profile} is of type S [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/Scorer.html... 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[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-summary.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractMatrixAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/CookbookMSA.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoDistanceTree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoLoadSubstMax.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/TestDNANeedlemanWunsch.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/class-use/DemoAlignProteins.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/package-use.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/allclasses-index.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/help-doc.html... [WARNING] 58 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/biojava-alignment-6.1.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 6.1.0 [5/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure --- [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 431 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure --- [INFO] Copying 55 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 100 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureWriter.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityHeuristics.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-structure --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/biojava-structure-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-structure --- [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] Loading source files for package org.biojava.nbio.structure... [WARNING] Loading source files for package org.biojava.nbio.structure.basepairs... [WARNING] Loading source files for package org.biojava.nbio.structure.cluster... [WARNING] Loading source files for package org.biojava.nbio.structure.secstruc... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.misc... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.core... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.internal... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.geometry... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.axis... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.utils... [WARNING] Loading source files for package org.biojava.nbio.structure.quaternary... [WARNING] Loading source files for package org.biojava.nbio.structure.io... 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[WARNING] Loading source files for package org.biojava.nbio.structure.jama... [WARNING] Loading source files for package org.biojava.nbio.structure.geometry... [WARNING] Loading source files for package org.biojava.nbio.structure.scop... [WARNING] Loading source files for package org.biojava.nbio.structure.xtal... [WARNING] Loading source files for package org.biojava.nbio.structure.xtal.io... [WARNING] Loading source files for package org.biojava.nbio.structure.contact... [WARNING] Loading source files for package org.biojava.nbio.structure.asa... [WARNING] Loading source files for package org.biojava.nbio.structure.chem... [WARNING] Loading source files for package org.biojava.nbio.structure.cath... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.WrappedAtom.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/AbstractStructureAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/AFP.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/AFPChain.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java:1311: warning: Tag @link: reference not found: org.biojava.nbio.structure.gui.JMatrixPanel [WARNING] * A {@link org.biojava.nbio.structure.gui.JMatrixPanel}, which is used in [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:56: warning: invalid input: '<' [WARNING] // AFP(k-1) < AFP(k)(refer AFP.h definition), [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/AFPChainFlipper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AFPChainScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/AfpChainWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java:59: warning: Parameter "name1" is documented more than once. [WARNING] * @param name1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/AFPTwister.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/AligMatEl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/Alignable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AlignmentProgressListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AlignmentResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AlignmentTools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:306: warning: invalid input: '<' [WARNING] * If none are found at n<=maxSymmetry, the alignment is reported as [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:317: warning: invalid input: '<' [WARNING] * @return The order of symmetry of alignment, or 1 if no order <= [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AligNPE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/AlignUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/AllChemCompProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AltAligComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AminoAcid.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AminoAcidImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:48: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:64: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:85: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/asa/AsaCalculator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java:621: warning: invalid usage of tag {@link Element().N [WARNING] * unknown type (element) the vdw radius of {@link Element().N} is returned [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/Astral.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/Astral.AstralSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/Atom.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java:263: warning: @return tag cannot be used in method with void return type. [WARNING] public void setCharge(short charge); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/AtomCache.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:227: warning: invalid input: '<' [WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:251: warning: invalid input: '<' [WARNING] * @throws StructureException if biassemblyId < 0 or other problems while loading structure [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:471: warning: Tag @link: reference not found: #setStrictSCOP(boolean) [WARNING] * see {@link #setStrictSCOP(boolean)} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:677: warning: Tag @link: reference not found: #isAutoFetch() [WARNING] * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:680: warning: @param argument "fetchFileEvenIfObsolete" is not a parameter name. [WARNING] * @param fetchFileEvenIfObsolete Whether to fetch obsolete records [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:681: warning: Tag @see: reference not found: #setFetchCurrent(boolean) [WARNING] * @see #setFetchCurrent(boolean) [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:691: warning: Tag @link: reference not found: #isAutoFetch() [WARNING] * such as when {@link #isAutoFetch()} is false. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:795: warning: @param argument "pdbId" is not a parameter name. [WARNING] * @param pdbId [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/AtomContact.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/AtomContactSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/AtomIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomPositionMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AtomPositionMap.GroupMatcher.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/AugmentedResidueRange.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/Author.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/AxisAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/BasePairParameters.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/BcifFileReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/BetaBridge.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/BioAssemblyIdentifier.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java:61: warning: @param argument "pdbCode" is not a parameter name. [WARNING] * @param pdbCode [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:51: warning: Tag @link: reference not found: #toString() [WARNING] * It is recommended that the {@link #toString()} method also return the [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:95: warning: Tag @see: reference not found: StructureTools#getReducedStructure(Structure, String) [WARNING] * @see StructureTools#getReducedStructure(Structure, String) [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BioAssemblyInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BioAssemblyTools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java:265: warning: @param argument "structure" is not a parameter name. [WARNING] * @param structure [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/BioJavaStructureAlignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/Block.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: Tag @see: reference not found: #setAlignRes() [WARNING] * @see #setAlignRes() [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: Tag @see: reference not found: #updateCoreLength() [WARNING] * @see #updateCoreLength() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/BlockImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:55: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockImpl a BlockImpl instance linked to its parent BlockSet. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java:72: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockImpl an identical copy of the input BlockImpl object. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: Tag @see: reference not found: #setAlignRes() [WARNING] * @see #setAlignRes() [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: Tag @see: reference not found: #updateCoreLength() [WARNING] * @see #updateCoreLength() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/BlockSet.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java:114: warning: @param argument "matrices" is not a parameter name. [WARNING] * @param matrices [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/BlockSetImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:58: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockSet an instance linked to the parent alignment. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java:79: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return BlockSet an identical copy of the input object. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/Bond.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java:29: warning: invalid input: '<' [WARNING] * @author Jules Jacobsen [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/BondImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:30: warning: invalid input: '<' [WARNING] * @author Jules Jacobsen [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java:47: warning: Tag @link: reference not found: #Bond(Atom, Atom, int, boolean) [WARNING] * {@link #Bond(Atom, Atom, int, boolean)} with the [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/BondMaker.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/BondType.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java:26: warning: invalid input: '<' [WARNING] * @author Jules Jacobsen [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/BoundingBox.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/BravaisLattice.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/BridgeType.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java:25: warning: invalid input: '<' [WARNING] * (i-1,i,i+1) and (j-1,j,j+1), where i------------------ [INFO] Building biojava-jcolorbrewer 6.1.0 [6/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-jcolorbrewer --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-jcolorbrewer --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-jcolorbrewer --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-jcolorbrewer --- [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] Loading source files for package org.jcolorbrewer.ui... [WARNING] Loading source files for package org.jcolorbrewer... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ColorBrewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/ColorPaletteChooserDialog.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:82: warning: Tag @see: reference not found: ColorChooserDialog [WARNING] * @see ColorChooserDialog [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java:436: warning: @param argument "color" is not a parameter name. [WARNING] * @param color the new color [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/ColorPanelSelectionModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/DivergingColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/PaletteIcon.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/QualitativeColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/SequentialColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/class-use/ColorBrewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/help-doc.html... [WARNING] 3 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/biojava-jcolorbrewer-6.1.0-javadoc.jar [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 6.1.0 [7/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 131 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure-gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 6 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure-gui --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-structure-gui --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-structure-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] Loading source files for package org.biojava.nbio.structure.gui... [WARNING] Loading source files for package org.biojava.nbio.structure.gui.util... [WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color... [WARNING] Loading source files for package org.biojava.nbio.structure.gui.events... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui... [WARNING] Loading source files for package org.biojava.nbio.structure.align.webstart... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.jmol... [WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AboutDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java:199: warning: @param argument "label" is not a parameter name. [WARNING] * @param label [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/AFPFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlignedPosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/AlignmentGuiDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/AligUIManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/BiojavaJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/BrowserOpener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ChooseDirAction.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ColorUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ConfigPDBInstallPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/ConfigXMLHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java:63: warning: @param argument "the" is not a parameter name. [WARNING] * @param the input value [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/CookBook.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/CoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoAlignmentFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoCE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoCeSymm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoFATCAT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoMultipleMC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoNWALignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoQuatSymmetryJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoRotationAxis.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowBiolAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowCATHDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoShowLargeAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoStructureFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/DemoSW3DAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DisplayAFP.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/DotPlotPanel.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java:59: warning: @param argument "background" is not a parameter name. [WARNING] * @param background [Optional]A matrix of 'background colors' over which to draw the alignment. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/GradientMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/GradientPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/HelpDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java:83: warning: @param argument "type" is not a parameter name. [WARNING] * @param type [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java:84: warning: @param argument "numcomponents" is not a parameter name. [WARNING] * @param numcomponents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/JMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.JmolLoggerAdapter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java:41: warning: @param argument "rotationGroup" is not a parameter name. [WARNING] * @param rotationGroup [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/JmolTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/JmolViewerImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/JNLPProxy.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/JPrintPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java:145: warning: @param argument "interpDirection" is not a parameter name. [WARNING] * @param interpDirection An array of size colorSpace.getNumComponents() [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.InterpolationDirection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/LogColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MemoryMonitor.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MemoryMonitor.Surface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MenuCreator.DotPlotListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java:157: warning: @param argument "multAln" is not a parameter name. [WARNING] * @param multAln [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java:158: warning: @param argument "colors" is not a parameter name. [WARNING] * @param colors [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyDistMaxListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyExportListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyOpenPdbFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MySaveFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/MyTableRowSorter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ParameterGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBDirPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBServerPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/PDBUploadPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/RenderStyle.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.GradientRenderer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/ScopSelectPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/Selection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/SelectionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/SelectPDBPanel.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/SequenceDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SequenceMouseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/SequenceScalePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/ShowPDBIDListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/ShowStructureInJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/SqrtColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/StatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/StructureLoaderThread.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/StructurePairSelector.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/StructureViewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java:107: warning: @param argument "msa" is not a parameter name. [WARNING] * @param msa [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/SystemInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/WebStartClientDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/WebStartMain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/WrapLayout.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-summary.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/WebStartClientDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowCATHDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoNWALignment.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowLargeAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/allclasses-index.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java:54: warning: invalid input: '&' [WARNING] * Tracks Memory allocated & used, displayed in graph form. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/help-doc.html... [WARNING] 20 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/biojava-structure-gui-6.1.0-javadoc.jar [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 6.1.0 [8/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-genome --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 51 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-genome --- [INFO] Copying 83 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 20 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-genome --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-genome --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/biojava-genome-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-genome --- [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] Loading source files for package org.biojava.nbio.genome.homology... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.geneid... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff... [WARNING] Loading source files for package org.biojava.nbio.genome... [WARNING] Loading source files for package org.biojava.nbio.genome.util... [WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq... [WARNING] Loading source files for package org.biojava.nbio.genome.query... [WARNING] Loading source files for package org.biojava.nbio.genome.uniprot... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/BlastHomologyHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/BlastXMLQuery.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/ChromosomeMappingTools.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:807: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Yana Valasatava [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java:854: warning: Tag @author cannot be used in method documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author Yana Valasatava [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/ChromPos.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/Cytoband.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/CytobandParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/Fastq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqVariant.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/FastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/Feature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/FeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/FeatureI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/FeatureList.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GCStats.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/GeneFeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GFF3Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/GFF3Writer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java:41: warning: @param argument "fileName" is not a parameter name. [WARNING] * @param fileName [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java:42: warning: @param argument "chromosomeSequence" is not a parameter name. [WARNING] * @param chromosomeSequence [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/IlluminaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/IlluminaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/Location.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:414: warning: invalid input: '<' [WARNING] * For position < 0, return Location( start, end + position ). [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java:456: warning: invalid input: '<' [WARNING] * For position < 0, return Location( end - position, end ). [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/LocIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/OutputHitsGFF.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/ParseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/ProteinMappingTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SangerFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SangerFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SolexaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/SolexaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/SplitFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/StainType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/StreamListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/UniprotToFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/help-doc.html... [WARNING] 7 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/biojava-genome-6.1.0-javadoc.jar [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 6.1.0 [9/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 23 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-modfinder --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-modfinder --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/biojava-modfinder-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-modfinder --- [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] Loading source files for package org.biojava.nbio.phosphosite... [WARNING] Loading source files for package org.biojava.nbio.protmod... [WARNING] Loading source files for package org.biojava.nbio.protmod.io... [WARNING] Loading source files for package org.biojava.nbio.protmod.structure... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/Component.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:33: warning: Tag @link: reference not found: register [WARNING] * you have to use one of the {@link register} and {@link of} methods. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java:112: warning: @param argument "pdbccIds" is not a parameter name. [WARNING] * @param pdbccIds possible Protein Data Bank ID. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/ComponentXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/Dataset.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationCategory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationCondition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationConditionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationLinkage.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:57: warning: @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent1 label of the atom on the first [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:60: warning: @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent2 label of the atom on the second [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:80: warning: @param argument "labelOfAtomOnComponent1" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent1 label of the atom on the first [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java:83: warning: @param argument "labelOfAtomOnComponent2" is not a parameter name. [WARNING] * @param labelOfAtomOnComponent2 label of the atom on the second [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ModificationOccurrenceType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/ModifiedCompound.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:50: warning: Tag @link: reference not found: ProteinModificationBean [WARNING] * @return {@link ProteinModificationBean} occurred on the residue. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning: Tag @see: reference not found: #getLinkedGroupPairs [WARNING] * @see #getLinkedGroupPairs [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:85: warning: @return tag cannot be used in method with void return type. [WARNING] public void setAtomLinkages(Set linkages); [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning: Tag @link: reference not found: addGroup [WARNING] * Add a linkage. Add new the involved groups first using {@link addGroup}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java:68: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [WARNING] * @return a {@link ModifiedCompound}. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:50: warning: Tag @link: reference not found: ProteinModificationBean [WARNING] * @return {@link ProteinModificationBean} occurred on the residue. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:76: warning: Tag @see: reference not found: #getLinkedGroupPairs [WARNING] * @see #getLinkedGroupPairs [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java:88: warning: Tag @link: reference not found: addGroup [WARNING] * Add a linkage. Add new the involved groups first using {@link addGroup}. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModification.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModificationImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModificationImpl.Builder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/ProteinModificationRegistry.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java:209: warning: @param argument "mod" is not a parameter name. [WARNING] * @param mod [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/Site.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureAtom.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureAtomLinkage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/StructureAtomXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/StructureUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/help-doc.html... [WARNING] 16 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/biojava-modfinder-6.1.0-javadoc.jar [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 6.1.0 [10/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 21 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ws --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-ws --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/biojava-ws-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-ws --- [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] Loading source files for package org.biojava.nbio.ws.hmmer... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment.qblast... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastJob.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastMatrixEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/HmmerDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/HmmerDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/HmmerResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/HmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:46: warning: invalid input: '&' [WARNING] * separatorSequence = "&"; [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java:79: warning: invalid input: '&' [WARNING] * {@code mappingSequence} is "=" and separator sequence is "&"; [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:140: warning: Tag @link: reference not found: NCBIQBlastService#printRemoteBlastInfo() [WARNING] * A list of available databases can be acquired by calling {@link NCBIQBlastService#printRemoteBlastInfo()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java:144: warning: @param argument "db" is not a parameter name. [WARNING] * @param db : a valid name to a NCBI blastable database [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/NCBIQBlastServiceDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/help-doc.html... [WARNING] 5 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/biojava-ws-6.1.0-javadoc.jar [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 6.1.0 [11/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-disorder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-disorder --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-protein-disorder --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-protein-disorder --- [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] Loading source files for package org.biojava.nbio.ronn... [WARNING] Loading source files for package org.biojava.nbio.data.sequence... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/FastaSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Jronn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Jronn.Range.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.Model.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ModelLoader.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/NullOutputStream.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ORonn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/ORonnModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/PredictDisorder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/RonnConstraint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/RonnConstraint.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/SequenceUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/Timer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/help-doc.html... [WARNING] 1 warning [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/biojava-protein-disorder-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 6.1.0 [12/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 33 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-aa-prop --- [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java: Recompile with -Xlint:removal for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-aa-prop --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-aa-prop --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-aa-prop --- [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] Loading source files for package org.biojava.nbio.aaproperties... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.xml... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/AminoAcidProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/BioJavaAADemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/CommandPrompt.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/CommandPrompt.PropertyName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/Constraints.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Charge.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Hydrophobicity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2NormalizedVanDerWaalsVolume.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2Polarizability.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SecondaryStructure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convert2SolventAccessibility.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:40: warning: Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @author kohchuanhock [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:41: warning: Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [WARNING] * @version 2011.06.09 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/Element.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/ElementTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/IPeptideProperties.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning: invalid input: '<' [WARNING] * here [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/SchemaGenerator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/Utils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.TRANSITION.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.GROUPING.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.ATTRIBUTE.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/index-all.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/help-doc.html... [WARNING] 61 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/biojava-aa-prop-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 6.1.0 [13/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-survival --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-survival --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 46 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-survival --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-survival --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-survival --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-survival --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/biojava-survival-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-survival --- [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] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... [WARNING] Loading source files for package org.biojava.nbio.survival.cox... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.stats... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.matrix... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators... [WARNING] Loading source files for package org.biojava.nbio.survival.data... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/AgScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatus.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/ChangeValue.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/ChiSq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/Cholesky2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/Chsolve2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/CompactCharSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxCC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxCoefficient.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxMart.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxMethod.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxR.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java:78: warning: invalid input: '<' [WARNING] * the percent change in loglikelihood is <= eps. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/CoxVariables.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/HeaderInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/Matrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/ResidualsCoxph.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/ResidualsCoxph.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/RiskInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/StdArrayIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/StrataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvFitInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfLower.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Error.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Method.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvivalInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvivalInfoHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/SurvivalInfoIndex.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/WaldTest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/WaldTestInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/WorkSheet.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java:1467: warning: @param argument "f" is not a parameter name. [WARNING] * @param f [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/help-doc.html... [WARNING] 3 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/biojava-survival-6.1.0-javadoc.jar [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 6.1.0 [14/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ontology --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ontology --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 36 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ontology --- [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ontology --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/test-classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java uses unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ontology --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-ontology --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/biojava-ontology-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-ontology --- [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] Loading source file /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/package-info.java... [WARNING] Loading source files for package org.biojava.nbio.ontology... [WARNING] Loading source files for package org.biojava.nbio.ontology.io... [WARNING] Loading source files for package org.biojava.nbio.ontology.utils... [WARNING] Loading source files for package org.biojava.nbio.ontology.obo... [WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/AbstractAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/AbstractTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/AlreadyExistsException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/Annotatable.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning: Tag @see: reference not found: org.biojavax.RichAnnotatable [WARNING] * @see org.biojavax.RichAnnotatable [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/Annotation.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning: Tag @see: reference not found: org.biojavax.RichAnnotation [WARNING] * @see org.biojavax.RichAnnotation [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/AssertionFailure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/DefaultOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/GOParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/IntegerOntology.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/IntegerOntology.IntTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/InvalidTermException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/KeyedWeakReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileEventListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java:41: 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] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/OboFileParser.SOPair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/OboParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Ontology.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java:43: warning: Tag @see: reference not found: org.biojavax.ontology.ComparableOntology [WARNING] * @see org.biojavax.ontology.ComparableOntology [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Ontology.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntologyTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/OntoTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/ParseGO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/RemoteTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/RemoteTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/SmallAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/SmallMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/StaticMemberPlaceHolder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Synonym.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/TabDelimParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Term.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:35: warning: Tag @link: reference not found: org.biojava.nbio.AnnotationAnnotation [WARNING] * A term in an ontology. This has an {@link org.biojava.nbio.Annotation Annotation} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:54: warning: Tag @see: reference not found: org.biojavax.ontology.ComparableTerm [WARNING] * @see org.biojavax.ontology.ComparableTerm [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Term.Impl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java:116: warning: Tag @see: reference not found: org.biojavax.ontology.SimpleComparableTermThis can be used to implement Ontology.createTerm [WARNING] * @see org.biojavax.ontology.SimpleComparableTerm [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Triple.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:44: warning: Tag @see: reference not found: org.biojavax.ontology.ComparableTriple [WARNING] * @see org.biojavax.ontology.ComparableTriple [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning: invalid input: '&' [WARNING] * return to.getSubject() == getSubject() && [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:98: warning: invalid input: '&' [WARNING] * return to.getSubject() == getSubject() && [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning: invalid input: '&' [WARNING] * to.getObject() == getObject() && [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:99: warning: invalid input: '&' [WARNING] * to.getObject() == getObject() && [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Triple.Impl.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java:114: warning: Tag @see: reference not found: org.biojavax.ontology.SimpleComparableTriple [WARNING] * @see org.biojavax.ontology.SimpleComparableTriple [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Variable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/Variable.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/WeakValueHashMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntoTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/DefaultOps.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/OboParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/GOParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/class-use/TabDelimParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AbstractAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/StaticMemberPlaceHolder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/AssertionFailure.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallAnnotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/KeyedWeakReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/SmallMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/Annotatable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/class-use/WeakValueHashMap.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileEventListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.SOPair.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/class-use/ParseGO.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/io/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/help-doc.html... [WARNING] 14 warnings [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/biojava-ontology-6.1.0-javadoc.jar [INFO] [INFO] ------------< org.biojava:biojava-protein-comparison-tool >------------- [INFO] Building biojava-protein-comparison-tool 6.1.0 [15/15] [INFO] --------------------------------[ jar ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-comparison-tool --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-comparison-tool --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-comparison-tool --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-protein-comparison-tool --- [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/biojava-protein-comparison-tool-6.1.0.jar [INFO] [INFO] --- maven-javadoc-plugin:3.4.1:jar (default-cli) @ biojava-protein-comparison-tool --- [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] Loading source files for package org.biojava.nbio.proteincomparisontool... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 [WARNING] Building tree for all the packages and classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/HelloWorld.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/class-use/HelloWorld.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/org/biojava/nbio/proteincomparisontool/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/overview-tree.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/apidocs/help-doc.html... [WARNING] 1 warning [INFO] Building jar: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/target/biojava-protein-comparison-tool-6.1.0-javadoc.jar [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [16/15] [INFO] --------------------------------[ pom ]--------------------------------- [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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian 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.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before. [INFO] [INFO] >>> maven-javadoc-plugin:3.4.1:aggregate (default-cli) > compile @ biojava >>> [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-core 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-core --- [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-core --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 188 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-forester 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-forester --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 359 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/TreePanel.java: Recompile with -Xlint:removal for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-alignment 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-alignment --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-alignment --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 53 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: Recompile with -Xlint:removal for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-structure 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure --- [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 431 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Recompile with -Xlint:removal for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-jcolorbrewer 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-structure-gui 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 131 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Some input files use or override a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/SequenceDisplay.java: Recompile with -Xlint:deprecation for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Some input files use or override a deprecated API that is marked for removal. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.java: Recompile with -Xlint:removal for details. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Some input files use unchecked or unsafe operations. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-genome 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-genome --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-genome --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 51 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-modfinder 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-modfinder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 23 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/classes [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-ws 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ws --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 21 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-protein-disorder 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/classes [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking biojava-aa-prop 6.1.0 [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Changes detected - recompiling the module! 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:56: warning: invalid input: '<' [WARNING] // AFP(k-1) < AFP(k)(refer AFP.h definition), [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:57: warning: invalid input: '<' [WARNING] // ie i(k-1) < i(k) and j(k-1) < j(k) [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/AFPChainFlipper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/AFPChainScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/model/AfpChainWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java:59: warning: Parameter "name1" is documented more than once. [WARNING] * @param name1 [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/AFPFromFasta.html... 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[WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex > [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:133: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning: invalid input: '<' [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner [WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor. [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/template/Aligner.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/routines/AlignerHelper.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning: Tag @link: reference not found: AlignedSequence [WARNING] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/alignment/Alignments.PairInProfileScorerType.html... 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[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:306: warning: invalid input: '<' [WARNING] * If none are found at n<=maxSymmetry, the alignment is reported as [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:317: warning: invalid input: '<' [WARNING] * @return The order of symmetry of alignment, or 1 if no order <= [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:474: warning: invalid input: '<' [WARNING] * List>> aln = getOptAlnAsList(AFPChain afpChain); [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:506: warning: invalid input: '<' [WARNING] * A Map can be viewed as a function from K to V. This class represents [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/pairwise/AligNPE.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/helper/AlignUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html... 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[WARNING] * @param cutsPerSection the number of cuts added to each section during each pass [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning: @param argument "cutsPerSection" is not a parameter name. [WARNING] * @param cutsPerSection the number of cuts added to each section during each pass [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:48: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:64: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:85: warning: @param argument "error" is not a parameter name. [WARNING] * @param error [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/Annotatable.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning: Tag @see: reference not found: org.biojavax.RichAnnotatable [WARNING] * @see org.biojavax.RichAnnotatable [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ontology/utils/Annotation.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning: Tag @see: reference not found: org.biojavax.RichAnnotation [WARNING] * @see org.biojavax.RichAnnotation [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/Annotation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/AnnotationParser.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/cox/stats/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/ws/hmmer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/analysis/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/application/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/applications/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/phylogeny/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/tools/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/archaeopteryx/webservices/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/datastructures/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/development/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/distance/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/character/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/matrix/distance/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/parsimony/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/evoinference/tools/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/go/etc/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nexus/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/nhx/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/phyloxml/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/tol/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/parsers/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/msa_compactor/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/pccx/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/data/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/factories/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/phylogeny/iterators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/protein/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sdi/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/species/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/surfacing/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/test/examples/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/tools/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/util/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/hmmer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/overview-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/deprecated-list.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/index.html... [WARNING] Building index for all classes... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/allclasses-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/allpackages-index.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/index-all.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/overview-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/help-doc.html... [WARNING] 100 warnings [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 25.759 s] [INFO] biojava-core ....................................... SUCCESS [ 9.438 s] [INFO] biojava-forester ................................... SUCCESS [ 12.138 s] [INFO] biojava-alignment .................................. SUCCESS [ 3.147 s] [INFO] biojava-structure .................................. SUCCESS [ 12.404 s] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.583 s] [INFO] biojava-structure-gui .............................. SUCCESS [ 4.893 s] [INFO] biojava-genome ..................................... SUCCESS [ 3.002 s] [INFO] biojava-modfinder .................................. SUCCESS [ 2.163 s] [INFO] biojava-ws ......................................... SUCCESS [ 1.854 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 1.850 s] [INFO] biojava-aa-prop .................................... SUCCESS [ 2.382 s] [INFO] biojava-survival ................................... SUCCESS [ 2.513 s] [INFO] biojava-ontology ................................... SUCCESS [ 2.239 s] [INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.120 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:27 min [INFO] Finished at: 2025-02-25T04:17:45Z [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' 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/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode test OpenJDK 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... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0 [WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava [pom] [INFO] biojava-core [jar] [INFO] biojava-forester [jar] [INFO] biojava-alignment [jar] [INFO] biojava-structure [jar] [INFO] biojava-jcolorbrewer [jar] [INFO] biojava-structure-gui [jar] [INFO] biojava-genome [jar] [INFO] biojava-modfinder [jar] [INFO] biojava-ws [jar] [INFO] biojava-protein-disorder [jar] [INFO] biojava-aa-prop [jar] [INFO] biojava-survival [jar] [INFO] biojava-ontology [jar] [INFO] biojava-protein-comparison-tool [jar] [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [1/15] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 6.1.0 [2/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-core --- [INFO] Copying 24 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-core --- [INFO] Copying 48 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-core --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.fasta.TestFASTAReader [INFO] Running org.biojava.nbio.core.util.SequenceToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.218 s - in org.biojava.nbio.core.util.SequenceToolsTest [INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.util.TestUncompressInputStream [INFO] Running org.biojava.nbio.core.util.EqualsTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.core.util.EqualsTest [INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.core.util.StringManipulationHelperTest [INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.259 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest [INFO] Running org.biojava.nbio.core.util.SoftHashMapTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.04 s - in org.biojava.nbio.core.util.SoftHashMapTest [INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.util.FlatFileCacheTest [INFO] Running org.biojava.nbio.core.util.HashcoderTest [INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.core.util.HashcoderTest [INFO] Running org.biojava.nbio.core.util.XMLHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 s - in org.biojava.nbio.core.util.XMLHelperTest [INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest 22 43.22 some text
2021-08-15
 SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest [INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.core.util.CRC64ChecksumTest [INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest [INFO] Running org.biojava.nbio.core.sequence.DNATest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.nbio.core.sequence.DNATest [INFO] Running org.biojava.nbio.core.sequence.location.LocationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.core.sequence.location.LocationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest [INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.core.sequence.location.LocationParserTest [INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.core.sequence.ExonComparatorTest [INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.core.sequence.RNASequenceTest [INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest [INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.TestSequenceEquals [INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.EditSequenceTest [INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.SequenceViewTest [INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.views.WindowViewTests [INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.444 s - in org.biojava.nbio.core.sequence.io.ABITracerTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [INFO] Running org.biojava.nbio.core.sequence.StrandTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.sequence.StrandTest [INFO] Running org.biojava.nbio.core.sequence.TranslationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 s - in org.biojava.nbio.core.sequence.TranslationTest [INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.071 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest [INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.sequence.ExonSequenceTest [INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest [INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.GeneSequenceTest [INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest [INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest [INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest [INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.158 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest [INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest [INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest [INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.core.alignment.SimpleProfileTest [INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [INFO] Running org.biojava.nbio.core.search.io.HspTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. getAlignment hashCode equals [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.search.io.HspTest [INFO] Running org.biojava.nbio.core.search.io.SearchIOTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.038 s - in org.biojava.nbio.core.search.io.SearchIOTest [INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest createObjects SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. getFileExtensions setFile [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.79 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest getFileExtensions SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. setFile [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.017 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 501, Failures: 0, Errors: 0, Skipped: 15 [INFO] [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 6.1.0 [3/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-forester --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-forester --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-forester --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-forester --- [INFO] No tests to run. [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 6.1.0 [4/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-alignment --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-alignment --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-alignment --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-alignment --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator [INFO] Running org.biojava.nbio.phylo.TestForesterWrapper SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.phylo.TestForesterWrapper [INFO] Running org.biojava.nbio.alignment.SmithWatermanTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.nbio.alignment.SmithWatermanTest [INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.SimpleProfilePairTest [INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading [INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.io.TestStockholmParser [INFO] Running org.biojava.nbio.alignment.GuideTreeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 s - in org.biojava.nbio.alignment.GuideTreeTest [INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest [INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest [INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.105 s - in org.biojava.nbio.alignment.TestSubOptimalMSA [INFO] Running org.biojava.nbio.alignment.TestDNAAlignment SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.934 s - in org.biojava.nbio.alignment.TestDNAAlignment [INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest [INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest [INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest [INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.LocalAlignmentTest [INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 s - in org.biojava.nbio.alignment.NeedlemanWunschTest [INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 127, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 6.1.0 [5/15] [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure --- [INFO] Copying 3 resources [INFO] Copying 61 resources [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure --- [INFO] Copying 55 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestExperimentalTechniques [INFO] Running org.biojava.nbio.structure.HetatomImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.structure.HetatomImplTest [INFO] Running org.biojava.nbio.structure.TestURLIdentifier SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.973 s - in org.biojava.nbio.structure.TestURLIdentifier [INFO] Running org.biojava.nbio.structure.TestKeywords SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.727 s - in org.biojava.nbio.structure.TestKeywords [INFO] Running org.biojava.nbio.structure.TestAtomCache SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.369 s - in org.biojava.nbio.structure.TestAtomCache [INFO] Running org.biojava.nbio.structure.TestStructureImpl SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestStructureImpl [INFO] Running org.biojava.nbio.structure.TestCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.structure.TestCalc [INFO] Running org.biojava.nbio.structure.ChemCompTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.241 s - in org.biojava.nbio.structure.ChemCompTest [INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters [INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.105 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster [INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor [INFO] Running org.biojava.nbio.structure.TestPdbId [1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100] [1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] [1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.TestPdbId [INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser [INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc [INFO] Running org.biojava.nbio.structure.AtomPositionMapTest [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.AtomPositionMapTest [INFO] Running org.biojava.nbio.structure.SiteTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.structure.SiteTest [INFO] Running org.biojava.nbio.structure.PDBStatusTest [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.PDBStatusTest [INFO] Running org.biojava.nbio.structure.TestParsingCalcium [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestParsingCalcium [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm [INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools [INFO] Running org.biojava.nbio.structure.TestEntityHeuristics SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.74 s - in org.biojava.nbio.structure.TestEntityHeuristics [INFO] Running org.biojava.nbio.structure.TestAltLocs SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.341 s - in org.biojava.nbio.structure.TestAltLocs [INFO] Running org.biojava.nbio.structure.SourceCompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.184 s - in org.biojava.nbio.structure.SourceCompoundTest [INFO] Running org.biojava.nbio.structure.io.TestShortLines SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.249 s - in org.biojava.nbio.structure.io.TestShortLines [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.065 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.816 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip [INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.918 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader [INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.876 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles [INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders [INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestSiftsParsing [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands [INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.476 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles [INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing [INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.553 s - in org.biojava.nbio.structure.io.TestHeaderOnly [INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures [INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest [INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.structure.io.TestDBRefParsing [INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestParseOnAsymId [INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest [INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestHardBioUnits [INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing [INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.3 s - in org.biojava.nbio.structure.io.TestMMCIFWriting [INFO] Running org.biojava.nbio.structure.io.TestTitleParsing [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.TestTitleParsing [INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB [INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.025 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId [INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType [INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. Using PDB_DIR=/tmp as temporary file directory [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.56 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider [INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.766 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes [INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.616 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader [INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.896 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest [INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestStructureCrossReferences [INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.align.util.RotationAxisTest [INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.088 s - in org.biojava.nbio.structure.align.util.AtomCacheTest [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.004 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.012 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer [INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion [INFO] Running org.biojava.nbio.structure.align.client.TestStructureName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.048 s - in org.biojava.nbio.structure.align.client.TestStructureName [INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency [INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment [INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest [INFO] Running org.biojava.nbio.structure.ElementTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ElementTest [INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestLoadStructureFromURL [INFO] Running org.biojava.nbio.structure.TestDNAAlignment [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.TestDNAAlignment [INFO] Running org.biojava.nbio.structure.Test2JA5 [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.Test2JA5 [INFO] Running org.biojava.nbio.structure.ResidueRangeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.051 s - in org.biojava.nbio.structure.ResidueRangeTest [INFO] Running org.biojava.nbio.structure.TestAtomIterator [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestAtomIterator [INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign [INFO] Running org.biojava.nbio.structure.TestStructureSerialization SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.054 s - in org.biojava.nbio.structure.TestStructureSerialization [INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.024 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions [INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.3 s - in org.biojava.nbio.structure.geometry.TestSuperPosition [INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP [INFO] Running org.biojava.nbio.structure.TestVeryLongFileName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestVeryLongFileName [INFO] Running org.biojava.nbio.structure.ResidueNumberTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ResidueNumberTest [INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.423 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.structure.xtal.TestCrystalCell [INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.82 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.025 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo [INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.446 s - in org.biojava.nbio.structure.TestEntityResIndexMapping [INFO] Running org.biojava.nbio.structure.TestChargeAdder [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestChargeAdder [INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.934 s - in org.biojava.nbio.structure.PdbFileFormat30Test [INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. Interface - 4.0 Interface - 5.477225575051661 Interface - 5.477225575051661 [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder [INFO] Running org.biojava.nbio.structure.contact.TestContactCalc [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.008 s - in org.biojava.nbio.structure.contact.TestContactCalc [INFO] Running org.biojava.nbio.structure.TestCloning [WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestCloning [INFO] Running org.biojava.nbio.structure.TestBond [WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBond [INFO] Running org.biojava.nbio.structure.TestNucleotides [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestNucleotides [INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.03 s - in org.biojava.nbio.structure.asa.TestAsaCalc [INFO] Running org.biojava.nbio.structure.Test4hhb SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.87 s - in org.biojava.nbio.structure.Test4hhb [INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.225 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider [INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 374, Failures: 0, Errors: 0, Skipped: 188 [INFO] [INFO] [INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------ [INFO] Building biojava-jcolorbrewer 6.1.0 [6/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-jcolorbrewer --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-jcolorbrewer --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-jcolorbrewer --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-jcolorbrewer --- [INFO] No tests to run. [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 6.1.0 [7/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure-gui --- [INFO] Copying 49 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-structure-gui --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-structure-gui --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-structure-gui --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-structure-gui --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest [INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.gui.RenderStyleTest [INFO] Running org.biojava.nbio.structure.gui.ViewerTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.nbio.structure.gui.ViewerTest [INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.structure.gui.TestAtomInfo [INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 6.1.0 [8/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-genome --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-genome --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-genome --- [INFO] Copying 83 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-genome --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-genome --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.io.fastq.FastqTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest [INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest [INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.genome.io.fastq.ConvertTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest [INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.nbio.genome.TestGenomeMapping [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.043 s - in org.biojava.nbio.genome.TestGenomeMapping [INFO] Running org.biojava.nbio.genome.TestIssue355 [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.TestIssue355 [INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.TestChromosomeMappingTools [INFO] Running org.biojava.nbio.genome.TestLocation [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.TestLocation [INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.473 s - in org.biojava.nbio.genome.GeneFeatureHelperTest [INFO] Running org.biojava.nbio.genome.FeatureListTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.genome.FeatureListTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 204, Failures: 0, Errors: 0, Skipped: 2 [INFO] [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 6.1.0 [9/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-modfinder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-modfinder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-modfinder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-modfinder --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.046 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest [INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.283 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest [INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 12, Failures: 0, Errors: 0, Skipped: 8 [INFO] [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 6.1.0 [10/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ws --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ws --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ws --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ws --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.057 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 6.1.0 [11/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-disorder --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-disorder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-disorder --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-disorder --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-disorder --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ronn.JronnTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.563 s - in org.biojava.nbio.ronn.JronnTest [INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.046 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 6.1.0 [12/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-aa-prop --- [INFO] Copying 11 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-aa-prop --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-aa-prop --- [INFO] Copying 7 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-aa-prop --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-aa-prop --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.454 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest [INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.371 s - in org.biojava.nbio.aaproperties.xml.ElementTest [INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 SequenceName,A,N,MolecularWeight NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 SequenceName,A,N,MolecularWeight NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint SAOV_0114,53660.5723,41370.0,41370.0,4.986 SAOV_0094,45884.0164,57760.0,57760.0,8.5193 SAA6008_00126,95002.026,55240.0,55740.0,5.7263 SequenceName,A,N,MolecularWeight SAOV_0114,0.101,0.0525,53660.5723 SAOV_0094,0.0537,0.0767,45884.0164 SAA6008_00126,0.0955,0.0414,95002.026 SequenceName,A,N,MolecularWeight SAOV_0114,0.101,0.0525,53660.5723 SAOV_0094,0.0537,0.0767,45884.0164 SAA6008_00126,0.0955,0.0414,95002.026 [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.369 s - in org.biojava.nbio.aaproperties.CommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest [INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [INFO] Running org.biojava.nbio.aaproperties.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 s - in org.biojava.nbio.aaproperties.CookBookTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 52, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 6.1.0 [13/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-survival --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-survival --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-survival --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-survival --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-survival --- [INFO] No tests to run. [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 6.1.0 [14/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-ontology --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-ontology --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-ontology --- [INFO] Copying 6 resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-ontology --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-ontology --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ontology.TestParseOBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.ontology.TestParseOBO [INFO] Running org.biojava.nbio.ontology.TestOboFileParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojava.nbio.ontology.TestOboFileParsing [INFO] Running org.biojava.nbio.ontology.TestParseSBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.ontology.TestParseSBO [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] ------------< org.biojava:biojava-protein-comparison-tool >------------- [INFO] Building biojava-protein-comparison-tool 6.1.0 [15/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ biojava-protein-comparison-tool --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-protein-comparison-tool --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ biojava-protein-comparison-tool --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-protein-comparison-tool --- [INFO] No tests to run. [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 0.002 s] [INFO] biojava-core ....................................... SUCCESS [09:50 min] [INFO] biojava-forester ................................... SUCCESS [ 0.038 s] [INFO] biojava-alignment .................................. SUCCESS [03:00 min] [INFO] biojava-structure .................................. SUCCESS [16:21 min] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.451 s] [INFO] biojava-structure-gui .............................. SUCCESS [01:00 min] [INFO] biojava-genome ..................................... SUCCESS [03:00 min] [INFO] biojava-modfinder .................................. SUCCESS [ 40.088 s] [INFO] biojava-ws ......................................... SUCCESS [ 10.046 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 20.034 s] [INFO] biojava-aa-prop .................................... SUCCESS [01:20 min] [INFO] biojava-survival ................................... SUCCESS [ 0.036 s] [INFO] biojava-ontology ................................... SUCCESS [ 30.029 s] [INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.111 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 36:13 min [INFO] Finished at: 2025-02-25T04:53:59Z [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/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Ddebian.package=libbiojava6-java -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install OpenJDK 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... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:6.1.0 [WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] biojava [pom] [INFO] biojava-core [jar] [INFO] biojava-forester [jar] [INFO] biojava-alignment [jar] [INFO] biojava-structure [jar] [INFO] biojava-jcolorbrewer [jar] [INFO] biojava-structure-gui [jar] [INFO] biojava-genome [jar] [INFO] biojava-modfinder [jar] [INFO] biojava-ws [jar] [INFO] biojava-protein-disorder [jar] [INFO] biojava-aa-prop [jar] [INFO] biojava-survival [jar] [INFO] biojava-ontology [jar] [INFO] biojava-protein-comparison-tool [jar] [INFO] [INFO] ------------------------< org.biojava:biojava >------------------------- [INFO] Building biojava 6.1.0 [1/15] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] --no-parent [INFO] [INFO] ----------------------< org.biojava:biojava-core >---------------------- [INFO] Building biojava-core 6.1.0 [2/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-core --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-core into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-forester >-------------------- [INFO] Building biojava-forester 6.1.0 [3/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-forester --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-forester into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-alignment >-------------------- [INFO] Building biojava-alignment 6.1.0 [4/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-alignment --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-alignment into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-structure >-------------------- [INFO] Building biojava-structure 6.1.0 [5/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-structure into /usr/share/java [INFO] [INFO] ------------------< org.biojava:biojava-jcolorbrewer >------------------ [INFO] Building biojava-jcolorbrewer 6.1.0 [6/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-jcolorbrewer --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-jcolorbrewer into /usr/share/java [INFO] [INFO] -----------------< org.biojava:biojava-structure-gui >------------------ [INFO] Building biojava-structure-gui 6.1.0 [7/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-structure-gui --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-structure-gui into /usr/share/java [INFO] [INFO] ---------------------< org.biojava:biojava-genome >--------------------- [INFO] Building biojava-genome 6.1.0 [8/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-genome --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-genome into /usr/share/java [INFO] [INFO] -------------------< org.biojava:biojava-modfinder >-------------------- [INFO] Building biojava-modfinder 6.1.0 [9/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-modfinder --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-modfinder into /usr/share/java [INFO] [INFO] -----------------------< org.biojava:biojava-ws >----------------------- [INFO] Building biojava-ws 6.1.0 [10/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ws --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-ws into /usr/share/java [INFO] [INFO] ----------------< org.biojava:biojava-protein-disorder >---------------- [INFO] Building biojava-protein-disorder 6.1.0 [11/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-protein-disorder --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-protein-disorder into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-aa-prop >--------------------- [INFO] Building biojava-aa-prop 6.1.0 [12/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-aa-prop --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-aa-prop into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-survival >-------------------- [INFO] Building biojava-survival 6.1.0 [13/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-survival --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-survival into /usr/share/java [INFO] [INFO] --------------------< org.biojava:biojava-ontology >-------------------- [INFO] Building biojava-ontology 6.1.0 [14/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-ontology --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-ontology into /usr/share/java [INFO] [INFO] ------------< org.biojava:biojava-protein-comparison-tool >------------- [INFO] Building biojava-protein-comparison-tool 6.1.0 [15/15] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ biojava-protein-comparison-tool --- [INFO] Cleaning pom file: /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-comparison-tool/pom.xml.save with options: [INFO] --keep-pom-version --package=libbiojava6-java [INFO] --rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/biojava6-live-6.1.0+dfsg/debian/maven.publishedRules [INFO] Install jar for biojava-protein-comparison-tool into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 0.384 s] [INFO] biojava-core ....................................... SUCCESS [ 0.043 s] [INFO] biojava-forester ................................... SUCCESS [ 0.040 s] [INFO] biojava-alignment .................................. SUCCESS [ 0.028 s] [INFO] biojava-structure .................................. SUCCESS [ 0.032 s] [INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.023 s] [INFO] biojava-structure-gui .............................. SUCCESS [ 0.028 s] [INFO] biojava-genome ..................................... SUCCESS [ 0.028 s] [INFO] biojava-modfinder .................................. SUCCESS [ 0.023 s] [INFO] biojava-ws ......................................... SUCCESS [ 0.024 s] [INFO] biojava-protein-disorder ........................... SUCCESS [ 0.030 s] [INFO] biojava-aa-prop .................................... SUCCESS [ 0.024 s] [INFO] biojava-survival ................................... SUCCESS [ 0.029 s] [INFO] biojava-ontology ................................... SUCCESS [ 0.023 s] [INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.033 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.978 s [INFO] Finished at: 2025-02-25T04:54:02Z [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore Analysing pom.xml... Analysing biojava-aa-prop/pom.xml... Checking the parent dependency in the sub project biojava-aa-prop/pom.xml Analysing biojava-alignment/pom.xml... Checking the parent dependency in the sub project biojava-alignment/pom.xml Analysing biojava-core/pom.xml... Checking the parent dependency in the sub project biojava-core/pom.xml Analysing biojava-forester/pom.xml... Checking the parent dependency in the sub project biojava-forester/pom.xml Analysing biojava-genome/pom.xml... Checking the parent dependency in the sub project biojava-genome/pom.xml Analysing biojava-jcolorbrewer/pom.xml... Checking the parent dependency in the sub project biojava-jcolorbrewer/pom.xml Analysing biojava-modfinder/pom.xml... Checking the parent dependency in the sub project biojava-modfinder/pom.xml Analysing biojava-ontology/pom.xml... Checking the parent dependency in the sub project biojava-ontology/pom.xml Analysing biojava-protein-comparison-tool/pom.xml... Checking the parent dependency in the sub project biojava-protein-comparison-tool/pom.xml Analysing biojava-protein-disorder/pom.xml... Checking the parent dependency in the sub project biojava-protein-disorder/pom.xml Analysing biojava-structure/pom.xml... Checking the parent dependency in the sub project biojava-structure/pom.xml Analysing biojava-structure-gui/pom.xml... Checking the parent dependency in the sub project biojava-structure-gui/pom.xml Analysing biojava-survival/pom.xml... Checking the parent dependency in the sub project biojava-survival/pom.xml Analysing biojava-ws/pom.xml... Checking the parent dependency in the sub project biojava-ws/pom.xml Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/libciftools-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/api/index.html > dpkg --search /usr/share/doc/libciftools-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/api/index.html > dpkg --search /usr/share/doc/libciftools-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java/apidocs/index.html > dpkg --search /usr/share/doc/libciftools-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libciftools-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-codec-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-codec-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/api/index.html > dpkg --search /usr/share/doc/libcommons-math-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java-doc/api/index.html > dpkg --search /usr/share/doc/libcommons-math-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-java/apidocs/index.html > dpkg --search /usr/share/doc/libcommons-math-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libcommons-math-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/libitext5-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/api/index.html > dpkg --search /usr/share/doc/libitext5-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/api/index.html > dpkg --search /usr/share/doc/libitext5-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java/apidocs/index.html > dpkg --search /usr/share/doc/libitext5-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libitext5-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java/api/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java-doc/api/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java/apidocs/index.html > dpkg --search /usr/share/doc/libjackson2-databind-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjackson2-databind-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-api-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/api/index.html > dpkg --search /usr/share/doc/libjaxb-api-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/api/index.html > dpkg --search /usr/share/doc/libjaxb-api-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-api-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/api/index.html > dpkg --search /usr/share/doc/libjaxb-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/api/index.html > dpkg --search /usr/share/doc/libjaxb-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java/apidocs/index.html > dpkg --search /usr/share/doc/libjaxb-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjaxb-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/api/index.html > dpkg --search /usr/share/doc/libjgrapht-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/api/index.html > dpkg --search /usr/share/doc/libjgrapht-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java/apidocs/index.html > dpkg --search /usr/share/doc/libjgrapht-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjgrapht-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjmol-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java/api/index.html > dpkg --search /usr/share/doc/libjmol-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java-doc/api/index.html > dpkg --search /usr/share/doc/libjmol-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java/apidocs/index.html > dpkg --search /usr/share/doc/libjmol-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjmol-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libjson-simple-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/api/index.html > dpkg --search /usr/share/doc/libjson-simple-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/api/index.html > dpkg --search /usr/share/doc/libjson-simple-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java/apidocs/index.html > dpkg --search /usr/share/doc/libjson-simple-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libjson-simple-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libmmtf-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/api/index.html > dpkg --search /usr/share/doc/libmmtf-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/api/index.html > dpkg --search /usr/share/doc/libmmtf-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java/apidocs/index.html > dpkg --search /usr/share/doc/libmmtf-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmmtf-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libslf4j-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/api/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/api/index.html > dpkg --search /usr/share/doc/libslf4j-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/apidocs/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libvecmath-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/api/index.html > dpkg --search /usr/share/doc/libvecmath-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/api/index.html > dpkg --search /usr/share/doc/libvecmath-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java/apidocs/index.html > dpkg --search /usr/share/doc/libvecmath-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libvecmath-java-doc/apidocs/index.html bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibbiojava6-java dh_install jh_installjavadoc debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' 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/biojava6-live-6.1.0+dfsg' dh_installchangelogs dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-4_all.deb'. dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/25528 and its subdirectories I: Current time: Mon Feb 24 16:59:34 -12 2025 I: pbuilder-time-stamp: 1740459574 Tue Jan 23 22:36:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Tue Jan 23 22:36:36 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Tue Jan 23 23:23:41 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Tue Jan 23 23:23:41 UTC 2024 I: biojava6-live_6.1.0+dfsg-4_i386.changes: Format: 1.8 Date: Tue, 07 Feb 2023 10:14:19 +0100 Source: biojava6-live Binary: libbiojava6-java libbiojava6-java-doc Architecture: all Version: 6.1.0+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: libbiojava6-java - Java API to biological data and applications (version 6) libbiojava6-java-doc - [Biology] Documentation for BioJava 6 Closes: 1030728 Changes: biojava6-live (6.1.0+dfsg-4) unstable; urgency=medium . * Excluding two more tests accessing the network during build-time tests, thanks to Hans Joachim Desserud! (Closes: #1030728) Checksums-Sha1: e5b12e895b62b51e3f87a8e30cd3784497817d9b 17866 biojava6-live_6.1.0+dfsg-4_i386.buildinfo 50b9ed2f2c1f097b460bcd5c41ba005098b2f424 2241440 libbiojava6-java-doc_6.1.0+dfsg-4_all.deb f86929e20ee031de1cd5cac091634972662bac98 5366668 libbiojava6-java_6.1.0+dfsg-4_all.deb Checksums-Sha256: e8b8685a954efef9fbc71432551286c82d15e9d9d81adc3daf7dd3a3087bdef2 17866 biojava6-live_6.1.0+dfsg-4_i386.buildinfo 313187cf8f71da967bbc92e039d08fe141f8c240ee1fda96e55e9c2e9fefaaae 2241440 libbiojava6-java-doc_6.1.0+dfsg-4_all.deb aa4c9f5916e8ad0cb81f885f5720b9385c4f76a05457bd711ed6f8b184fc08de 5366668 libbiojava6-java_6.1.0+dfsg-4_all.deb Files: 5bbf760639ac596f7f6ffe90af847be0 17866 java optional biojava6-live_6.1.0+dfsg-4_i386.buildinfo 81f339909d3c800b9eb962e78a2f77f8 2241440 doc optional libbiojava6-java-doc_6.1.0+dfsg-4_all.deb 126c3ac54f58819dbb4c09bb34671f3b 5366668 java optional libbiojava6-java_6.1.0+dfsg-4_all.deb Tue Jan 23 23:23:43 UTC 2024 I: diffoscope 254 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/biojava6-live_6.1.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/biojava6-live_6.1.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/biojava6-live_6.1.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/b1/biojava6-live_6.1.0+dfsg-4_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/b2/biojava6-live_6.1.0+dfsg-4_i386.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 22.733s) 9.793s 9 calls diff 9.242s 10 calls xxd 1.632s 11 calls js-beautify 1.267s 11 calls html2text 0.736s 6 calls xz 0.031s 2 calls cmp 0.031s 2 calls cmp (external) 0.001s 9 calls cmp (internal) ## compare_files (cumulative) (total time: 166.286s) 34.734s 1 call abc.DotChangesFile 34.703s 1 call abc.DebFile 34.674s 2 calls abc.XzFile 33.799s 1 call abc.DebDataTarFile 16.597s 1 call abc.JavaScriptFile 11.558s 1 call abc.HtmlFile 0.124s 1 call abc.TarFile 0.099s 1 call abc.Md5sumsFile ## container_extract (total time: 2.325s) 1.572s 7008 calls diffoscope.comparators.deb.DebTarContainer 0.736s 6 calls diffoscope.comparators.xz.XzContainer 0.010s 8 calls diffoscope.comparators.deb.DebContainer 0.007s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.606s) 0.606s 133 calls linediff ## has_same_content_as (total time: 0.033s) 0.022s 1 call abc.DebDataTarFile 0.010s 2 calls abc.DebFile 0.000s 2 calls abc.Md5sumsFile 0.000s 2 calls abc.TextFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.JavaScriptFile 0.000s 1 call abc.HtmlFile ## main (total time: 38.249s) 38.244s 2 calls outputs 0.005s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer ## output (total time: 2.737s) 2.202s 1 call html 0.353s 1 call text 0.182s 1 call json ## recognizes (total time: 0.232s) 0.099s 578 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.075s 12 calls diffoscope.comparators.binary.FilesystemFile 0.046s 260 calls diffoscope.comparators.utils.archive.ArchiveMember 0.012s 108 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.113s) 0.113s 13 calls specialize Tue Jan 23 23:24:22 UTC 2024 E: biojava6-live failed to build reproducibly in bookworm on i386. Tue Jan 23 23:24:22 UTC 2024 E: diffoscope 254 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bookworm/i386/biojava6-live_6.1.0+dfsg-4.diffoscope.html Tue Jan 23 23:24:30 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Jan 23 23:24:30 UTC 2024 I: Submitting 20K b1/biojava6-live_6.1.0+dfsg-4_i386.buildinfo.asc Tue Jan 23 23:24:32 UTC 2024 I: Submitting 20K b2/biojava6-live_6.1.0+dfsg-4_i386.buildinfo.asc Tue Jan 23 23:24:33 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 23 23:24:33 UTC 2024 I: Done submitting .buildinfo files. Tue Jan 23 23:24:33 UTC 2024 I: Removing signed biojava6-live_6.1.0+dfsg-4_i386.buildinfo.asc files: removed './b1/biojava6-live_6.1.0+dfsg-4_i386.buildinfo.asc' removed './b2/biojava6-live_6.1.0+dfsg-4_i386.buildinfo.asc'