Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/biojava-live/biojava-live_1.7.1-9_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/biojava-live-1.7.1-9c2jwyofd/biojava-live_1.7.1-9_all.buildinfo Get source package info: biojava-live=1:1.7.1-9 Source URL: http://snapshot.notset.fr/mr/package/biojava-live/1:1.7.1-9/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=ant=1.10.9-1 ant-optional=1.10.9-1 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-6 binutils-common=2.35.1-6 binutils-x86-64-linux-gnu=2.35.1-6 bsdextrautils=2.36.1-4 bsdutils=1:2.36.1-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20200601 ca-certificates-java=20190909 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-3 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debianutils=4.11.2 default-jdk=2:1.11-72 default-jdk-headless=2:1.11-72 default-jre=2:1.11-72 default-jre-headless=2:1.11-72 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-5 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.0-1 g++-10=10.2.1-3 gcc=4:10.2.0-1 gcc-10=10.2.1-3 gcc-10-base=10.2.1-3 gettext=0.21-3 gettext-base=0.21-3 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 java-common=0.72 junit4=4.13.1-1 libacl1=2.2.53-9 libarchive-zip-perl=1.68-1 libasan6=10.2.1-3 libasound2=1.2.4-1.1 libasound2-data=1.2.4-1.1 libatomic1=10.2.1-3 libattr1=1:2.4.48-6 libaudit-common=1:3.0-1 libaudit1=1:3.0-1 libavahi-client3=0.8-3 libavahi-common-data=0.8-3 libavahi-common3=0.8-3 libbinutils=2.35.1-6 libblkid1=2.36.1-4 libbrotli1=1.0.9-2+b2 libbsd0=0.10.0-1 libbytecode-java=0.92.svn.20090106-2.1 libbz2-1.0=1.0.8-4 libc-bin=2.31-7 libc-dev-bin=2.31-7 libc6=2.31-7 libc6-dev=2.31-7 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-3 libcom-err2=1.45.6-1 libcommons-collections3-java=3.2.2-2 libcommons-dbcp-java=1.4-7 libcommons-pool-java=1.6-3.1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-6 libctf0=2.35.1-6 libcups2=2.3.3op1-4 libdb5.3=5.3.28+dfsg1-0.6 libdbus-1-3=1.12.20-1 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdpkg-perl=1.20.5 libdrm-amdgpu1=2.4.103-2 libdrm-common=2.4.103-2 libdrm-intel1=2.4.103-2 libdrm-nouveau2=2.4.103-2 libdrm-radeon1=2.4.103-2 libdrm2=2.4.103-2 libedit2=3.1-20191231-2+b1 libelf1=0.182-2 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libgcc-10-dev=10.2.1-3 libgcc-s1=10.2.1-3 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgif7=5.1.9-1 libgl1=1.3.2-1 libgl1-mesa-dri=20.3.2-1 libglapi-mesa=20.3.2-1 libglib2.0-0=2.66.4-1 libglvnd0=1.3.2-1 libglx-mesa0=20.3.2-1 libglx0=1.3.2-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-5 libgomp1=10.2.1-3 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libhamcrest-java=1.3-9 libharfbuzz0b=2.6.7-1 libhogweed6=3.6-2 libhsqldb-java=2.5.1-1 libicu67=67.1-5 libidn2-0=2.3.0-4 libisl23=0.23-1 libitm1=10.2.1-3 libjpeg62-turbo=1:2.0.5-2 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblcms2-2=2.9-4+b1 libllvm11=1:11.0.1~+rc2-1 liblsan0=10.2.1-3 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-4 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.6-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.29-1 libnss3=2:3.60-1 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpciaccess0=0.16-1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libpcsclite1=1.9.0-1 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpng16-16=1.6.37-3 libquadmath0=10.2.1-3 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsensors-config=1:3.6.0-2 libsensors5=1:3.6.0-2 libservlet-api-java=4.0.1-2 libsigsegv2=2.12-3 libsmartcols1=2.36.1-4 libsqlite3-0=3.34.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-3 libstdc++6=10.2.1-3 libsub-override-perl=0.09-2 libsystemd0=247.2-4 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-14 libtsan0=10.2.1-3 libubsan1=10.2.1-3 libuchardet0=0.0.7-1 libudev1=247.2-4 libunistring2=0.9.10-4 libuuid1=2.36.1-4 libvulkan1=1.2.154.1-1 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libx11-xcb1=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb-dri2-0=1.14-2.1 libxcb-dri3-0=1.14-2.1 libxcb-glx0=1.14-2.1 libxcb-present0=1.14-2.1 libxcb-shm0=1.14-2.1 libxcb-sync1=1.14-2.1 libxcb-xfixes0=1.14-2.1 libxcb1=1.14-2.1 libxdamage1=1:1.1.5-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxfixes3=1:5.0.3-2 libxi6=2:1.7.10-1 libxml2=2.9.10+dfsg-6.3+b1 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxtst6=2:1.2.3-1 libxxf86vm1=1:1.1.4-1+b2 libz3-4=4.8.9-1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.4-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openjdk-11-jdk=11.0.10+8-1 openjdk-11-jdk-headless=11.0.10+8-1 openjdk-11-jre=11.0.10+8-1 openjdk-11-jre-headless=11.0.10+8-1 openssl=1.1.1i-1 patch=2.7.6-6 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 ucf=3.0043 util-linux=2.36.1-4 x11-common=1:7.7+21 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210105T023154Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d biojava-live=1:1.7.1-9 && mkdir -p /build/biojava-live-XHkm1f && dpkg-source --no-check -x /*.dsc /build/biojava-live-XHkm1f/biojava-live-1.7.1 && chown -R builduser:builduser /build/biojava-live-XHkm1f" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/biojava-live-XHkm1f/biojava-live-1.7.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609774933" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/biojava-live-XHkm1f /tmp/biojava-live-1.7.1-9c2jwyofd bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210105T023154Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.neTAR4OCFg as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.neTAR4OCFg Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210105T023154Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210105T023154Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (872 kB/s) Selecting previously unselected package libfakeroot: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 ... 4647 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210105T023154Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.neTAR4OCFg Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210105T023154Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1183 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.neTAR4OCFg I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d biojava-live=1:1.7.1-9 && mkdir -p /build/biojava-live-XHkm1f && dpkg-source --no-check -x /*.dsc /build/biojava-live-XHkm1f/biojava-live-1.7.1 && chown -R builduser:builduser /build/biojava-live-XHkm1f"' exec /tmp/mmdebstrap.neTAR4OCFg Reading package lists... NOTICE: 'biojava-live' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/biojava-live.git Please use: git clone https://salsa.debian.org/med-team/biojava-live.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 11.1 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main biojava-live 1:1.7.1-9 (dsc) [2430 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main biojava-live 1:1.7.1-9 (tar) [11.0 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main biojava-live 1:1.7.1-9 (diff) [9580 B] Fetched 11.1 MB in 9s (1278 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'biojava-live_1.7.1-9.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting biojava-live in /build/biojava-live-XHkm1f/biojava-live-1.7.1 dpkg-source: info: unpacking biojava-live_1.7.1.orig.tar.gz dpkg-source: info: unpacking biojava-live_1.7.1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying buildxml.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying java8_instead_of_11.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/biojava-live-XHkm1f/biojava-live-1.7.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609774933" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.neTAR4OCFg dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.7.1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean dh_auto_clean ant clean Buildfile: /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml init: [tstamp] Honouring environment variable SOURCE_DATE_EPOCH which has been set to 1609774933 [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-11-openjdk-amd64 [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true clean: BUILD SUCCESSFUL Total time: 2 seconds debian/rules override_dh_clean make[1]: Entering directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' ant clean # most probably this is not needed when using dh - leave it to be sure ... Buildfile: /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml init: [tstamp] Honouring environment variable SOURCE_DATE_EPOCH which has been set to 1609774933 [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-11-openjdk-amd64 [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true clean: BUILD SUCCESSFUL Total time: 2 seconds dh_clean make[1]: Leaving directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i dh_auto_configure -i debian/rules override_dh_auto_build make[1]: Entering directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' find . -name "*.java" -o -name ReadMe -o -name "*.fa" -o -name "*.html" | xargs -r chmod 644 # circumvent Debian's difficulties with libjgrapht - deleting all usage of that library rm -rf src/org/biojavax/bio/phylo/io/nexus/ \ src/org/biojavax/bio/phylo/DistanceBasedTreeMethod.java \ src/org/biojavax/bio/phylo/ParsimonyTreeMethod.java dh_auto_build ant -Duser.name debian Buildfile: /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml init: [tstamp] Honouring environment variable SOURCE_DATE_EPOCH which has been set to 1609774933 [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-11-openjdk-amd64 [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true prepare: [mkdir] Created dir: /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build prepare-biojava: [mkdir] Created dir: /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/classes/biojava [mkdir] Created dir: /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/biojava [mkdir] Created dir: /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/check/biojava compile-biojava: [javac] /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml:247: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 1444 source files to /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/classes/biojava [javac] Support for javac --release has been added in Java9 ignoring it [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:37: warning: as of release 9, '_' is a keyword, and may not be used as an identifier [javac] private static final AtomicSymbol _; [javac] ^ [javac] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:53: warning: as of release 9, '_' is a keyword, and may not be used as an identifier [javac] _ = (AtomicSymbol) sTok.parseToken(" "); [javac] ^ [javac] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:72: warning: as of release 9, '_' is a keyword, and may not be used as an identifier [javac] return _; [javac] ^ [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 unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 4 warnings [javac] Creating empty /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/classes/biojava/org/biojava/bio/program/fastq/package-info.class package-biojava: [jar] Building jar: /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/biojava.jar BUILD SUCCESSFUL Total time: 2 minutes 36 seconds # Add here commands to compile the package. ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava Buildfile: /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml init: [tstamp] Honouring environment variable SOURCE_DATE_EPOCH which has been set to 1609774933 [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-11-openjdk-amd64 [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true prepare: prepare-biojava: compile-biojava: [javac] /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml:247: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds package-biojava: BUILD SUCCESSFUL Total time: 8 seconds #ant compile-demos ant javadocs-biojava Buildfile: /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml init: [tstamp] Honouring environment variable SOURCE_DATE_EPOCH which has been set to 1609774933 [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-11-openjdk-amd64 [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true prepare: prepare-biojava: javadocs-biojava: [javadoc] Generating Javadoc [javadoc] Using javadoc -source 1.5 is no longer supported, switching to 6 [javadoc] Debian build on Java 9+ detected: Adding the --ignore-source-errors option [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.bibliography... 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[javadoc] Loading source files for package org.biojava.stats.svm... [javadoc] Loading source files for package org.biojava.stats.svm.tools... [javadoc] Loading source files for package org.biojava.utils... [javadoc] Loading source files for package org.biojava.utils.automata... [javadoc] Loading source files for package org.biojava.utils.cache... [javadoc] Loading source files for package org.biojava.utils.candy... [javadoc] Loading source files for package org.biojava.utils.io... [javadoc] Loading source files for package org.biojava.utils.lsid... [javadoc] Loading source files for package org.biojava.utils.math... [javadoc] Loading source files for package org.biojava.utils.net... [javadoc] Loading source files for package org.biojava.utils.process... [javadoc] Loading source files for package org.biojava.utils.regex... [javadoc] Loading source files for package org.biojava.utils.stax... [javadoc] Loading source files for package org.biojava.utils.walker... 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[javadoc] Loading source files for package org.biojavax.ga.functions... [javadoc] Loading source files for package org.biojavax.ga.impl... [javadoc] Loading source files for package org.biojavax.ga.util... [javadoc] Loading source files for package org.biojavax.ontology... [javadoc] Loading source files for package org.biojavax.utils... [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:37: warning: as of release 9, '_' is a keyword, and may not be used as an identifier [javadoc] private static final AtomicSymbol _; [javadoc] ^ [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:53: warning: as of release 9, '_' is a keyword, and may not be used as an identifier [javadoc] _ = (AtomicSymbol) sTok.parseToken(" "); [javadoc] ^ [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/proteomics/StructureTools.java:72: warning: as of release 9, '_' is a keyword, and may not be used as an identifier [javadoc] return _; [javadoc] ^ [javadoc] Constructing Javadoc information... [javadoc] Standard Doclet version 11.0.10-ea [javadoc] Building tree for all the packages and classes... [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bibliography/BiblioScope.java:49: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bibliography/BibRefQuery.java:625: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/AnnotationType.java:578: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/alignment/EditableAlignment.java:35: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/alignment/EditableAlignment.java:35: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/alignment/SequenceAlignment.java:36: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/alignment/SequenceAlignment.java:36: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/alignment/SubstitutionMatrix.java:60: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/alignment/SubstitutionMatrix.java:60: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/chromatogram/ChromatogramTools.java:67: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/chromatogram/graphic/ChromatogramGraphic.java:1074: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/MarkovModel.java:42: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/MarkovModel.java:42: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/symbol/SymbolList.java:148: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/symbol/SymbolList.java:148: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/StatePath.java:34: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/StatePath.java:36: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/StatePath.java:38: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/StatePath.java:47: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/StatePath.java:48: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/StatePath.java:50: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/TransitionTrainer.java:34: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/dp/TransitionTrainer.java:34: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/gui/LogoPainter.java:30: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/gui/glyph/RectangleGlyph.java:32: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/gui/glyph/RectangleGlyph.java:32: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/gui/sequence/SequencePanel.java:398: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/gui/sequence/SequencePoster.java:406: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/molbio/RestrictionEnzymeManager.java:229: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/molbio/RestrictionEnzymeManager.java:229: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/program/BlastLikeToXMLConverter.java:61: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/program/BlastLikeToXMLConverter.java:61: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/program/blast2html/HTMLRenderer.java:116: warning - invalid usage of tag < [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/program/blast2html/SimpleAlignmentStyler.java:30: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:74: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/utils/AbstractChangeable.java:84: warning - invalid usage of tag & [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/symbol/SymbolList.java:148: warning - invalid usage of tag > [javadoc] /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bio/symbol/SymbolList.java:148: warning - invalid usage of tag > [javadoc] javadoc: warning - invalid usage of tag &cvsroot [javadoc] javadoc: warning - invalid usage of tag &content [javadoc] javadoc: warning - invalid usage of tag &cvsroot [javadoc] javadoc: warning - invalid usage of tag &content [javadoc] javadoc: warning - invalid usage of tag &cvsroot [javadoc] javadoc: warning - invalid usage of tag &content [javadoc] javadoc: warning - invalid usage of tag &cvsroot [javadoc] javadoc: warning - invalid usage of tag &content [javadoc] javadoc: warning - invalid usage of tag &cvsroot [javadoc] javadoc: warning - invalid usage of tag &content [javadoc] Generating /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/package-summary.html... [javadoc] Copying file /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_corba.jpg to directory /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_soap.jpg to directory /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_simple.jpg to directory /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-XHkm1f/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/bibobjects_java.jpg to directory /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Building index for all classes... [javadoc] Generating /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/biojava/help-doc.html... [javadoc] 100 warnings BUILD SUCCESSFUL Total time: 2 minutes 53 seconds touch build-stamp make[1]: Leaving directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' dh_auto_test -i create-stamp debian/debhelper-build-stamp dh_prep -i dh_installdirs -i dh_auto_install -i debian/rules override_dh_install make[1]: Entering directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' dh_install cp ant-build/biojava.jar /build/biojava-live-XHkm1f/biojava-live-1.7.1/debian/libbiojava1.7-java/usr/share/java/biojava1.7.1.jar d=/build/biojava-live-XHkm1f/biojava-live-1.7.1/debian/libbiojava-java-doc/usr/share/doc/libbiojava-java/api; \ [ -d $d ] || mkdir -p $d ; \ cp -r ant-build/docs/biojava/* $d for i in /build/biojava-live-XHkm1f/biojava-live-1.7.1/debian/libbiojava-java*; do \ if [ -d "" ]; then \ find -name ".svn" | xargs -r rm -r ; \ fi ; \ done ant runtests Buildfile: /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml init: [tstamp] Honouring environment variable SOURCE_DATE_EPOCH which has been set to 1609774933 [echo] Building biojava-1.7.1 [echo] Java Home: /usr/lib/jvm/java-11-openjdk-amd64 [echo] JUnit present: true [echo] JUnit supported by Ant: true [echo] HSQLDB driver present: true [echo] XSLT support: true prepare: prepare-tests: [mkdir] Created dir: /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/classes/tests [mkdir] Created dir: /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/docs/tests [mkdir] Created dir: /build/biojava-live-XHkm1f/biojava-live-1.7.1/reports/tests prepare-biojava: compile-biojava: [javac] /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml:247: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds package-biojava: compile-tests: [javac] /build/biojava-live-XHkm1f/biojava-live-1.7.1/build.xml:265: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 184 source files to /build/biojava-live-XHkm1f/biojava-live-1.7.1/ant-build/classes/tests [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [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 unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 warning runtests: [echo] Running tests: ** [junit] Running org.biojava.bio.AnnotationTypeTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec [junit] Running org.biojava.bio.MergeAnnotationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec [junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.alignment.SubstitutionMatrixTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.dist.DistSerTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.788 sec [junit] Running org.biojava.bio.dist.DistributionTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.dist.DistributionToolsTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.286 sec [junit] Running org.biojava.bio.dist.TranslatedDistributionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.dp.DPSerializationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.311 sec [junit] Running org.biojava.bio.dp.EmissionStateEventTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec [junit] Running org.biojava.bio.dp.MarkovModelEventTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec [junit] Running org.biojava.bio.program.fastq.FastqBuilderTest [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.program.fastq.FastqTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.FastqVariantTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.189 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqReaderTest [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.program.indexdb.IndexToolsTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.694 sec [junit] Running org.biojava.bio.program.phred.PhredToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec [junit] Running org.biojava.bio.program.sax.BlastTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.793 sec [junit] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 sec [junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.613 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.405 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.993 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.101 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.007 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.591 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.407 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.554 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.762 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.405 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.892 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.411 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.303 sec [junit] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.proteomics.MassCalcTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexTest [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec [junit] Running org.biojava.bio.search.MaxMismatchPatternTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.search.SeqContentPatternTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.CircularSequenceTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.seq.DNAToolsTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.FeatureFilterTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec [junit] Running org.biojava.bio.seq.FeatureHolderUtilsTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.seq.FilterUtilsTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec [junit] Running org.biojava.bio.seq.MergeFeatureHolderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 sec [junit] Running org.biojava.bio.seq.ProteinToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.RNAToolsTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec [junit] Running org.biojava.bio.seq.SeqSerializationTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 sec [junit] Running org.biojava.bio.seq.SimpleAssemblyTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 sec [junit] Running org.biojava.bio.seq.db.HashSequenceDBTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 1.302 sec [junit] Test org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest FAILED [junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.filter.FilterTransformerTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec [junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.impl.GappedSequenceTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.seq.impl.SubSequenceTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec [junit] Running org.biojava.bio.seq.impl.ViewSequenceTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.seq.io.LocationFormatterTest [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.299 sec [junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.seq.io.SeqIOToolsTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.312 sec [junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.512 sec [junit] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 sec [junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.structure.MMcifTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.009 sec [junit] Running org.biojava.bio.structure.PDBFileParserTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.structure.PdbFileFormat30Test [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec [junit] Running org.biojava.bio.structure.SourceCompoundTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.87 sec [junit] Running org.biojava.bio.structure.StructurePairAlignerTest [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 12.1 sec [junit] Test org.biojava.bio.structure.StructurePairAlignerTest FAILED [junit] Running org.biojava.bio.structure.StructureTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.396 sec [junit] Running org.biojava.bio.structure.StructureToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 sec [junit] Running org.biojava.bio.symbol.AlphabetManagerTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.AlphabetSerializationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 sec [junit] Running org.biojava.bio.symbol.BetweenLocationTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec [junit] Running org.biojava.bio.symbol.CircularLocationTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.CodonPrefToolsTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 sec [junit] Running org.biojava.bio.symbol.CompoundLocationTest [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.197 sec [junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.399 sec [junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec [junit] Running org.biojava.bio.symbol.DoubleAlphabetTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec [junit] Running org.biojava.bio.symbol.GappedSymbolListTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec [junit] Running org.biojava.bio.symbol.IndexedNoAmbPackTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.IntegerAlphabetTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.LinearAlphabetIndexTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.MergeLocationTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.MotifToolsTest [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.NameTokenizationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec [junit] Running org.biojava.bio.symbol.PointLocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.RangeLocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolListTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec [junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SymbolListTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.215 sec [junit] Running org.biojava.bio.symbol.SymbolSerializationTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.TranslationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.189 sec [junit] Running org.biojava.directory.OBDARegistryParserTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec [junit] Running org.biojava.directory.RegistryConfigurationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.directory.SystemRegistryTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.853 sec [junit] Running org.biojava.naming.ObdaInitialContextFactoryTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.156 sec [junit] Running org.biojava.naming.ObdaUriParserTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.ontology.OntologyTest [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.ontology.ParseOBOFileTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.694 sec [junit] Running org.biojava.ontology.TermImplTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.ontology.TripleImplTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.utils.ListToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.utils.RepeatedCharSequenceTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.utils.SmallMapTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.utils.automata.NfaTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.utils.process.ExternalProcessTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.506 sec [junit] Running org.biojava.utils.regex.PatternCheckerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec [junit] Running org.biojava.utils.regex.RegexTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.utils.walker.WalkerFactoryTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec [junit] Running org.biojava.utils.walker.WalkerTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec [junit] Running org.biojavax.CrossReferenceResolutionExceptionTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.DummyCrossReferenceResolverTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.EmptyRichAnnotationTest [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.SimpleCommentTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.SimpleCrossRefTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.SimpleDocRefAuthorTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.SimpleDocRefTest [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.SimpleNamespaceTest [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.006 sec [junit] Test org.biojavax.SimpleNamespaceTest FAILED [junit] Running org.biojavax.SimpleNoteTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.SimpleRankedCrossRefTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 sec [junit] Running org.biojavax.SimpleRankedDocRefTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 sec [junit] Running org.biojavax.SimpleRichAnnotationTest [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.bio.SimpleBioEntryTest [junit] Tests run: 32, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec [junit] Test org.biojavax.bio.SimpleBioEntryTest FAILED [junit] Running org.biojavax.bio.seq.CompoundRichLocationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec [junit] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.bio.seq.SimpleRichFeatureTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.bio.seq.SimpleRichLocationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojavax.bio.seq.io.Bug2249_2248Test [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec [junit] Running org.biojavax.bio.seq.io.Bug2250_2256Test [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 sec [junit] Running org.biojavax.bio.seq.io.Bug2255Test [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 sec [junit] Running org.biojavax.bio.seq.io.EMBLFormatTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.bio.seq.io.GenbankFormatTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 sec [junit] Running org.biojavax.bio.seq.io.INSDseqFormatTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 sec [junit] Running org.biojavax.bio.seq.io.UniProtFormatTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.186 sec [junit] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ga.functions.ProportionalSelectionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec [junit] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ga.functions.SimpleMutationFunctionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec [junit] Running org.biojavax.ga.impl.SimpleOrganismTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ga.impl.SimplePopulationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ga.util.GAToolsTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ga.util.WeightedSetTest [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ontology.SimpleComparableOntologyTest [junit] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.ontology.SimpleComparableTermTest [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec [junit] Running org.biojavax.ontology.SimpleComparableTripleTest [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec BUILD SUCCESSFUL Total time: 3 minutes 10 seconds make[1]: Leaving directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' dh_installdocs -i dh_installchangelogs -i debian/rules override_dh_installexamples make[1]: Entering directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' dh_installexamples dh_installexamples -plibbiojava-java-demos demos/* make[1]: Leaving directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' dh_perl -i debian/rules override_dh_link make[1]: Entering directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' dh_link -p libbiojava-java /usr/share/java/biojava1.7.1.jar /usr/share/java/biojava.jar # thinking about svn snapshots if [ "1.7" != "1.7.1" ]; then \ dh_link -p libbiojava1.7-java \ /usr/share/java/biojava1.7.1.jar \ /usr/share/java/biojava1.7.jar; \ fi dh_link # use .link files for version independant linking make[1]: Leaving directory '/build/biojava-live-XHkm1f/biojava-live-1.7.1' dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dpkg-gencontrol: warning: Depends field of package libbiojava1.7-java: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.7.1-9_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.7.1-9_all.deb'. dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-9_all.deb'. dpkg-deb: building package 'libbiojava-java-demos' in '../libbiojava-java-demos_1.7.1-9_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../biojava-live_1.7.1-9_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/biojava-live-XHkm1f 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I: done I: removing tempdir /tmp/mmdebstrap.neTAR4OCFg... I: success in 1161.9872 seconds md5: libbiojava-java-demos_1.7.1-9_all.deb: OK md5: libbiojava-java-doc_1.7.1-9_all.deb: OK md5: libbiojava-java_1.7.1-9_all.deb: OK md5: libbiojava1.7-java_1.7.1-9_all.deb: OK sha1: libbiojava-java-demos_1.7.1-9_all.deb: OK sha1: libbiojava-java-doc_1.7.1-9_all.deb: OK sha1: libbiojava-java_1.7.1-9_all.deb: OK sha1: libbiojava1.7-java_1.7.1-9_all.deb: OK sha256: libbiojava-java-demos_1.7.1-9_all.deb: OK sha256: libbiojava-java-doc_1.7.1-9_all.deb: OK sha256: libbiojava-java_1.7.1-9_all.deb: OK sha256: libbiojava1.7-java_1.7.1-9_all.deb: OK Checksums: OK