I: pbuilder: network access will be disabled during build I: Current time: Wed May 15 05:25:39 +14 2024 I: pbuilder-time-stamp: 1715700339 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biojava4-live_4.2.12+dfsg-8.dsc] I: copying [./biojava4-live_4.2.12+dfsg.orig.tar.xz] I: copying [./biojava4-live_4.2.12+dfsg-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Dec 11 21:26:50 2022 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava4-live_4.2.12+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting biojava4-live in biojava4-live-4.2.12+dfsg dpkg-source: info: unpacking biojava4-live_4.2.12+dfsg.orig.tar.xz dpkg-source: info: unpacking biojava4-live_4.2.12+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_itext_class_updates dpkg-source: info: applying use_simple_json dpkg-source: info: applying fix_import dpkg-source: info: applying faketest dpkg-source: info: applying fix_ascii_characters_mapping dpkg-source: info: applying skip_network_related_tests dpkg-source: info: applying remove_openchart_use dpkg-source: info: applying ignore_fake_tests dpkg-source: info: applying fix_ambiguous_method_call.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/730688/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 14 15:25 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/730688/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/730688/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=38e253a0d6064a20838bcdfc7672dbf3 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=730688 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.SCcUH7bj/pbuilderrc_8g7f --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SCcUH7bj/b2 --logfile b2/build.log biojava4-live_4.2.12+dfsg-8.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 14 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/730688/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), ant, javahelper, libcommons-dbcp-java, libhsqldb-java, libcommons-collections3-java, libcommons-pool-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libguava-java, libcommons-codec-java, libitext5-java, libjmol-java, libvecmath-java, default-jdk-headless, junit4, ant-optional, ant-contrib, libhamcrest-java, libjson-simple-java, liblog4j2-java, libslf4j-java, libxmlunit-java, libjgrapht0.8-java, libjaxb-api-java, libjaxb-java, libnetx-java, default-jdk-doc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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 ant; however: Package ant is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on libcommons-dbcp-java; however: Package libcommons-dbcp-java is not installed. pbuilder-satisfydepends-dummy depends on libhsqldb-java; however: Package libhsqldb-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-collections3-java; however: Package libcommons-collections3-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-pool-java; however: Package libcommons-pool-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however: Package libcommons-logging-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math-java; however: Package libcommons-math-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-cli-java; however: Package libcommons-cli-java is not installed. pbuilder-satisfydepends-dummy depends on libguava-java; however: Package libguava-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 libitext5-java; however: Package libitext5-java is not installed. pbuilder-satisfydepends-dummy depends on libjmol-java; however: Package libjmol-java is not installed. pbuilder-satisfydepends-dummy depends on libvecmath-java; however: Package libvecmath-java is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-headless; however: Package default-jdk-headless is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 is not installed. pbuilder-satisfydepends-dummy depends on ant-optional; however: Package ant-optional is not installed. pbuilder-satisfydepends-dummy depends on ant-contrib; however: Package ant-contrib is not installed. pbuilder-satisfydepends-dummy depends on libhamcrest-java; however: Package libhamcrest-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 libslf4j-java; however: Package libslf4j-java is not installed. pbuilder-satisfydepends-dummy depends on libxmlunit-java; however: Package libxmlunit-java is not installed. pbuilder-satisfydepends-dummy depends on libjgrapht0.8-java; however: Package libjgrapht0.8-java is not installed. pbuilder-satisfydepends-dummy depends on 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 libnetx-java; however: Package libnetx-java is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-doc; however: Package default-jdk-doc is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-contrib{a} ant-optional{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk-doc{a} default-jdk-headless{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{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} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit{a} junit4{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libassuan0{a} libatinject-jsr330-api-java{a} libb-hooks-op-check-perl{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-dbcp-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-pool-java{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastinfoset-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} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgoogle-gson-java{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libhsqldb-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} 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} libitext5-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjgraph-java{a} libjgrapht0.8-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} libjsr305-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblightcouch-java{a} liblog4j1.2-java{a} liblog4j2-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libnaga-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnetx-java{a} libnpth0t64{a} libnspr4{a} libnss3{a} libparams-classify-perl{a} libpcsclite1{a} libpipeline1{a} libplexus-archiver-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-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox2-java{a} libreadline8t64{a} librelaxng-datatype-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{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} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} liburi-perl{a} libvecmath-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libxbean-reflect-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxmlunit-java{a} libxsom-java{a} libxz-java{a} m4{a} man-db{a} media-types{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk-headless{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} wdiff{a} The following packages are RECOMMENDED but will NOT be installed: curl debian-keyring dput dput-ng dupload equivs javascript-common libarchive-cpio-perl libasound2t64 libcups2t64 libdata-dump-perl libdistro-info-perl libfontconfig1 libfreetype6 libgit-wrapper-perl libgitlab-api-v4-perl libharfbuzz0b libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjansi-java libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace unzip wget 0 packages upgraded, 225 newly installed, 0 to remove and 0 not upgraded. Need to get 213 MB of archives. After unpacking 748 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 java-common all 0.75 [6640 B] Get: 29 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 35 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 36 http://deb.debian.org/debian trixie/main amd64 ant all 1.10.14-1 [2162 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 ant-contrib all 1.0~b3+svn177-12 [262 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 ant-optional all 1.10.14-1 [455 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 52 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 openjdk-17-doc all 17.0.11+9-1 [12.8 MB] Get: 64 http://deb.debian.org/debian trixie/main amd64 default-jdk-doc amd64 2:1.17-75 [3148 B] Get: 65 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 66 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.40-3 [565 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.40-3 [793 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.40-3 [1094 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 gnupg-utils amd64 2.2.40-3 [928 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.40-3 [950 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.40-3 [695 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 gpg-wks-client amd64 2.2.40-3 [541 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 gpg-wks-server amd64 2.2.40-3 [532 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.40-3 [671 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.40-3 [847 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 88 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 116 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.23.7 [1068 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 javahelper all 0.79 [84.6 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 junit all 3.8.2-10 [108 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 junit4 all 4.13.2-4 [349 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 134 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 135 http://deb.debian.org/debian trixie/main amd64 libargs4j-java all 2.33-2 [138 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libasm-java all 9.7-1 [394 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 138 http://deb.debian.org/debian trixie/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 139 http://deb.debian.org/debian trixie/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 153 http://deb.debian.org/debian trixie/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 159 http://deb.debian.org/debian trixie/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libmaven3-core-java all 3.8.7-2 [1573 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.0-2 [29.0 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get: 171 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libxz-java all 1.9-1 [143 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libcommons-pool-java all 1.6-5 [109 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libcommons-dbcp-java all 1.4-8 [157 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libcommons-math-java all 2.2-8 [926 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libexec-maven-plugin-java all 3.1.0-2 [66.7 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libxsom-java all 2.3.0.1-10.1 [400 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libhsqldb-java all 2.7.2-1 [1657 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libinchi1 amd64 1.03+dfsg-4+b2 [436 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 libitext5-java all 5.5.13.3-4 [2667 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 librngom-java all 2.3.0.1-10.1 [290 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libjgrapht0.8-java all 0.8.3-6 [214 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-jni amd64 0.8+dfsg-7 [9064 B] Get: 208 http://deb.debian.org/debian trixie/main amd64 libmaven-shared-incremental-java all 1.1-4 [9924 B] Get: 209 http://deb.debian.org/debian trixie/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libplexus-compiler-java all 2.12.1-2 [99.0 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libjni-inchi-java all 0.8+dfsg-7 [33.2 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libnaga-java all 3.0+svn80-5 [43.5 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libjmol-java all 16.2.9+dfsg-1 [8951 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libnetx-java all 0.5-4 [138 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libxmlunit-java all 1.6-2 [100 kB] Fetched 213 MB in 7s (28.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.11-minimal:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libnpth0t64:amd64 (1.6-3.1) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.40-8) ... Setting up java-common (0.75) ... Setting up libnetx-java (0.5-4) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libqdox2-java (2.0.3-1) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libcommons-exec-java (1.3-2) ... Setting up libvecmath-java (1.5.2-7) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libasm-java (9.7-1) ... Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up liblog4j1.2-java (1.2.17-11) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up file (1:5.45-3) ... Setting up libjson-simple-java (2.3.0-1) ... Setting up libassuan0:amd64 (2.5.6-1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libsnappy1v5:amd64 (1.2.0-2) ... Setting up libexec-maven-plugin-java (3.1.0-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue May 14 15:27:23 UTC 2024. Universal Time is now: Tue May 14 15:27:23 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up autotools-dev (20220109.1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up junit (3.8.2-10) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up gnupg-l10n (2.2.40-3) ... Setting up libapache-pom-java (29-2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up libitext5-java (5.5.13.3-4) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.9-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libcommons-pool-java (1.6-5) ... Setting up autopoint (0.21-14) ... Setting up binfmt-support (2.2.2-7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libjgraph-java (5.12.4.2+dfsg-7) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libcommons-math-java (2.2-8) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up openssl (3.2.1-3) ... Setting up libcdi-api-java (1.2-3) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up libargs4j-java (2.33-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libinchi1 (1.03+dfsg-4+b2) ... Setting up libnaga-java (3.0+svn80-5) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+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 (1.2.1-3+b2) ... Setting up libdom4j-java (2.1.4-1) ... 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 libcommons-dbcp-java (1.4-8) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.21-14+b1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up libjgrapht0.8-java (0.8.3-6) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libhsqldb-java (2.7.2-1) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libmaven-parent-java (35-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxmlunit-java (1.6-2) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up librngom-java (2.3.0.1-10.1) ... Setting up libjni-inchi-jni (0.8+dfsg-7) ... Setting up groff-base (1.23.0-4) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up gpgconf (2.2.40-3) ... Setting up openjdk-17-doc (17.0.11+9-1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libxsom-java (2.3.0.1-10.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.16.0-1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.40-3) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.40-3) ... Setting up default-jdk-doc (2:1.17-75) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-3) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gpg-wks-server (2.2.40-3) ... Setting up libhttpclient-java (4.5.14-1) ... 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 libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up gnupg (2.2.40-3) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.79) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libmaven3-core-java (3.8.7-2) ... Setting up libmaven-shared-incremental-java (1.1-4) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-compiler-java (2.12.1-2) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libjni-inchi-java (0.8+dfsg-7) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libjmol-java (16.2.9+dfsg-1) ... Processing triggers for libc-bin (2.38-10) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up default-jre-headless (2:1.17-75) ... Setting up ant-contrib (1.0~b3+svn177-12) ... Setting up ant-optional (1.10.14-1) ... Setting up default-jdk-headless (2:1.17-75) ... Setting up libistack-commons-java (3.0.6-5) ... 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 ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/730688/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/730688/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-8_source.changes dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dpkg: warning: --compare-versions used with obsolete relation operator '>' dh clean --with javahelper jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' dh_clean rm -rf build rm -rf dist rm -rf javadoc rm -rf test rm -f biojava-*/build.xml rm -rf biojavadoc rm -rf doc find . -name "*.class" -delete rm -rf buildtest find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print make[1]: Leaving directory '/build/reproducible-path/biojava4-live-4.2.12+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/biojava4-live-4.2.12+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' dh_auto_configure sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml sed -e 's/BJLIB/biojava4-core/g' debian/build.xml > biojava-core/build.xml sed -e 's/BJLIB/biojava4-alignment/g' debian/build.xml > biojava-alignment/build.xml sed -e 's/BJLIB/biojava4-genome/g' debian/build.xml > biojava-genome/build.xml sed -e 's/BJLIB/biojava4-modfinder/g' debian/build.xml > biojava-modfinder/build.xml sed -e 's/BJLIB/biojava4-phylo/g' debian/build.xml > biojava-phylo/build.xml sed -e 's/BJLIB/biojava4-sequencing/g' debian/build.xml > biojava-sequencing/build.xml sed -e 's/BJLIB/biojava4-protein-disorder/g' debian/build.xml > biojava-protein-disorder/build.xml sed -e 's/BJLIB/biojava4-structure/g' debian/build.xml > biojava-structure/build.xml sed -e 's/BJLIB/biojava4-ws/g' debian/build.xml > biojava-ws/build.xml sed -e 's/BJLIB/biojava4-structure-gui/g' debian/build.xml > biojava-structure-gui/build.xml sed -e 's/BJLIB/biojava4-ontology/g' debian/build.xml > biojava-ontology/build.xml sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml make[1]: Leaving directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' 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 cd biojava-jcolorbrewer && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 9 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Warning: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/src/main/resources does not exist. jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL Total time: 5 seconds cd biojava-forester && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 359 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use or override a deprecated API that is marked for removal. [javac] Note: Recompile with -Xlint:removal for details. [copy] Warning: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-forester/src/main/resources does not exist. jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL Total time: 19 seconds cd biojava-core && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 176 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes [javac] Note: Some input files use or override a deprecated API that is marked for removal. [javac] Note: Recompile with -Xlint:removal for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 24 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL Total time: 11 seconds cd biojava-phylo && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 8 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [copy] Copying 2 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL Total time: 4 seconds cd biojava-alignment && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 45 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API that is marked for removal. [javac] Note: Recompile with -Xlint:removal for details. [copy] Copying 1 file to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL Total time: 6 seconds cd biojava-aa-prop && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 32 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] Creating empty /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/xml/package-info.class [javac] Creating empty /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/package-info.class [javac] Creating empty /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/convertor/package-info.class [javac] Creating empty /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/package-info.class [copy] Copying 11 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL Total time: 5 seconds cd biojava-genome && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 30 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 1 file to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL Total time: 6 seconds cd biojava-sequencing && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 19 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] Creating empty /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes/org/biojava/nbio/sequencing/io/fastq/package-info.class [copy] Warning: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-sequencing/src/main/resources does not exist. jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL Total time: 3 seconds cd biojava-structure && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 483 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use or override a deprecated API that is marked for removal. [javac] Note: Recompile with -Xlint:removal for details. [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 64 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL Total time: 19 seconds cd biojava-structure-gui && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 136 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.java uses or overrides a deprecated API that is marked for removal. [javac] Note: Recompile with -Xlint:removal for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 49 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL Total time: 17 seconds cd biojava-modfinder && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 23 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 2 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL Total time: 8 seconds cd biojava-ontology && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 34 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] Note: Some input files use or override a deprecated API that is marked for removal. [javac] Note: Recompile with -Xlint:removal for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 2 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL Total time: 6 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 13 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] Creating empty /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/ronn/package-info.class [javac] Creating empty /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/data/sequence/package-info.class [copy] Copying 11 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL Total time: 7 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 1 source file to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [copy] Warning: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/src/main/resources does not exist. jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL Total time: 3 seconds cd biojava-ws && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 20 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [copy] Warning: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ws/src/main/resources does not exist. jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL Total time: 4 seconds cd biojava-survival && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml compile: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 46 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [copy] Copying 1 file to /build/reproducible-path/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes jar: [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL Total time: 7 seconds # make doc rm -rf biojavadoc mkdir biojavadoc cp -r biojava-*/src biojavadoc/ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml cd biojavadoc && ant javadocs Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/build.xml javadocs: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/javadoc [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava [javadoc] Generating Javadoc [javadoc] Debian build on Java 9+ detected: Adding the --ignore-source-errors option [javadoc] Debian build on Java 9+ detected: Adding the -Xdoclint:none option [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.nbio.aaproperties... 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[javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.chem... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.model... [javadoc] Loading source files for package org.biojava.nbio.structure.io.sifts... [javadoc] Loading source files for package org.biojava.nbio.structure.io.util... [javadoc] Loading source files for package org.biojava.nbio.structure.jama... [javadoc] Loading source files for package org.biojava.nbio.structure.math... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary.io... [javadoc] Loading source files for package org.biojava.nbio.structure.rcsb... [javadoc] Loading source files for package org.biojava.nbio.structure.scop... [javadoc] Loading source files for package org.biojava.nbio.structure.scop.server... [javadoc] Loading source files for package org.biojava.nbio.structure.secstruc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.analysis... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.core... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.geometry... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.internal... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.misc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.utils... [javadoc] Loading source files for package org.biojava.nbio.structure.validation... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal.io... [javadoc] Loading source files for package org.biojava.nbio.survival.cox... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.comparators... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.matrix... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.stats... [javadoc] Loading source files for package org.biojava.nbio.survival.data... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment.qblast... [javadoc] Loading source files for package org.biojava.nbio.ws.hmmer... [javadoc] Loading source files for package org.forester.analysis... [javadoc] Loading source files for package org.forester.application... [javadoc] Loading source files for package org.forester.applications... [javadoc] Loading source files for package org.forester.archaeopteryx... [javadoc] Loading source files for package org.forester.archaeopteryx.phylogeny.data... [javadoc] Loading source files for package org.forester.archaeopteryx.tools... [javadoc] Loading source files for package org.forester.archaeopteryx.webservices... [javadoc] Loading source files for package org.forester.datastructures... [javadoc] Loading source files for package org.forester.development... [javadoc] Loading source files for package org.forester.evoinference... [javadoc] Loading source files for package org.forester.evoinference.distance... [javadoc] Loading source files for package org.forester.evoinference.matrix.character... [javadoc] Loading source files for package org.forester.evoinference.matrix.distance... [javadoc] Loading source files for package org.forester.evoinference.parsimony... [javadoc] Loading source files for package org.forester.evoinference.tools... [javadoc] Loading source files for package org.forester.go... [javadoc] Loading source files for package org.forester.go.etc... [javadoc] Loading source files for package org.forester.io.parsers... [javadoc] Loading source files for package org.forester.io.parsers.nexus... [javadoc] Loading source files for package org.forester.io.parsers.nhx... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml.data... [javadoc] Loading source files for package org.forester.io.parsers.tol... [javadoc] Loading source files for package org.forester.io.parsers.util... [javadoc] Loading source files for package org.forester.io.writers... [javadoc] Loading source files for package org.forester.msa... [javadoc] Loading source files for package org.forester.msa_compactor... [javadoc] Loading source files for package org.forester.pccx... [javadoc] Loading source files for package org.forester.phylogeny... [javadoc] Loading source files for package org.forester.phylogeny.data... [javadoc] Loading source files for package org.forester.phylogeny.factories... [javadoc] Loading source files for package org.forester.phylogeny.iterators... [javadoc] Loading source files for package org.forester.protein... [javadoc] Loading source files for package org.forester.rio... [javadoc] Loading source files for package org.forester.sdi... [javadoc] Loading source files for package org.forester.sequence... [javadoc] Loading source files for package org.forester.species... [javadoc] Loading source files for package org.forester.surfacing... [javadoc] Loading source files for package org.forester.test... [javadoc] Loading source files for package org.forester.test.examples... [javadoc] Loading source files for package org.forester.tools... [javadoc] Loading source files for package org.forester.util... [javadoc] Loading source files for package org.forester.ws.hmmer... [javadoc] Loading source files for package org.forester.ws.seqdb... [javadoc] Loading source files for package org.forester.ws.wabi... [javadoc] Loading source files for package org.jcolorbrewer... [javadoc] Loading source files for package org.jcolorbrewer.ui... [javadoc] Constructing Javadoc information... [javadoc] error: Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/ (java.net.UnknownHostException: java.sun.com) [javadoc] Building index for all the packages and classes... [javadoc] Standard Doclet version 17.0.11+9-Debian-1 [javadoc] Building tree for all the packages and classes... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/aa.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/aaa.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/AAindexFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/AboutDialog.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java:199: warning: @param argument "label" is not a parameter name. [javadoc] * @param label [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/AbstractAnnotation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/AbstractBean.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/AbstractCompound.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/AbstractFeature.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/AbstractLocation.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: Tag @link: reference not found: #getAllSubLocations() [javadoc] * {@link #getAllSubLocations()}. [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/AbstractMatrixAligner.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/AbstractRenderer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/AbstractScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/AbstractScoresCache.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/AbstractSequence.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java:160: warning: @param argument "bioBegin" is not a parameter name. [javadoc] * @param bioBegin the bioBegin to set [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java:178: warning: @param argument "bioEnd" is not a parameter name. [javadoc] * @param bioEnd the bioEnd to set [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java:210: warning: @param argument "annotation" is not a parameter name. [javadoc] * @param annotation the annotation to set [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java:345: warning: @param argument "featureType" is not a parameter name. [javadoc] * @param featureType [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java:496: warning: @param argument "species" is not a parameter name. [javadoc] * @param species the species to set [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java:555: warning: @param argument "begin" is not a parameter name. [javadoc] * @param begin [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java:556: warning: @param argument "end" is not a parameter name. [javadoc] * @param end [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/AbstractSequence.AnnotationType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/AbstractStructureAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/AbstractTerm.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/AccesionedLocation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Accession.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Accession.Source.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/Accessioned.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/AccessionID.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/AccessionParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/AdjactantDirectedCombinableDomains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/model/AFP.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/model/AFPChain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:54: warning: invalid input: '<' [javadoc] // AFP(k-1) < AFP(k)(refer AFP.h definition), [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:55: warning: invalid input: '<' [javadoc] // ie i(k-1) < i(k) and j(k-1) < j(k) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java:55: warning: invalid input: '<' [javadoc] // ie i(k-1) < i(k) and j(k-1) < j(k) [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/AFPChainFlipper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/AFPChainScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/model/AfpChainWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLParser.java:59: warning: Parameter "name1" is documented more than once. [javadoc] * @param name1 [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/AFPTwister.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/stats/AgScore.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/AligMatEl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/Alignable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/AlignedPosition.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/AlignedSequence.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner [javadoc] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<' [javadoc] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex > [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:117: warning: invalid input: '<' [javadoc] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:141: warning: invalid input: '<' [javadoc] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner [javadoc] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor. [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/Aligner.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/AlignerHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/AlignerHelper.Anchor.QueryIndexComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/AlignerHelper.Cut.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/AlignerHelper.Last.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/AlignerHelper.Subproblem.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/AlignmentCalc.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/AlignmentCalc.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/AlignmentCalcDB.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/AlignmentCalculationRunnable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/AlignmentGui.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/events/AlignmentPositionListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/events/AlignmentProgressListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/AlignmentProgressListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/AlignmentResult.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/Alignments.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:312: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/Alignments.PairInProfileScorerType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/Alignments.PairwiseSequenceAlignerType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/Alignments.PairwiseSequenceScorerType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/Alignments.ProfileProfileAlignerType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/Alignments.RefinerType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/AlignmentTextPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/AlignmentTools.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:499: warning: invalid input: '<' [javadoc] * A Map can be viewed as a function from K to V. This class represents [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:299: warning: invalid input: '<' [javadoc] * If none are found at n<=maxSymmetry, the alignment is reported as [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:310: warning: invalid input: '<' [javadoc] * @return The order of symmetry of alignment, or 1 if no order <= [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:467: warning: invalid input: '<' [javadoc] * List>> aln = getOptAlnAsList(AFPChain afpChain); [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:467: warning: invalid input: '<' [javadoc] * List>> aln = getOptAlnAsList(AFPChain afpChain); [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/AlignmentTools.IdentityMap.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java:499: warning: invalid input: '<' [javadoc] * A Map can be viewed as a function from K to V. This class represents [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/AligNPE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/AlignTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/AligPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/AligPanelMouseMotionListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/webstart/AligUIManager.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/AlreadyExistsException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/AltAligComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/AlternativeAlignmentFrame.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/AmbiguityDNARNAHybridCompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/AmbiguityRNACompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/AminoAcid.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/AminoAcidImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/analysis/AncestralTaxonomyInference.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/analysis/AncestralTaxonomyInferenceException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning: invalid input: '<' [javadoc] * counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning: @param argument "cutsPerSection" is not a parameter name. [javadoc] * @param cutsPerSection the number of cuts added to each section during each pass [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning: @param argument "cutsPerSection" is not a parameter name. [javadoc] * @param cutsPerSection the number of cuts added to each section during each pass [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:48: warning: @param argument "error" is not a parameter name. [javadoc] * @param error [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:64: warning: @param argument "error" is not a parameter name. [javadoc] * @param error [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java:85: warning: @param argument "error" is not a parameter name. [javadoc] * @param error [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/AngleOutlier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/Annotatable.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java:78: warning: Tag @see: reference not found: org.biojavax.RichAnnotatable [javadoc] * @see org.biojavax.RichAnnotatable [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/Annotation.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java:56: warning: Tag @see: reference not found: org.biojavax.RichAnnotation [javadoc] * @see org.biojavax.RichAnnotation [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Annotation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/AnnotationParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/annotator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/App.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/App.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/AptxUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/AptxUtil.GraphicsExportType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/Archaeopteryx.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/ArchaeopteryxA.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/ArchaeopteryxE.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:544: 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. [javadoc] * @author Herve Menager [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:574: 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. [javadoc] * @author Herve Menager [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/asa/AsaCalculator.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java:114: warning: Tag @see: reference not found: StructureTools.getAllNonHAtomArray [javadoc] * @see StructureTools.getAllNonHAtomArray [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java:462: warning: invalid usage of tag {@link #Element().N [javadoc] * unknown type (element) the vdw radius of {@link #Element().N} is returned [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/AsciiHistogram.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/AssertionFailure.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/AssignmentXMLSerializer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/Astral.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/Astral.AstralSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Atom.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/Atom.java:248: warning: @return tag cannot be used in method with void return type. [javadoc] public void setCharge(short charge); [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/AtomCache.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:711: warning: Tag @link: reference not found: FileParsingParameters#getObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:727: warning: Tag @link: reference not found: FileParsingParameters#getObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:808: warning: Tag @link: reference not found: FileParsingParameters#setObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#setObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:826: warning: Tag @link: reference not found: FileParsingParameters#setObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#setObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:262: 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. [javadoc] * @author Peter Rose [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:711: warning: Tag @link: reference not found: FileParsingParameters#getObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:708: warning: invalid input: '&' [javadoc] * N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:727: warning: Tag @link: reference not found: FileParsingParameters#getObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:721: warning: invalid input: '&' [javadoc] * N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:724: 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. [javadoc] * @author Amr AL-Hossary [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:725: warning: Tag @see: reference not found: #fetchCurrent [javadoc] * @see #fetchCurrent [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:808: warning: Tag @link: reference not found: FileParsingParameters#setObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#setObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:801: warning: invalid input: '&' [javadoc] * N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:805: 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. [javadoc] * @author Amr AL-Hossary [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:803: warning: @param argument "fetchCurrent" is not a parameter name. [javadoc] * @param fetchCurrent [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:826: warning: Tag @link: reference not found: FileParsingParameters#setObsoleteBehavior() [javadoc] * @deprecated Use {@link FileParsingParameters#setObsoleteBehavior()} instead (4.0.0) [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:822: warning: invalid input: '&' [javadoc] * N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:860: warning: @param argument "fetchFileEvenIfObsolete" is not a parameter name. [javadoc] * @param fetchFileEvenIfObsolete Whether to fetch obsolete records [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java:921: warning: @param argument "strictSCOP" is not a parameter name. [javadoc] * @param strictSCOP Ignored [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/AtomContact.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/AtomContactSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/AtomIdentifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/AtomImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/AtomInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/AtomInfoParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/AtomIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/AtomPositionMap.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java:362: warning: @param argument "map" is not a parameter name. [javadoc] * @param map [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/AtomPositionMap.GroupMatcher.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/AtomSite.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/AtomSites.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/AuditAuthor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/AugmentedResidueRange.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Author.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/autosuggest/AutoSuggestProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/AxisAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/BasicBinaryDomainCombination.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/BasicCombinableDomains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/BasicDescriptiveStatistics.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/BasicDomain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/BasicDomainSimilarityCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/BasicGenomeWideCombinableDomains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/BasicGoRelationship.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/BasicGoSubset.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/BasicGoTerm.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/BasicGoXRef.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/BasicMsa.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/webservices/BasicPhylogeniesWebserviceClient.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/BasicProtein.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/BasicSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sequence/BasicSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/species/BasicSpecies.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/BasicTable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/BasicTableParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/BerkeleyScopInstallation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/BetaBridge.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/BinaryCharacters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/BinaryDomainCombination.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/BinaryDomainCombination.DomainCombinationType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/BinaryDomainCombination.OutputFormat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/BioAssemblyIdentifier.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:50: warning: Tag @link: reference not found: #toString() [javadoc] * It is recommended that the {@link #toString()} method also return the [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/BioAssemblyInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/BioAssemblyTools.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java:265: warning: @param argument "structure" is not a parameter name. [javadoc] * @param structure [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/BiojavaJmol.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/BioJavaStructureAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java:165: warning: @param argument "assemblyId" is not a parameter name. [javadoc] * @param assemblyId Id of the macromolecular assembly to be generated [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/BioUnitDataProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/BioUnitDataProviderFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/BitSequenceReader.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&' [javadoc] * Class is immutable & so this is unsupported [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&' [javadoc] * Class is immutable & so this is unsupported [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&' [javadoc] * Class is immutable & so this is unsupported [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&' [javadoc] * Class is immutable & so this is unsupported [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/Blast.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/homology/BlastHomologyHits.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/BlastHspBuilder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/BlastJob.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/BlastMatrixEnum.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/BlastResult.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/BlastTabularParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/BlastXMLParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/query/BlastXMLQuery.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/Block.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: Tag @see: reference not found: #setAlignRes() [javadoc] * @see #setAlignRes() [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: Tag @see: reference not found: #updateCoreLength() [javadoc] * @see #updateCoreLength() [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/BlockImpl.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/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. [javadoc] * @return BlockImpl a BlockImpl instance linked to its parent BlockSet. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/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. [javadoc] * @return BlockImpl an identical copy of the input BlockImpl object. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:75: warning: Tag @see: reference not found: #setAlignRes() [javadoc] * @see #setAlignRes() [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java:111: warning: Tag @see: reference not found: #updateCoreLength() [javadoc] * @see #updateCoreLength() [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/BlockSet.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java:114: warning: @param argument "matrices" is not a parameter name. [javadoc] * @param matrices [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/BlockSetImpl.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/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. [javadoc] * @return BlockSet an instance linked to the parent alignment. [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/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. [javadoc] * @return BlockSet an identical copy of the input object. [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Bond.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/Bond.java:27: warning: invalid input: '<' [javadoc] * @author Jules Jacobsen [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/BondImpl.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/BondImpl.java:31: warning: invalid input: '<' [javadoc] * @author Jules Jacobsen [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/BondImpl.java:48: warning: Tag @link: reference not found: #Bond(Atom, Atom, int, boolean) [javadoc] * {@link #Bond(Atom, Atom, int, boolean)} with the [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/BondMaker.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/BondOutlier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/BondType.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/BondType.java:26: warning: invalid input: '<' [javadoc] * @author Jules Jacobsen [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/tools/BootstrapResampler.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/BoundingBox.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/BranchColor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/BranchCountingBasedScoringMethod.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning: invalid input: '<' [javadoc] * SortedMap in which the external node [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/BranchData.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/BranchLengthBasedScoringMethod.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/BranchWidth.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/BranchWidthParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/BravaisLattice.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/BridgeType.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java:25: warning: invalid input: '<' [javadoc] * (i-1,i,i+1) and (j-1,j,j+1), where i each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning: Tag @link: reference not found: Profile [javadoc] * @param each {@link Sequence} of the {@link Profile} pair is of type S [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning: Tag @link: reference not found: AlignedSequence [javadoc] * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/CallableStructureAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/CartesianProduct.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathCategory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathDatabase.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathDomain.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java:50: warning: Tag @link: reference not found: #toString() [javadoc] * It is recommended that the {@link #toString()} method also return the [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathFragment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathInstallation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathNode.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/CathSegment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/CDSComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/CDSSequence.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:34: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [javadoc] * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml} [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:85: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml [javadoc] * {@link http://www.sequenceontology.org/gff3.shtml} [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:86: warning: invalid usage of tag {@link http://biowiki.org/~yam/bioe131/GFF.ppt [javadoc] * {@link http://biowiki.org/~yam/bioe131/GFF.ppt} [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CECalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeCPMain.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:60: warning: invalid input: '&' [javadoc] * 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain [javadoc] ^ [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java:60: warning: invalid input: '&' [javadoc] * 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeCPMain.CPRange.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CECPParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CECPParameters.DuplicationHint.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeCPUserArgumentProcessor.CeCPStartupParams.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/Cell.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeMain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatus.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeParameters.html... [javadoc] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java:361: warning: @param argument "maxNrIterationsForOptimization" is not a parameter name. [javadoc] * @param maxNrIterationsForOptimization [javadoc] ^ [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeParameters.ScoringStrategy.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeSideChainMain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeSideChainUserArgumentProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/CeSymm.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.OrderDetectorMethod.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.RefineMethod.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.SymmetryType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeUserArgumentProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeUserArgumentProcessor.CeStartupParams.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Chain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/ChainClusterer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/ChainImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/misc/ChainSignature.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/data/ChangeValue.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/CharacterStateMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/CharacterStateMatrix.BinaryStates.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/CharacterStateMatrix.Format.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/CharacterStateMatrix.GainLossStates.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/CharacterStateMatrix.NucleotideStates.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/ChargeAdder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa_compactor/Chart.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/check_fasta.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/ChemComp.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/ChemCompAtom.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/ChemCompBond.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/ChemCompConsumer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/ChemCompDescriptor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/ChemCompProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/chem/ChemCompTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/stats/ChiSq.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/stats/Cholesky2.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/jama/CholeskyDecomposition.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/ChooseDirAction.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/util/ChromosomeMappingTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/ChromosomeSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/genename/ChromPos.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/stats/Chsolve2.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/CIFLabel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/Clash.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/util/ClasspathResource.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/CliTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/ClustalOmega.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ClusterAltAligs.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/ClusterDomains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/ClusterMerger.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/ClusterProteinChains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/CodonCompound.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/CollectionTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ColorBrewer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/ColorConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/ColorInterpolator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/ColorPaletteChooserDialog.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/ColorPanelSelectionModel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/ColorParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/ColorUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/CombinableDomains.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/CoreSuperimposer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/count_support.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/CountProgressListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/Coverage.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/CoverageCalculationMethod.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/CoverageCalculationOptions.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/CRC64Checksum.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/CrystalBuilder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/CrystalCell.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/CrystalTransform.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/Cut.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/CutDomain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/CutSites.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phosphosite/Dataset.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/DataSource.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Date.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/DateParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/DBRef.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/DBReferenceInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/DBResultTable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/DBSearchGUI.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/decorator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/decoratorX.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/autosuggest/DefaultAutoSuggestProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/DefaultMatrixMapper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/DefaultOps.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/DeleteableMsa.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/DescriptiveStatistics.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/DevelopmentTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DirectedBinaryDomainCombination.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DirectedCombinableDomains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/DisplayAFP.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/distance/DistanceMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/distance/DistanceMatrix.Format.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/DistanceMatrixCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/DistanceTreeEvaluator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Distribution.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/DistributionParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/DivergingColorPalettePanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/DNACompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/DNASequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/DNASequence.DNAType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/DNASequenceCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/parsimony/DolloParsimony.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/dom_dup.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/Domain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/Domain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/DomainArchitecture.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainCountsDifferenceUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainLengths.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainLengthsTable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/domainloss_replacement.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainParsimonyCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/DomainProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/DomainProviderFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainSimilarity.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/DomainSimilarity.DomainSimilarityScoring.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/FastqReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/FastqTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/FastqVariant.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/FastqWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/FatCat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/FatCatRigid.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/FatCatUserArgumentProcessor.FatCatStartupParams.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/Feature.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/FeatureHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/FeatureI.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/FeatureInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/FeatureList.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/FeatureRetriever.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/FileConvert.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/util/FileDownloadUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/FileParsingParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/parsimony/FitchParsimony.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/FlatFileCache.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/FontChooser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/ForesterConstants.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/ForesterConstants.PhylogeneticTreeFormats.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/ForesterUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/ForesterWrapper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.FourBitArrayWorker.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/FractionalIdentityScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/FractionalSimilarityScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/FragmentPair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/Frame.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/FuzzyPoint.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/GapArray.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa_compactor/GapContribution.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/GapPenalty.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/GapPenalty.Type.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/GCStats.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenbankReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenbankWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/gene_tree_preprocess.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/genename/GeneChromosomePosition.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/GeneFeatureHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/GeneIDGFF2Reader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/GeneMarkGTFReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/genename/GeneName.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/GeneralMsaParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/GeneralTable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/GeneSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/genome_counts_for_once_appearing_dcs.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/GenomeWideCombinableDomains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/get_distances.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/get_genome_counts_per_char.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/get_loss_nodes.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/get_shared_chars.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/get_subtree_specific_chars.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/GetDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/GetRepresentatives.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/GFF3Reader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/GFF3Writer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/goac.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoId.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoNameSpace.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoNameSpace.GoNamespaceType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/io/GOParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoRelationship.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoRelationship.Type.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoSubset.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoSubset.Type.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoTerm.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/Gotoh.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoXRef.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/GoXRef.Type.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/GradientMapper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/GradientPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/Grid.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/GridCell.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Group.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/asa/GroupAsa.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/GroupContact.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/GroupContactSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/GroupIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/GroupToSDF.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/GroupType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/gsdi.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/GSDI.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/GSDII.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/GSDIR.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/GuanUberbacher.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/GuideTree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/GuideTree.Node.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/GuideTreeNode.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/GUIFarmJobRunnable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/GuiWrapper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/Hashcoder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/HasResultXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/HBond.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/data/HeaderInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/Helix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/HelixAxisAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/HelixExtender.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/HelixLayers.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/HelixSolver.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/Hello3d.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/HelpDialog.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/HetatomImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/HetatomImpl.PerformanceBehavior.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/HierarchicalClusterer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/Hit.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/hmmer/HmmerDomain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/HmmerRest.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/hmmer/HmmerResult.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/hmmer/HmmerScan.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/HmmPfamOutputParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/HmmPfamOutputParser.FilterType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/HmmPfamOutputParser.ReturnType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/HmmscanPerDomainTableParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/HmmscanPerDomainTableParser.FilterType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/HmmscanPerDomainTableParser.ReturnType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/Hsp.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/HTTPConnectionTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Identifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Identifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/IdentifierParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/IdxComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/IgnoreField.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/IllegalFormatUseException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/ImageLoader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/IndexPair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/InferenceManager.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/InputStreamProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/InsdcLocations.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/IntegerOntology.IntTerm.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/datastructures/IntMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/IntronSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/InvalidTermException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/inverted_dcs.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/util/IOUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/util/IOUtils.ReaderProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/IPeptideProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.ATTRIBUTE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.DISTRIBUTION.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.GROUPING.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.TRANSITION.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/Isotope.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/IteratingPhylogenyParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/IUPACParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/IUPACParser.IUPACTable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/JFatCatClient.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/JMatrixPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/events/JmolAlignedPositionListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.JmolLoggerAdapter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/JmolTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/JmolViewerImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/webstart/JNLPProxy.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/JobKillException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/JointFragments.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/JournalArticle.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/JPrintPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/Jronn.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/Jronn.Range.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/KeyedWeakReference.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/Ladder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/iterators/LevelOrderTreeIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/LightweightProfile.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/LightweightProfile.StringFormat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/LocalScopDatabase.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/Location.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/Location.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/Location.Tools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/LocationHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/LocIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/LogBranchLengthBasedScoringMethod.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/LogColorMapper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/jama/LUDecomposition.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/Mafft.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/MainFrame.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/MainFrameApplet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/MainFrameApplication.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/MainPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/map_lengths.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/Mapping.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/MappingResults.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/jama/Maths.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/jama/Matrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/matrix/Matrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/MatrixAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/MatrixListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/mcc.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MemoryMonitor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MemoryMonitor.Surface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MenuCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/MenuCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MenuCreator.DotPlotListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/exceptions/Messages.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/meta_ontologizer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/chem/MetalBondDistance.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/MetalBondParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/etc/MetaOntologizer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/MmCifBiolAssemblyProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/MMCIFFileReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/MMcifParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/MmCifPDBBiolAssemblyProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/ModelingUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/ModelledSubgroup.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/ModelLoader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/ModelLoader.Model.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/ModelLoader.Threshold.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ModificationCategory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ModificationCondition.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ModificationConditionImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ModificationLinkage.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ModificationOccurrenceType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/ModifiedCompound.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/MogAngleOutlier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/MogBondOutlier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sequence/MolecularSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sequence/MolecularSequence.TYPE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/MomentsOfInertia.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/MomentsOfInertia.SymmetryClass.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/Msa.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/msa_compactor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/Msa.MSA_FORMAT.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa_compactor/MsaCompactor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/MsaFormatException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/MsaInferrer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/MsaMethods.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa_compactor/MsaProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/MsaRenderer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/MultipleAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentDisplay.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanelMouseMotionListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/mc/MultipleMcParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/MultipleStructureAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/MultipleSuperimposer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/MultipleUris.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/MultiThreadedDBSearch.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/MutableProfile.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/MutableProfilePair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/MutableSequencePair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Mutator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MyAlignmentLoadListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MyDistMaxListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MyExportListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MyOpenPdbFileListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MySaveFileListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/MyTableRowSorter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/Name2Count.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/NexusCharactersParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/NexusConstants.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/NexusFormatException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/NexusPhylogeniesParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nhx/NHXFormatException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nhx/NHXParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nhx/NHXParser.TAXONOMY_EXTRACTION.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nhx/NHXtags.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/nj.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/NodeData.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/NodeDataField.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/NodeVisualData.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/NodeVisualData.FontType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/NodeVisualData.NodeFill.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/NodeVisualData.NodeShape.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/NucleotideCompound.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/NucleotideImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/NullOutputStream.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/ObjectFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/obo_tool.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/obo/OboFileEventListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/obo/OboFileHandler.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/obo/OboFileParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/obo/OboFileParser.SOPair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/io/OboParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/OBOparser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/OBOparser.ReturnType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/Octahedron.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/etc/OntologizerResult.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/etc/OntologizerResult.TYPE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/Ontology.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/Ontology.Impl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/OntologyException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/OntologyFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/OntologyOps.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/OntologyTerm.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/OntologyTerm.Impl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/OntoTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/OperatorResolver.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/OptimalCECPMain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/OptimalCECPParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/Options.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/Options.CLADOGRAM_TYPE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/Options.NODE_LABEL_DIRECTION.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/Options.PHYLOGENY_GRAPHICS_TYPE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/OrderDetector.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/OrderedPair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/ORonn.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/ORonnModel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/query/OutputHitsGFF.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/Pair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/PairInProfileScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/PairwiseAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/distance/PairwiseDistanceCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/distance/PairwiseDistanceCalculator.PWD_DISTANCE_METHOD.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/PairwiseDomainSimilarity.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/PairwiseDomainSimilarityCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/PairwiseGenomeComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/PairwiseSequenceScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/PaletteIcon.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/ParameterGUI.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/ParseListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/exceptions/ParserException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/util/ParserUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/PartitionRefiner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/PassthroughIdentifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/PaupLogParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/pccx.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/PDBBioAssemblyParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/PDBBioUnitDataProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/PDBCrystallographicInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/PDBDirPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/PDBDomainProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/PDBFileParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/PDBFileReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/PDBHeader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/PdbIdLists.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/PdbPair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/PdbPairsMessage.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/PdbPairXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/PDBParseException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/PDBRecord.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/PDBServerPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/PDBStatus.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/PDBStatus.Status.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/util/PDBTemporaryStorageUtils.LinkRecord.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/PDBUploadPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxChemCompDescriptor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxChemCompIdentifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxEntityNonPoly.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxNonPolyScheme.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxPolySeqScheme.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssembly.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssemblyGen.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssemblyGenXMLContainer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxStructAssemblyXMLContainer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperList.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/PdbxStructOperListXMLContainer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/PDPDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/PDPDomain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/PDPParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/PDPProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/PeptideProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/PeptideProperties.SingleLetterAACode.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/utils/PermutationGenerator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/PermutationGroup.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/pfam_go.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/pfam2go_extractor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/pfamacc2go.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/pfamacc2pfamid.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/PfamToGoMapping.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/PfamToGoParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/phylo2coloredgraphics.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/phylo2graphics.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/PhylogeneticInferrer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/PhylogeneticInferrer.MSA_PRG.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/Phylogeny.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/PhylogenyBranch.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/PhylogenyData.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/PhylogenyDataUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/tools/PhylogenyDecorator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/tools/PhylogenyDecorator.FIELD.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/factories/PhylogenyFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/PhylogenyMethods.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/PhylogenyMethods.PhylogenyNodeField.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/PhylogenyNode.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/iterators/PhylogenyNodeIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/PhylogenyParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/util/PhylogenyParserException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/writers/PhylogenyWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/writers/PhylogenyWriter.FORMAT.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/PhyloInferenceDialog.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/phylostrip.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/phyloxml_converter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/PhyloXmlException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/PhyloXmlHandler.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/PhyloXmlMapping.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/writers/PhyloXmlNodeWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/PhyloXmlParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/PhyloXmlUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/PlainFastaHeaderParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/Point.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Point.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/Point.Resolver.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/PointParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Polygon.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/PolygonParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/Polyhedron.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/chem/PolymerType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/PositionInQueueXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/iterators/PostOrderStackObject.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/iterators/PostorderTreeIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/iterators/PreorderTreeIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/PrettyXMLWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/Prism.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/ProcessPool.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/ProcessRunning.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/Profile.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/Profile.StringFormat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/ProfilePair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/ProfileProfileAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/ProfileProfileScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/ProfileView.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/Program.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/Programs.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/PropertiesMap.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Property.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Property.AppliesTo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/PropertyParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/Protein.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/ProteinChainExtractor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/misc/ProteinComplexSignature.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/ProteinDomain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/ProteinId.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ProteinModification.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ProteinModificationImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ProteinModificationImpl.Builder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/ProteinModificationRegistry.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/ProteinSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/ProteinSequenceClusterer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/ProxySequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/jama/QRDecomposition.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/Qualifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/QualitativeColorPalettePanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/QualityFeature.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/QuantityFeature.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/QuatSymmetryParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/QuatSymmetryScores.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySolver.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/datastructures/Queue.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/RandomThing.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/RasmolCommandListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/RawBioUnitDataProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBDescription.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBDescriptionFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBLigand.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBLigands.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBLigandsFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBMacromolecule.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBPolymer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBTaxonomy.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/RCSBUpdates.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/ReadUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/ReducedChemCompProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Reference.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/ReferenceParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/ReferenceSuperimposer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/Refine.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/RefinerFailedException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/reinv_count.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/RemoteBioUnitDataProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/RemoteDomainProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentOutputProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentProperties.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/RemotePairwiseAlignmentService.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/RemotePDPProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/RemoteRawBioUnitDataProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/RemoteScopInstallation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/RemoteTerm.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/RemoteTerm.Impl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/phylogeny/data/RenderableMsaSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/phylogeny/data/RenderableVector.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/RenderStyle.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/RepresentativeXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/ResampleableMsa.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/RescoreRefiner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/ResidualsCoxph.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/ResidualsCoxph.Type.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/ResidueNumber.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/ResidueRange.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/ResidueRangeAndLength.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/ResidueRenderer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/chem/ResidueType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/ResourceManager.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/RestUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/Result.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/ResultFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/views/ReversedSequenceView.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/rio.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/rio/RIO.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/rio/RIO.REROOTING.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/rio/RIOException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/RiskInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/RNACompoundSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/RNASequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/RNASequenceCreator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/views/RnaSequenceView.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/RonnConstraint.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/RonnConstraint.Threshold.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/Rotation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/RotationAxis.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/RotationAxisAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/RotationGroup.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/RotationSolver.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/RunnableProcess.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/SandboxStyleStructureProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/SangerFastqReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/parsimony/SankoffParsimony.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/distance/Sarray.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/ScaleableMatrixPanel.GradientRenderer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/analysis/ScanSymmetry.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/SchemaGenerator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopCategory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopDatabase.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopDescription.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/server/ScopDescriptions.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopDomain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/server/ScopDomains.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopInstallation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/ScopInstallationInstance.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopIOException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopMirror.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/ScopNode.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/server/ScopNodes.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/ScopSelectPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/Scorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/ScoresCache.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/ScoringMethodForExternalNode.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/SDI.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/SDIException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/SDIR.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/SDIutil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/SDIutil.ALGORITHM.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/SDIutil.TaxonomyComparisonBase.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/SearchIO.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/SecStrucCalc.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/SecStrucElement.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/SecStrucInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/SecStrucState.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/SecStrucTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/SecStrucType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/Segment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/SegmentComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/Selection.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/SelectionImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/SelectPDBPanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/SeqMisMatch.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/SeqMisMatchImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/SeqRes2AtomAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/Sequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Sequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/SequenceAccessionTools.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/seqdb/SequenceDbWsTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/SequenceDisplay.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionOrderDetector.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/SequenceLocation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/SequenceMixin.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/SequenceMixin.SequenceIterator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/SequenceMouseListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/SequenceOptimizationHints.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceCollection.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceUsage.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/SequencePair.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/SequenceParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/SequenceProxyView.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/SequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/SequenceRelation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/SequenceRelation.SEQUENCE_RELATION_TYPE.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/SequenceScalePanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/SequenceTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/data/sequence/SequenceUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/SequenceView.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/writers/SequenceWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/writers/SequenceWriter.SEQ_FORMAT.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/SequentialColorPalettePanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/SerializableCache.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/set_comparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/shared_chars_in_ext_nodes.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/ShortSegmentRemover.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/ShowPDBIDListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/SiftsChainEntry.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/SiftsEntity.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/SiftsResidue.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/SiftsSegment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/SigEva.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/simple_node_processor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/SimpleAlignedSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/SimpleDomain.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/StartCodonSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/StartupParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/StaticMemberPlaceHolder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/StatusDisplay.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/matrix/StdArrayIO.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/io/StockholmFileAnnotation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/io/StockholmFileAnnotation.StockholmFileAnnotationReference.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/io/StockholmFileParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/io/StockholmStructure.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/StopCodonSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/Strand.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/StrataInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/StrCompAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/StreamListener.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/StringInt.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/StringInt.DescendingIntComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/StringManipulationHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/StrucAligParameters.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/Struct.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructAsym.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructConn.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructKeywords.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructNcsOper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructRef.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructRefSeq.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructRefSeqDif.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructSite.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/StructSiteGen.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/Structure.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/StructureAlignment.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/StructureAlignmentDisplay.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/StructureAlignmentFactory.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/StructureAtom.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/StructureAtomLinkage.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/io/StructureAtomXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/StructureException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/StructureGroup.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/StructureIdentifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/StructureImpl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/StructureInterface.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/StructureInterfaceCluster.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/StructureInterfaceList.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/StructureIO.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/StructureIO.StructureFiletype.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/StructureIOFile.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/StructureLoaderThread.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/StructureName.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/StructureName.Source.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/StructurePairAligner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/StructurePairSelector.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/StructureProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/StructureSequenceMatcher.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/StructureTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/StructureUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/StructureViewer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/SubstitutionMatrixScorer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/SubstructureIdentifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/subtree_feature_count.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/SubunitGraph.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/Subunits.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/SurvFitInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfLower.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.ConfType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Error.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.Method.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/SurvivalInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/SurvivalInfoHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/SurvivalInfoIndex.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/SVDSuperimposer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/math/SymbolTable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/SymmClash.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/SymmetricalDistanceMatrixParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/SymmetricalDistanceMatrixParser.InputMatrixType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/Symmetry.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/SystemInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/io/TabDelimParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/Table.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/Table.CaseInsensitiveTriplet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/Table.Codon.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/table2fasta.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/tax_code_cleaner.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Taxonomy.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/TaxonomyColors.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/analysis/TaxonomyDataManager.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/TaxonomyID.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/TaxonomyParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/TaxonomyUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/Term.html... 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[javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/rio/TestRIO.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/TestSurfacing.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/TextFeature.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/Time.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/Timer.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/tol/TolParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/tol/TolXmlHandler.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/tol/TolXmlMapping.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.Builder.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/TranscriptSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/io/TransfAlgebraicAdapter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/TransformType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/exceptions/TranslationException.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/TreeColorSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/TreeConstructor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/TreeConstructorType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/TreeFontSet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/io/TreeMapSpaceGroupWrapper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/TreePanel.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/TreePanelUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/server/TreeSetStringWrapper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/tools/TreeSplitMatrix.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/TreeType.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/Triple.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/Triple.Impl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/twobit/TwoBitParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.TwoBitArrayWorker.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/TxSearch.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/TxSearch.RANKS.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/TxSearch.TAX_NAME_CLASS.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/TxSearch.TAX_RANK.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/UncompressInputStream.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/seqdb/UniProtEntry.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/seqdb/UniProtTaxonomy.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/uniprot/UniprotToFasta.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/UniqueSequenceList.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/Uri.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/UriParser.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/URLIdentifier.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/UrlTreeReader.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/UserArgumentProcessor.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/UserConfiguration.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/Utils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/Variable.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/Variable.Impl.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/WabiTools.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/WaldTest.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/WaldTestInfo.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/WeakValueHashMap.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/webservices/WebservicesManager.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/webservices/WebservicesManager.WsPhylogenyFormat.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/webservices/WebserviceUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/webstart/WebStartDBSearch.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/webstart/WebStartDBSearchResults.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/webstart/WebStartMain.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/wiki_examples.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/views/WindowedSequence.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/WindowsUtils.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/data/WorkSheet.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/WrapLayout.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/WwPDBValidationInformation.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/XmlElement.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/XMLHelper.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/server/XMLUtil.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/XMLWriter.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/convertor/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/profeat/convertor/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/aaproperties/xml/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/routines/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/alignment/template/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/matrices/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/alignment/template/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/exceptions/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/exceptions/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/search/io/blast/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/compound/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/edits/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/edits/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/features/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/template/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/template/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/io/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/loader/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/loader/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/location/template/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/storage/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/template/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/transcription/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/views/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/sequence/views/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/core/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/data/sequence/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/data/sequence/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/homology/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/homology/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/cytoband/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/cytoband/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/geneid/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/geneid/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/genename/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/genename/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/gff/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/twobit/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/parsers/twobit/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/query/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/query/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/uniprot/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/uniprot/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/genome/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/obo/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/obo/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ontology/utils/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phosphosite/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phosphosite/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/phylo/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/proteincomparisontool/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/proteincomparisontool/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/protmod/structure/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ronn/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/sequencing/io/fastq/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/client/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/events/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/events/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/fatcat/calc/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/aligpanel/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/autosuggest/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/autosuggest/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/gui/jmol/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/helper/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/model/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/model/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/mc/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/mc/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/multiple/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/pairwise/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/seq/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/seq/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/webstart/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/webstart/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/xml/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/asa/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/asa/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/cath/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/contact/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/domain/pdp/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/ecod/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/ecod/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/events/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/events/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/gui/util/color/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/chem/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/chem/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/mmcif/model/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/sifts/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/io/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/jama/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/jama/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/math/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/math/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/quaternary/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/rcsb/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/server/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/scop/server/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/secstruc/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/analysis/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/analysis/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/core/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/geometry/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/gui/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/gui/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/internal/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/misc/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/misc/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/utils/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/symmetry/utils/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/validation/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/io/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/xtal/io/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/comparators/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/comparators/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/matrix/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/matrix/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/stats/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/cox/stats/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/data/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/data/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/alignment/qblast/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/hmmer/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/ws/hmmer/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/analysis/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/analysis/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/application/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/applications/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/phylogeny/data/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/phylogeny/data/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/tools/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/webservices/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/archaeopteryx/webservices/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/datastructures/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/datastructures/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/development/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/distance/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/distance/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/character/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/distance/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/matrix/distance/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/parsimony/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/parsimony/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/tools/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/evoinference/tools/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/etc/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/go/etc/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nexus/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nhx/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/nhx/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/phyloxml/data/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/tol/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/tol/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/parsers/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/writers/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/io/writers/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa_compactor/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/msa_compactor/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/pccx/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/data/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/factories/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/factories/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/iterators/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/phylogeny/iterators/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/protein/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/rio/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/rio/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sdi/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sequence/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/sequence/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/species/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/species/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/surfacing/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/test/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/test/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/test/examples/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/test/examples/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/tools/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/tools/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/util/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/hmmer/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/hmmer/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/seqdb/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/seqdb/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/forester/ws/wabi/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/package-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/org/jcolorbrewer/ui/package-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/constant-values.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/serialized-form.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/overview-tree.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/deprecated-list.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/index.html... [javadoc] Building index for all classes... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/allclasses-index.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/allpackages-index.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/index-all.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/overview-summary.html... [javadoc] Generating /build/reproducible-path/biojava4-live-4.2.12+dfsg/doc/biojava/help-doc.html... [javadoc] 1 error [javadoc] 100 warnings BUILD SUCCESSFUL Total time: 45 seconds # rm -rf biojavadoc make[1]: Leaving directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' * The following test is ignored since under certain circumstances it might fail * echo '* Please check the result! *' * Please check the result! * echo '* More information can be found in the Debian BTS at *' * More information can be found in the Debian BTS at * echo '* https://bugs.debian.org/843712 *' * https://bugs.debian.org/843712 * echo '*********************************************************************************' ********************************************************************************* cd biojava-core && (ant test || true) Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile-test: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 30 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 21 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [copy] Copying 176 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes test: [echo] Using java version 17.0.11 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.132 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.132 sec [junit] [junit] Testcase: testGetIndexOf took 0.042 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.004 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0.001 sec [junit] Testcase: testGetSequenceIndexAt took 0.006 sec [junit] Testcase: testGetAccession took 0.001 sec [junit] Testcase: testToString took 0.007 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0.001 sec [junit] Testcase: testCountCompounds took 0.006 sec [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.005 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.003 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.007 sec [junit] Testcase: testGetOriginalSequence took 0.001 sec [junit] Testcase: testGetCompoundAt took 0.001 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetEnd took 0 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec [junit] Testcase: testGetOverlapCount took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetLocationInAlignment took 0.001 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetSequenceAsString took 0 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.005 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.25 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.25 sec [junit] [junit] Testcase: testGetIndexOf took 0.086 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.002 sec [junit] Testcase: testGetAlignedSequenceInt took 0.005 sec [junit] Testcase: testToStringInt took 0.018 sec [junit] Testcase: testToString took 0.005 sec [junit] Testcase: testToStringFormatted took 0.032 sec [junit] Testcase: testSimpleProfile took 0.001 sec [junit] Testcase: testGetSize took 0.002 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec [junit] Testcase: testGetAlignedSequences took 0.001 sec [junit] Testcase: testGetOriginalSequences took 0.001 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0.001 sec [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec [junit] Testcase: testGetIndicesAt took 0.002 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.002 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.004 sec [junit] Testcase: testGetCompoundAtIntInt took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundSet took 0.001 sec [junit] Testcase: testGetCompoundsAt took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.002 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0 sec [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0.005 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.003 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.074 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0.002 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.004 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumIdenticals took 0.002 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.002 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumSimilars took 0.003 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.101 sec [junit] Testcase: testHashCode took 0.001 sec [junit] Testcase: testEquals took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.224 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.224 sec [junit] ------------- Standard Error ----------------- [junit] May 15, 2024 5:31:34 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] May 15, 2024 5:31:34 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testConstructorWithEvalueHspFilter took 0 sec [junit] SKIPPED: Attemps to use the network [junit] Testcase: testConstructorWithFactoryGuess took 0.205 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0 sec [junit] SKIPPED: Attemps to use the network [junit] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.1 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.1 sec [junit] ------------- Standard Output --------------- [junit] createObjects [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] ------------- Standard Error ----------------- [junit] May 15, 2024 5:31:35 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] May 15, 2024 5:31:35 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 2 hits approximately in all results [junit] May 15, 2024 5:31:35 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] May 15, 2024 5:31:35 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 117713 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testCreateObjects took 1.988 sec [junit] Testcase: testGetFileExtensions took 0 sec [junit] Testcase: testSetFile took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.055 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.055 sec [junit] ------------- Standard Output --------------- [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testCreateObjects took 0 sec [junit] SKIPPED: Attempts to use the network [junit] Testcase: testStoreObjects took 0.006 sec [junit] Testcase: testSetDatabaseReferences took 0 sec [junit] SKIPPED [junit] Testcase: testGetFileExtensions took 0.023 sec [junit] Testcase: testSetQueryReferences took 0 sec [junit] SKIPPED [junit] Testcase: testSetFile took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.DNATest [junit] Testsuite: org.biojava.nbio.core.sequence.DNATest [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 sec [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 sec [junit] [junit] Testcase: sequenceEquality took 0.077 sec [junit] Testcase: subSequence took 0.013 sec [junit] Testcase: singleCompoundSequence took 0.009 sec [junit] Testcase: translateToRna took 0.137 sec [junit] Testcase: kmerNonOverlap took 0.019 sec [junit] Testcase: twoBit took 0.01 sec [junit] Testcase: composition took 0.004 sec [junit] Testcase: fourBit took 0.006 sec [junit] Testcase: complement took 0.008 sec [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.005 sec [junit] Testcase: at took 0.002 sec [junit] Testcase: gc took 0.008 sec [junit] Testcase: basesEqual took 0.001 sec [junit] Testcase: bogusSequence took 0.008 sec [junit] Testcase: kmerOverlap took 0.002 sec [junit] Testcase: reverseComplement took 0.014 sec [junit] Testcase: reverse took 0.002 sec [junit] Testcase: respectCase took 0.002 sec [junit] Testcase: basesEquivalent took 0.002 sec [junit] Testcase: badTwoBit took 0.002 sec [junit] Running org.biojava.nbio.core.sequence.EditSequenceTest [junit] Testsuite: org.biojava.nbio.core.sequence.EditSequenceTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec [junit] [junit] Testcase: badSubstitute took 0.068 sec [junit] Testcase: delete took 0.006 sec [junit] Testcase: insert took 0.002 sec [junit] Testcase: substitute took 0.002 sec [junit] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.225 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.225 sec [junit] [junit] Testcase: empty took 0.078 sec [junit] Testcase: canScan took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [junit] Testsuite: org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec [junit] [junit] Testcase: testGetCompoundsAt took 0.044 sec [junit] Running org.biojava.nbio.core.sequence.SequenceViewTest [junit] Testsuite: org.biojava.nbio.core.sequence.SequenceViewTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec [junit] [junit] Testcase: testLastIndexOf took 0.056 sec [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testInverse took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.TranslationTest [junit] Testsuite: org.biojava.nbio.core.sequence.TranslationTest [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.339 sec [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.339 sec [junit] [junit] Testcase: translateN took 0.111 sec [junit] Testcase: basicTranslation took 0.004 sec [junit] Testcase: translateBrca2 took 0.554 sec [junit] Testcase: translateStopAtInternalStops took 0.013 sec [junit] Testcase: getUniversal took 0.001 sec [junit] Testcase: translateInternalStops took 0.02 sec [junit] Testcase: multiFrameTranslation took 0.009 sec [junit] Testcase: waitForStartCodon took 0.003 sec [junit] Testcase: translateInitMet took 0.002 sec [junit] Testcase: lowerCases took 0.001 sec [junit] Testcase: testHashCollision took 0.002 sec [junit] Testcase: translateBrca2ExonOne took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [junit] Testsuite: org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 sec [junit] [junit] Testcase: testAmbiguity took 0.059 sec [junit] Testcase: testBasicAmbiguity took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 sec [junit] [junit] Testcase: testConstructor took 0.071 sec [junit] Running org.biojava.nbio.core.sequence.io.FastaReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.FastaReaderTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.FastaReaderTest - process [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testSmallFasta2 took 0.033 sec [junit] Testcase: testProcess took 0.153 sec [junit] Testcase: testSmallFasta took 0.002 sec [junit] Running org.biojava.nbio.core.sequence.io.FastaWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.FastaWriterTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.26 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.26 sec [junit] [junit] Testcase: writeBasicFasta took 0.216 sec [junit] Testcase: writeFastaEqualToLineLength took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankCookbookTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.517 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.517 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - DNA Sequence: AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - Protein Sequence: MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - DNA Sequence: {NM_000266=AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA} [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - Protein Sequence: {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS} [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testProcess took 0.46 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankReaderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - process protein [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - process DNA [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - CDS Test [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - protein sequences: {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS} [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testProcess took 0.16 sec [junit] Testcase: CDStest took 0.015 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankWriterTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 sec [junit] [junit] Testcase: testProcess took 0.357 sec [junit] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest - parseHeader [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testParseHeader took 0.026 sec [junit] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.864 sec [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.864 sec [junit] [junit] Testcase: testProteinSequenceFactoring[0] took 0.005 sec [junit] Testcase: testFeatures[0] took 0.002 sec [junit] Testcase: testProteinSequenceFactoring[1] took 0 sec [junit] Testcase: testFeatures[1] took 0.002 sec [junit] Testcase: testProteinSequenceFactoring[2] took 0 sec [junit] Testcase: testFeatures[2] took 0 sec [junit] Testcase: testProteinSequenceFactoring[3] took 0.001 sec [junit] Testcase: testFeatures[3] took 0.002 sec [junit] Testcase: testProteinSequenceFactoring[4] took 0.001 sec [junit] Testcase: testFeatures[4] took 0 sec [junit] Testcase: testProteinSequenceFactoring[5] took 0.001 sec [junit] Testcase: testFeatures[5] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[6] took 0 sec [junit] Testcase: testFeatures[6] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[7] took 0.001 sec [junit] Testcase: testFeatures[7] took 0.006 sec [junit] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.638 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.638 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest - test wrong sequence [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testWrongSequence took 0.62 sec [junit] Running org.biojava.nbio.core.sequence.location.InsdcParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.InsdcParserTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.261 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.261 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - test accession [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - simple location: complement(CP001663.1:6463934..6465826) [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - test accession [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - simple location: complement(NC_000932.1:69611..69724) [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: extractAccessionTest[0] took 0.188 sec [junit] Testcase: extractAccessionTest[1] took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.location.LocationParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.LocationParserTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.095 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.095 sec [junit] [junit] Testcase: moreComplex took 0 sec [junit] SKIPPED [junit] Testcase: basicLocationTests took 0 sec [junit] SKIPPED [junit] Running org.biojava.nbio.core.sequence.location.LocationTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.LocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.277 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.277 sec [junit] [junit] Testcase: testWithStrandSwitch took 0.069 sec [junit] Testcase: modulateCircular took 0.002 sec [junit] Testcase: testStrandFlip took 0.002 sec [junit] Testcase: testBasicCircularLocation took 0.008 sec [junit] Testcase: badLocations took 0.001 sec [junit] Testcase: completePasses took 0.001 sec [junit] Testcase: testSubLocations took 0.007 sec [junit] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec [junit] [junit] Testcase: locationTest[0] took 0.035 sec [junit] Testcase: locationTest[1] took 0.001 sec [junit] Testcase: locationTest[2] took 0.001 sec [junit] Testcase: locationTest[3] took 0.001 sec BUILD SUCCESSFUL Total time: 50 seconds cd biojava-alignment && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile-test: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 22 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 10 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 45 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes test: [echo] Using java version 17.0.11 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 sec [junit] [junit] Testcase: testGetQuery took 0.07 sec [junit] Testcase: testGetScore took 0.032 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.615 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.615 sec [junit] [junit] Testcase: testGetQuery took 0.121 sec [junit] Testcase: testGetScore took 0.027 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.002 sec [junit] Testcase: testGetMinScore took 0.025 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0.002 sec [junit] Testcase: testGetMaxScore took 0.008 sec [junit] Running org.biojava.nbio.alignment.GuideTreeTest [junit] Testsuite: org.biojava.nbio.alignment.GuideTreeTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.146 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.146 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGuideTree took 0.146 sec [junit] Testcase: testToString took 0.005 sec [junit] Testcase: testGetScoreMatrix took 0.024 sec [junit] Testcase: testGetRoot took 0.04 sec [junit] Testcase: testGetSequences took 0.007 sec [junit] Testcase: testGetDistanceMatrix took 0.004 sec [junit] Testcase: testGetAllPairsScores took 0.005 sec [junit] Testcase: testIterator took 0.013 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.242 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.242 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.121 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.45 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.45 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.071 sec [junit] Testcase: testGetGapPenalty took 0.002 sec [junit] Testcase: testGetComputationTime took 0.034 sec [junit] Testcase: should_align_middle_anchor took 0.044 sec [junit] Testcase: testGetQuery took 0.005 sec [junit] Testcase: testGetScore took 0.004 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec [junit] Testcase: should_align_all_anchored took 0.003 sec [junit] Testcase: testGetScoreMatrix took 0.002 sec [junit] Testcase: testGetPair took 0.003 sec [junit] Testcase: should_align_multiple_anchors took 0.004 sec [junit] Testcase: testAnchoredDNAAlignment took 0.013 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: should_align_ending_anchor took 0.003 sec [junit] Testcase: testIsStoringScoreMatrix took 0.004 sec [junit] Testcase: testComplex took 0.013 sec [junit] Testcase: testGetScoreMatrixAsString took 0.033 sec [junit] Testcase: should_align_starting_anchor took 0.002 sec [junit] Testcase: anchors_should_not_change_score took 0.002 sec [junit] Testcase: testGetTarget took 0.002 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: testIntOverflowBug took 0.168 sec [junit] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.508 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.508 sec [junit] [junit] Testcase: testOpenPenalty took 0.006 sec [junit] Testcase: testType took 0.001 sec [junit] Testcase: testExtensionPenalty took 0.001 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0.001 sec [junit] Testcase: testSimpleGapPenalty took 0.001 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.131 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.131 sec [junit] [junit] Testcase: testGetQuery took 0.263 sec [junit] Testcase: testGetTarget took 0.005 sec [junit] Testcase: testSimpleProfilePair took 0.013 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.959 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.959 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.176 sec [junit] Testcase: testGetGapPenalty took 0.022 sec [junit] Testcase: testGetComputationTime took 0.004 sec [junit] Testcase: testGetQuery took 0.012 sec [junit] Testcase: testGetScore took 0.003 sec [junit] Testcase: testGetScoreMatrix took 0.003 sec [junit] Testcase: testGetPair took 0.011 sec [junit] Testcase: testGetProfile took 0.008 sec [junit] Testcase: testGetMinScore took 0.014 sec [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec [junit] Testcase: testGetScoreMatrixAsString took 0.08 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.003 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec [junit] Testcase: testGetTarget took 0.005 sec [junit] Testcase: testGetMaxScore took 0.003 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.014 sec [junit] Testcase: testSetDescription took 0.057 sec [junit] Testcase: testToString took 0.059 sec [junit] Testcase: testCaseEquivalence took 0.003 sec [junit] Testcase: test took 0.031 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.008 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.006 sec [junit] Testcase: testSetName took 0.006 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.006 sec [junit] Running org.biojava.nbio.alignment.SmithWatermanTest [junit] Testsuite: org.biojava.nbio.alignment.SmithWatermanTest [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.634 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.634 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.189 sec [junit] Testcase: testGetGapPenalty took 0.001 sec [junit] Testcase: testGetComputationTime took 0.071 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.008 sec [junit] Testcase: testGetScoreMatrix took 0.014 sec [junit] Testcase: testGetPair took 0.015 sec [junit] Testcase: testSmithWaterman took 0.001 sec [junit] Testcase: testGetProfile took 0.006 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0.008 sec [junit] Testcase: testGetScoreMatrixAsString took 0.255 sec [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.195 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.195 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.05 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.008 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0.001 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0.002 sec [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.002 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0.001 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0.001 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.119 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.119 sec [junit] [junit] Testcase: testGetComputationTime took 0.148 sec [junit] Testcase: testGuanUberbacher took 0.002 sec [junit] Testcase: testGetScore took 0.002 sec [junit] Testcase: testGetPair took 0.005 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0.003 sec [junit] Testcase: should_align_shorter_target took 0.034 sec [junit] Testcase: should_align_multiple_cuts took 0.002 sec [junit] Testcase: testGetMaxScore took 0.003 sec [junit] Testcase: should_align_shorter_query took 0.002 sec BUILD SUCCESSFUL Total time: 34 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile-test: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 9 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] Note: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java uses or overrides a deprecated API that is marked for removal. [javac] Note: Recompile with -Xlint:removal for details. [copy] Copying 7 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [copy] Copying 32 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes test: [echo] Using java version 17.0.11 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.611 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.611 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 [junit] SAOV_0094,45884.0164,57760.0,57760.0,8.5193 [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testAdvancedXMLExample took 1.044 sec [junit] Testcase: testExample1 took 0.327 sec [junit] Testcase: testExample2 took 0.032 sec [junit] Testcase: testExample3 took 0.016 sec [junit] Testcase: testExample1WithCSV took 0.319 sec [junit] Testcase: testWithCases took 0.009 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.817 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.817 sec [junit] [junit] Testcase: shortExample1 took 0.075 sec [junit] Testcase: shortExample2 took 0.653 sec [junit] Testcase: shortExample3 took 0.094 sec [junit] Testcase: shortExample4 took 0.01 sec [junit] Testcase: shortExample5 took 0.047 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.478 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.478 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testAdvancedXMLExample took 1.151 sec [junit] Testcase: testExample1 took 0.19 sec [junit] Testcase: testExample2 took 0.028 sec [junit] Testcase: testExample3 took 0.023 sec [junit] Testcase: testExample1WithCSV took 0.169 sec [junit] Testcase: testWithCases took 0.015 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.93 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.93 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Molecular weight is 0.0, can't divide by 0: setting absorbance to 0.0 [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Molecular weight is 0.0, can't divide by 0: setting absorbance to 0.0 [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate average hydropathy: setting average hydropathy to 0 [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'Z are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '0''1''2''3''4''6''7''8''- are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate instability index: setting instability index value to 0.0 [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testAbsorbance took 0.324 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 0.607 sec [junit] Testcase: testEnrichment took 0.044 sec [junit] Testcase: testApliphaticIndex took 0.01 sec [junit] Testcase: testMolecularWeightXMLNull took 0.019 sec [junit] Testcase: testApliphaticIndexNull took 0.001 sec [junit] Testcase: testIsoelectricPointExpasy took 0.006 sec [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0 sec [junit] Testcase: testAverageHydropathy took 0.002 sec [junit] Testcase: testExtinctionCoefficient took 0.002 sec [junit] Testcase: testAAComposition took 0.003 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.143 sec [junit] Testcase: testMolecularWeight took 0.009 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.011 sec [junit] Testcase: testNetChargeNull took 0.002 sec [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec [junit] Testcase: testNetCharge took 0.227 sec [junit] Testcase: testEnrichmentNull took 0.001 sec [junit] Testcase: testInstabilityIndexNull took 0.001 sec [junit] Testcase: testAverageHydropathyNull took 0.001 sec [junit] Testcase: testMolecularWeightXML took 0.17 sec [junit] Testcase: testInstabilityIndex took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 sec [junit] [junit] Testcase: testFake took 0.014 sec [junit] Running org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.174 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.174 sec [junit] [junit] Testcase: testFakeTest took 0.044 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.979 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.979 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'J are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: generateSchema took 1.273 sec [junit] Testcase: readWithIDXml took 0.176 sec [junit] Testcase: readMinXml took 0.13 sec [junit] Testcase: readAdvancedXml took 0.06 sec [junit] Testcase: generateXml took 0.119 sec [junit] Testcase: readXml took 0.084 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.922 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.922 sec [junit] [junit] Testcase: generateSchema took 1.149 sec [junit] Testcase: generateXml took 0.357 sec [junit] Testcase: readXml took 0.347 sec [junit] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.545 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.545 sec [junit] [junit] Testcase: testFake took 0.047 sec BUILD SUCCESSFUL Total time: 41 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile-test: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 2 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 2 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 8 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes test: [echo] Using java version 17.0.11 BUILD SUCCESSFUL Total time: 7 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile-test: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 14 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 74 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 19 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes test: [echo] Using java version 17.0.11 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.969 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.969 sec [junit] [junit] Testcase: testConvert took 0.734 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec [junit] [junit] Testcase: testBuildAppendSequence took 0.031 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0.001 sec [junit] Testcase: testBuild took 0.008 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0.001 sec [junit] Testcase: testBuildNullAppendSequence took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec [junit] Testcase: testBuildNullSequence took 0.007 sec [junit] Testcase: testBuildMissingDescription took 0.001 sec [junit] Testcase: testBuildNullVariant took 0 sec [junit] Testcase: testBuildDefault took 0 sec [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0 sec [junit] Testcase: testBuildMultiple took 0 sec [junit] Testcase: testConstructor took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec [junit] [junit] Testcase: testImmutable took 0.004 sec [junit] Testcase: testBuilder took 0.02 sec [junit] Testcase: testVariant took 0 sec [junit] Testcase: testQuality took 0.01 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Testcase: testConstructor took 0 sec [junit] Testcase: testSequence took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.367 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.367 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.003 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.002 sec [junit] Testcase: testConvertNullVariant took 0 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.002 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.08 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0.001 sec [junit] Testcase: testConvertNullFastq took 0.001 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.002 sec [junit] Testcase: testCreateErrorProbabilities took 0.001 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.001 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.003 sec [junit] Testcase: testConvertQualitiesNullVariant took 0.001 sec [junit] Testcase: testConvertSameVariant took 0 sec [junit] Testcase: testQualityScores took 0.01 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0.001 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testToList took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec [junit] Testcase: testErrorProbabilities took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec [junit] [junit] Testcase: testParseFastqVariant took 0.005 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.002 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec [junit] Testcase: testIsSanger took 0.007 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec [junit] Testcase: testIsSolexa took 0.001 sec [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.58 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.58 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.129 sec [junit] Testcase: testWrappingAsIllumina took 0.014 sec [junit] Testcase: testValidateDescription took 0.024 sec [junit] Testcase: testValidateRepeatDescription took 0.027 sec [junit] Testcase: testMiscDnaAsIllumina took 0.003 sec [junit] Testcase: testMiscRnaAsIllumina took 0.002 sec [junit] Testcase: testLongReadsAsIllumina took 0.013 sec [junit] Testcase: testParseNullReadable took 0.002 sec [junit] Testcase: testReadRoundTripSingleFile took 0.135 sec [junit] Testcase: testReadEmptyFile took 0.001 sec [junit] Testcase: testErrorExamples took 0.074 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.01 sec [junit] Testcase: testReadEmptyInputStream took 0.004 sec [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0.002 sec [junit] Testcase: testMultipleWrappedQuality took 0.006 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.002 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.005 sec [junit] Testcase: testWrappedQuality took 0.006 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.032 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.025 sec [junit] Testcase: testWriteFileIterable took 0.149 sec [junit] Testcase: testWriteOutputStreamIterable took 0.004 sec [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.04 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.071 sec [junit] Testcase: testFullRangeAsSanger took 0.009 sec [junit] Testcase: testWrappingOriginal took 0.003 sec [junit] Testcase: testLongReadsOriginal took 0.022 sec [junit] Testcase: testMiscDnaOriginal took 0.002 sec [junit] Testcase: testMiscRnaOriginal took 0.006 sec [junit] Testcase: testValidateDescription took 0.015 sec [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testFullRangeOriginal took 0.005 sec [junit] Testcase: testWrappingAsSanger took 0.008 sec [junit] Testcase: testLongReadsAsSanger took 0.007 sec [junit] Testcase: testMiscDnaAsSanger took 0.006 sec [junit] Testcase: testParseNullReadable took 0.007 sec [junit] Testcase: testReadRoundTripSingleFile took 0.086 sec [junit] Testcase: testReadEmptyFile took 0.006 sec [junit] Testcase: testErrorExamples took 0.04 sec [junit] Testcase: testParse took 0.006 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.002 sec [junit] Testcase: testReadEmptyInputStream took 0.004 sec [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0.002 sec [junit] Testcase: testMultipleWrappedQuality took 0.002 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.224 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.224 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.018 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.032 sec [junit] Testcase: testWriteFileIterable took 0.09 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.008 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.663 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.663 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.079 sec [junit] Testcase: testFullRangeAsSolexa took 0.005 sec [junit] Testcase: testValidateDescription took 0.025 sec [junit] Testcase: testValidateRepeatDescription took 0.005 sec [junit] Testcase: testWrappingAsSolexa took 0.007 sec [junit] Testcase: testLongReadsAsSolexa took 0.006 sec [junit] Testcase: testMiscDnaAsSolexa took 0.009 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.108 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.058 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.007 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0.001 sec [junit] Testcase: testMultipleWrappedQuality took 0.003 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.238 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.238 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.01 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.007 sec [junit] Testcase: testWriteFileIterable took 0.165 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.005 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] [junit] Testcase: testStreamNullVariant took 0.003 sec [junit] Testcase: testStreamNullListener took 0.005 sec [junit] Testcase: testStreamNullReadable took 0.002 sec BUILD SUCCESSFUL Total time: 32 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure #cd biojava-protein-disorder && ant test # Requires remote access and tmp directory write access #cd biojava-structure && ant test cd biojava-structure-gui && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile-test: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 5 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [copy] Warning: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure-gui/src/test/resources does not exist. [copy] Copying 141 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes test: [echo] Using java version 17.0.11 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec [junit] [junit] Testcase: testMe took 0.002 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] [junit] Testcase: testSomeMethod took 0.009 sec [junit] Running org.biojava.nbio.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.StructureViewerTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec [junit] [junit] Testcase: testGetColor took 0.015 sec [junit] Testcase: testSetStructure took 0.001 sec [junit] Testcase: testClear took 0.007 sec [junit] Testcase: testGetSelection took 0.006 sec [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0.001 sec [junit] Testcase: testSetStyle took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL Total time: 16 seconds cd biojava-ontology && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile-test: [mkdir] Created dir: /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [javac] /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml:95: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 2 source files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 5 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 36 files to /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes test: [echo] Using java version 17.0.11 BUILD SUCCESSFUL Total time: 6 seconds make[1]: Leaving directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_install jh_installjavadoc dh_installdocs 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 dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-8_all.deb'. dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-8_all.deb'. dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-8_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava4-live_4.2.12+dfsg-8_amd64.buildinfo dpkg-genchanges --build=binary -O../biojava4-live_4.2.12+dfsg-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/730688/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/730688/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/730688 and its subdirectories I: Current time: Wed May 15 05:36:40 +14 2024 I: pbuilder-time-stamp: 1715701000