Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/biojava4-live/biojava4-live_4.2.12+dfsg-3.1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/biojava4-live-4.2.12+dfsg-3.1d61rk52o/biojava4-live_4.2.12+dfsg-3.1_all.buildinfo Get source package info: biojava4-live=4.2.12+dfsg-3.1 Source URL: http://snapshot.notset.fr/mr/package/biojava4-live/4.2.12+dfsg-3.1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 ant=1.10.8-1 ant-contrib=1.0~b3+svn177-11 ant-optional=1.10.8-1 autoconf=2.69-11.1 automake=1:1.16.2-3 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.35-1 binutils-common=2.35-1 binutils-x86-64-linux-gnu=2.35-1 bsdextrautils=2.36-1 bsdutils=1:2.36-1 build-essential=12.8 bzip2=1.0.8-4 ca-certificates=20200601 ca-certificates-java=20190909 coreutils=8.32-3 cpp=4:10.1.0-1 cpp-10=10.2.0-3 dash=0.5.10.2-7 dctrl-tools=2.24-3+b1 debconf=1.5.74 debhelper=13.2 debianutils=4.11 default-jdk-doc=2:1.11-72 default-jdk-headless=2:1.11-72 default-jre-headless=2:1.11-72 devscripts=2.20.4 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dirmngr=2.2.20-1 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 fakeroot=1.24-1 file=1:5.38-5 findutils=4.7.0-1 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.1.0-1 g++-10=10.2.0-3 gcc=4:10.1.0-1 gcc-10=10.2.0-3 gcc-10-base=10.2.0-3 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gnupg=2.2.20-1 gnupg-l10n=2.2.20-1 gnupg-utils=2.2.20-1 gpg=2.2.20-1 gpg-agent=2.2.20-1 gpg-wks-client=2.2.20-1 gpg-wks-server=2.2.20-1 gpgconf=2.2.20-1 gpgsm=2.2.20-1 gpgv=2.2.20-1 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 java-common=0.72 javahelper=0.75 junit=3.8.2-9 junit4=4.12-8 libacl1=2.2.53-8 libactivation-java=1.2.0-2 libaopalliance-java=20070526-6 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libargs4j-java=2.33-1 libasan6=10.2.0-3 libasound2=1.2.2-2.3 libasound2-data=1.2.2-2.3 libassuan0=2.5.3-7.1 libatinject-jsr330-api-java=1.0+ds1-5 libatomic1=10.2.0-3 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libavahi-client3=0.8-3 libavahi-common-data=0.8-3 libavahi-common3=0.8-3 libb-hooks-op-check-perl=0.22-1+b2 libbinutils=2.35-1 libblkid1=2.36-1 libbrotli1=1.0.7-7 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-2 libc-dev-bin=2.31-2 libc6=2.31-2 libc6-dev=2.31-2 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-3 libcdi-api-java=1.2-2 libclass-method-modifiers-perl=2.13-1 libcodemodel-java=2.6+jaxb2.3.0.1-9 libcom-err2=1.45.6-1 libcommons-cli-java=1.4-1 libcommons-codec-java=1.14-1 libcommons-collections3-java=3.2.2-2 libcommons-compress-java=1.20-1 libcommons-dbcp-java=1.4-7 libcommons-io-java=2.6-2 libcommons-lang3-java=3.11-1 libcommons-logging-java=1.2-2 libcommons-math-java=2.2-7 libcommons-parent-java=43-1 libcommons-pool-java=1.6-3 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.35-1 libctf0=2.35-1 libcups2=2.3.3-1 libdb5.3=5.3.28+dfsg1-0.6 libdbus-1-3=1.12.20-1 libdebconfclient0=0.253 libdebhelper-perl=13.2 libdevel-callchecker-perl=0.008-1+b1 libdom4j-java=2.1.1-4 libdpkg-perl=1.20.5 libdtd-parser-java=1.2~svn20110404-1 libdynaloader-functions-perl=0.003-1 libelf1=0.180-1 libencode-locale-perl=1.05-1 libexpat1=2.2.9-1 libfakeroot=1.24-1 libfastinfoset-java=1.2.12-3 libffi7=3.3-4 libfile-homedir-perl=1.004-1 libfile-listing-perl=6.04-1 libfile-stripnondeterminism-perl=1.9.0-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.2+dfsg-3 libgcc-10-dev=10.2.0-3 libgcc-s1=10.2.0-3 libgcrypt20=1.8.6-2 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgeronimo-annotation-1.3-spec-java=1.0-1 libgeronimo-interceptor-3.0-spec-java=1.0.1-4 libglib2.0-0=2.64.4-1 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.14-2+b1 libgomp1=10.2.0-3 libgoogle-gson-java=2.8.6-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libguava-java=29.0-5 libguice-java=4.2.1-1 libhamcrest-java=1.3-9 libhogweed6=3.6-2 libhsqldb-java=2.5.1-1 libhtml-parser-perl=3.72-5 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.08-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.25-1 libhttp-negotiate-perl=6.01-1 libhttpclient-java=4.5.11-1 libhttpcore-java=4.4.13-1 libicu67=67.1-3 libidn2-0=2.3.0-1 libimport-into-perl=1.002005-1 libio-html-perl=1.001-1 libio-pty-perl=1:1.12-1 libio-socket-ssl-perl=2.067-1 libipc-run-perl=20200505.0-1 libisl22=0.22.1-1 libistack-commons-java=3.0.6-4 libitext5-java=5.5.13.1-1 libitm1=10.2.0-3 libjaxb-api-java=2.3.1-1 libjaxb-java=2.3.0.1-9 libjaxen-java=1.1.6-4 libjgraph-java=5.12.4.2+dfsg-5 libjgrapht0.8-java=0.8.3-5 libjmol-java=14.6.4+2016.11.05+dfsg1-4 libjpeg62-turbo=1:2.0.5-1 libjson-simple-java=2.3.0-1 libjsoup-java=1.10.2-2 libjsr305-java=0.1~+svn49-11 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libksba8=1.4.0-2 liblcms2-2=2.9-4+b1 libldap-2.4-2=2.4.50+dfsg-1+b1 libldap-common=2.4.50+dfsg-1 liblightcouch-java=0.0.6-1 liblog4j2-java=2.11.2-1 liblsan0=10.2.0-3 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.09-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmaven-file-management-java=3.0.0-1 libmaven-parent-java=31-2 libmaven-resolver-java=1.4.2-1 libmaven-shared-io-java=3.0.0-3 libmaven-shared-utils-java=3.3.0-1 libmaven3-core-java=3.6.3-1 libmodule-runtime-perl=0.016-1 libmongodb-java=3.6.3-2 libmoo-perl=2.004000-1 libmount1=2.36-1 libmpc3=1.1.0-1 libmpdec2=2.4.2-3 libmpfr6=4.1.0-3 libnaga-java=3.0+svn80-4 libncursesw6=6.2-1 libnet-http-perl=6.19-1 libnet-ssleay-perl=1.88-3 libnettle8=3.6-2 libnetx-java=0.5-4 libnpth0=1.6-2 libnspr4=2:4.25-1 libnss3=2:3.53.1-1 libp11-kit0=0.23.20-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libparams-classify-perl=0.015-1+b2 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libpcsclite1=1.9.0-1 libperl5.30=5.30.3-4 libpipeline1=1.5.2-2 libplexus-archiver-java=3.6.0-2 libplexus-cipher-java=1.7-3 libplexus-classworlds-java=2.6.0-1 libplexus-component-annotations-java=2.1.0-1 libplexus-interpolation-java=1.26-1 libplexus-io-java=3.2.0-1 libplexus-sec-dispatcher-java=1.4-4 libplexus-utils2-java=3.3.0-1 libpng16-16=1.6.37-2 libpython3-stdlib=3.8.2-3 libpython3.8-minimal=3.8.5-1 libpython3.8-stdlib=3.8.5-1 libquadmath0=10.2.0-3 libreadline8=8.0-4 librelaxng-datatype-java=1.0+ds1-3 librngom-java=2.3.0.1-9 librole-tiny-perl=2.001004-1 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.3-1+b1 libselinux1=3.1-2 libsemanage-common=3.1-1 libsemanage1=3.1-1 libsepol1=3.1-1 libservlet-api-java=4.0.1-2 libsigsegv2=2.12-2 libsisu-guice-java=4.2.0-1 libsisu-inject-java=0.3.3-1 libsisu-ioc-java=2.3.0-11 libsisu-plexus-java=0.3.3-3 libslf4j-java=1.7.25-3 libsmartcols1=2.36-1 libsnappy-java=1.1.7.5-1 libsnappy-jni=1.1.7.5-1 libsnappy1v5=1.1.8-1 libsqlite3-0=3.32.3-1 libssl1.1=1.1.1g-1 libstax-ex-java=1.7.8-3 libstdc++-10-dev=10.2.0-3 libstdc++6=10.2.0-3 libstreambuffer-java=1.5.4-1 libstrictures-perl=2.000006-1 libsub-override-perl=0.09-2 libsub-quote-perl=2.006006-1 libsystemd0=245.6-3 libtasn1-6=4.16.0-2 libtimedate-perl=2.3300-1 libtinfo6=6.2-1 libtool=2.4.6-14 libtry-tiny-perl=0.30-1 libtsan0=10.2.0-3 libtxw2-java=2.3.0.1-9 libubsan1=10.2.0-3 libuchardet0=0.0.7-1 libudev1=245.6-3 libunistring2=0.9.10-4 liburi-perl=1.76-2 libuuid1=2.36-1 libvecmath-java=1.5.2-7 libwagon-http-java=3.3.4-1 libwagon-provider-api-java=3.3.4-1 libwww-perl=6.46-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.6.9-2+b1 libx11-data=2:1.6.9-2 libxau6=1:1.0.8-1+b2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxi6=2:1.7.10-1 libxml-commons-resolver1.1-java=1.2-10 libxml2=2.9.10+dfsg-5+b1 libxmlunit-java=1.6-2 libxrender1=1:0.9.10-1 libxsom-java=2.3.0.1-9 libxtst6=2:1.2.3-1 libxz-java=1.8-2 libzstd1=1.4.5+dfsg-3 linux-libc-dev=5.7.10-1 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 mime-support=3.64 ncurses-base=6.2-1 ncurses-bin=6.2-1 netbase=6.1 openjdk-11-doc=11.0.8+10-1 openjdk-11-jdk-headless=11.0.8+10-1 openjdk-11-jre-headless=11.0.8+10-1 openssl=1.1.1g-1 passwd=1:4.8.1-1 patch=2.7.6-6 patchutils=0.4.2-1 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 perl-openssl-defaults=5 pinentry-curses=1.1.0-4 po-debconf=1.0.21 python3=3.8.2-3 python3-minimal=3.8.2-3 python3.8=3.8.5-1 python3.8-minimal=3.8.5-1 rdfind=1.4.1-1+b3 readline-common=8.0-4 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 ucf=3.0043 util-linux=2.36-1 wdiff=1.2.2-2+b1 x11-common=1:7.7+20 xz-utils=5.2.4-1+b1 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/20200727T204945Z/ 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 biojava4-live=4.2.12+dfsg-3.1 && mkdir -p /build/biojava4-live-bkYa0a && dpkg-source --no-check -x /*.dsc /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg && chown -R builduser:builduser /build/biojava4-live-bkYa0a" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1594668511" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/biojava4-live-bkYa0a /tmp/biojava4-live-4.2.12+dfsg-3.1d61rk52o bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200727T204945Z 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.EEB_CeeJGh 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.EEB_CeeJGh Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200727T204945Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200727T204945Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (705 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 ... 4578 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-2) ... 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/20200727T204945Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.EEB_CeeJGh Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200727T204945Z 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 20s (1118 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.EEB_CeeJGh I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d biojava4-live=4.2.12+dfsg-3.1 && mkdir -p /build/biojava4-live-bkYa0a && dpkg-source --no-check -x /*.dsc /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg && chown -R builduser:builduser /build/biojava4-live-bkYa0a"' exec /tmp/mmdebstrap.EEB_CeeJGh Reading package lists... NOTICE: 'biojava4-live' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/biojava4-live.git Please use: git clone https://salsa.debian.org/med-team/biojava4-live.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 12.2 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main biojava4-live 4.2.12+dfsg-3.1 (dsc) [2489 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main biojava4-live 4.2.12+dfsg-3.1 (tar) [12.2 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main biojava4-live 4.2.12+dfsg-3.1 (diff) [15.8 kB] Fetched 12.2 MB in 10s (1271 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'biojava4-live_4.2.12+dfsg-3.1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting biojava4-live in /build/biojava4-live-bkYa0a/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-3.1.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 I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1594668511" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.EEB_CeeJGh dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-3.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Paul Gevers dpkg-source --before-build . fakeroot 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/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg' debian/rules build-indep dpkg: warning: --compare-versions used with obsolete relation operator '>' dh build-indep --with javahelper dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg' jh_linkjars -i debian/rules override_dh_auto_build make[1]: Entering directory '/build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [javac] Note: /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL Total time: 17 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/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. [copy] Warning: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-forester/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL Total time: 2 minutes 5 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-core/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 unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 24 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL Total time: 1 minute 23 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [copy] Copying 2 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL Total time: 15 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] Note: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 1 file to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL Total time: 36 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] Creating empty /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/xml/package-info.class [javac] Creating empty /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/package-info.class [javac] Creating empty /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/convertor/package-info.class [javac] Creating empty /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/package-info.class [copy] Copying 11 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL Total time: 31 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] Note: /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL Total time: 40 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] Creating empty /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes/org/biojava/nbio/sequencing/io/fastq/package-info.class [copy] Warning: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-sequencing/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL Total time: 17 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/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: /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL Total time: 2 minutes 3 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/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: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 49 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL Total time: 1 minute 24 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] Note: /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL Total time: 25 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/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 unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [copy] Copying 2 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL Total time: 21 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] Creating empty /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/ronn/package-info.class [javac] Creating empty /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL Total time: 18 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [copy] Warning: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL Total time: 9 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [copy] Warning: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-ws/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL Total time: 16 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml compile: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [copy] Copying 1 file to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes jar: [jar] Building jar: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL Total time: 40 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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/build.xml javadocs: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/javadoc [mkdir] Created dir: /build/biojava4-live-bkYa0a/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] Javadoc execution [javadoc] Loading source files for package org.biojava.nbio.aaproperties... 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[javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag < [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:261: warning - invalid usage of tag > [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:122: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] javadoc: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:107: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:38: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java:39: warning - Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, module, package, class/interface. [javadoc] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning - @param argument "dbReference" is not a parameter name. [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning - invalid usage of tag < [javadoc] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning - invalid usage of tag < [javadoc] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:33: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:36: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning - Tag @link: reference not found: AlignedSequence [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning - Tag @link: reference not found: Profile [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:105: warning - invalid usage of tag > [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:130: warning - invalid usage of tag > [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:133: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:141: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:149: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:157: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:165: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:173: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:181: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:189: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:197: warning - invalid usage of tag & [javadoc] /build/biojava4-live-bkYa0a/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] /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning - invalid usage of tag < [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Building index for all classes... [javadoc] Generating /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/doc/biojava/help-doc.html... [javadoc] 100 warnings BUILD SUCCESSFUL Total time: 3 minutes 16 seconds # rm -rf biojavadoc make[1]: Leaving directory '/build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] Note: /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [copy] Copying 176 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes test: [echo] Using java version 11.0.8 [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: 0.405 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.405 sec [junit] [junit] Testcase: testGetIndexOf took 0.186 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetNumGaps took 0.004 sec [junit] Testcase: testGetStart took 0 sec [junit] Testcase: testGetSequenceIndexAt took 0 sec [junit] Testcase: testGetAccession took 0.001 sec [junit] Testcase: testToString took 0.002 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec [junit] Testcase: testCountCompounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAt took 0.073 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.003 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.002 sec [junit] Testcase: testGetOriginalSequence took 0 sec [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testGetLength took 0 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 0.002 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: 0.911 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.911 sec [junit] [junit] Testcase: testGetIndexOf took 0.394 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.005 sec [junit] Testcase: testGetAlignedSequenceInt took 0.005 sec [junit] Testcase: testToStringInt took 0.014 sec [junit] Testcase: testToString took 0.002 sec [junit] Testcase: testToStringFormatted took 0.106 sec [junit] Testcase: testSimpleProfile took 0.001 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0.003 sec [junit] Testcase: testGetAlignedSequences took 0.001 sec [junit] Testcase: testGetOriginalSequences took 0 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0.001 sec [junit] Testcase: testGetAlignedSequencesSArray took 0 sec [junit] Testcase: testGetIndicesAt took 0.002 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.003 sec [junit] Testcase: testGetCompoundAtIntInt took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.003 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.002 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.002 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetLastIndexOf took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0 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: 0.508 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.508 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.302 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetIndexInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.075 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.004 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumIdenticals took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumSimilars took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 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: 0.689 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.689 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.417 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 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: 0, Time elapsed: 25.675 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 25.675 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Read finished [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Query for hits in /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - 71 results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Parsing of /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml finished. [junit] Oct 18, 2021 1:23:09 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Oct 18, 2021 1:23:09 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Read finished [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Query for hits in /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - 71 results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Parsing of /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml finished. [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testConstructorWithEvalueHspFilter took 14.867 sec [junit] Testcase: testConstructorWithFactoryGuess took 0.32 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 10.322 sec [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: 8.779 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.779 sec [junit] ------------- Standard Output --------------- [junit] createObjects [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] ------------- Standard Error ----------------- [junit] Oct 18, 2021 1:23:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Oct 18, 2021 1:23:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 2 hits approximately in all results [junit] Oct 18, 2021 1:23:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Oct 18, 2021 1:23:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 117713 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testCreateObjects took 8.615 sec [junit] Testcase: testGetFileExtensions took 0.001 sec [junit] Testcase: testSetFile took 0 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: 2, Time elapsed: 4.576 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 4.576 sec [junit] ------------- Standard Output --------------- [junit] createObjects [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Read finished [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Query for hits in /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - 1 results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Parsing of /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml finished. [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testCreateObjects took 4.467 sec [junit] Testcase: testStoreObjects took 0 sec [junit] Testcase: testSetDatabaseReferences took 0 sec [junit] SKIPPED [junit] Testcase: testGetFileExtensions took 0 sec [junit] Testcase: testSetQueryReferences took 0 sec [junit] SKIPPED [junit] Testcase: testSetFile took 0 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: 1.402 sec [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.402 sec [junit] [junit] Testcase: sequenceEquality took 0.192 sec [junit] Testcase: subSequence took 0.004 sec [junit] Testcase: singleCompoundSequence took 0.003 sec [junit] Testcase: translateToRna took 0.387 sec [junit] Testcase: kmerNonOverlap took 0.002 sec [junit] Testcase: twoBit took 0.011 sec [junit] Testcase: composition took 0.001 sec [junit] Testcase: fourBit took 0.015 sec [junit] Testcase: complement took 0.099 sec [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.001 sec [junit] Testcase: at took 0.001 sec [junit] Testcase: gc took 0.001 sec [junit] Testcase: basesEqual took 0 sec [junit] Testcase: bogusSequence took 0 sec [junit] Testcase: kmerOverlap took 0 sec [junit] Testcase: reverseComplement took 0.001 sec [junit] Testcase: reverse took 0 sec [junit] Testcase: respectCase took 0 sec [junit] Testcase: basesEquivalent took 0 sec [junit] Testcase: badTwoBit took 0.001 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: 0.376 sec [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 sec [junit] [junit] Testcase: badSubstitute took 0.197 sec [junit] Testcase: delete took 0.084 sec [junit] Testcase: insert took 0.002 sec [junit] Testcase: substitute took 0 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: 0.308 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.308 sec [junit] [junit] Testcase: empty took 0.229 sec [junit] Testcase: canScan took 0 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: 0.208 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 sec [junit] [junit] Testcase: testGetCompoundsAt took 0.106 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: 0.322 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.322 sec [junit] [junit] Testcase: testLastIndexOf took 0.213 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: 2.702 sec [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.702 sec [junit] [junit] Testcase: translateN took 0.587 sec [junit] Testcase: basicTranslation took 0.002 sec [junit] Testcase: translateBrca2 took 1.671 sec [junit] Testcase: translateStopAtInternalStops took 0.015 sec [junit] Testcase: getUniversal took 0 sec [junit] Testcase: translateInternalStops took 0.008 sec [junit] Testcase: multiFrameTranslation took 0.008 sec [junit] Testcase: waitForStartCodon took 0.001 sec [junit] Testcase: translateInitMet took 0.001 sec [junit] Testcase: lowerCases took 0.001 sec [junit] Testcase: testHashCollision took 0 sec [junit] Testcase: translateBrca2ExonOne took 0 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: 0.288 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 sec [junit] [junit] Testcase: testAmbiguity took 0.005 sec [junit] Testcase: testBasicAmbiguity took 0 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: 0.291 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.291 sec [junit] [junit] Testcase: testConstructor took 0.194 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: 0.583 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.FastaReaderTest - process [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testSmallFasta2 took 0.089 sec [junit] Testcase: testProcess took 0.402 sec [junit] Testcase: testSmallFasta took 0.078 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: 0.296 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec [junit] [junit] Testcase: writeBasicFasta took 0.188 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: 0.795 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.795 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 0.606 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: 1.279 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.279 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 0.874 sec [junit] Testcase: CDStest took 0.106 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: 0.913 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.913 sec [junit] [junit] Testcase: testProcess took 0.805 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: 0.202 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest - parseHeader [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testParseHeader took 0.016 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: 0.213 sec [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 sec [junit] [junit] Testcase: testProteinSequenceFactoring[0] took 0.001 sec [junit] Testcase: testFeatures[0] took 0 sec [junit] Testcase: testProteinSequenceFactoring[1] took 0 sec [junit] Testcase: testFeatures[1] took 0 sec [junit] Testcase: testProteinSequenceFactoring[2] took 0 sec [junit] Testcase: testFeatures[2] took 0 sec [junit] Testcase: testProteinSequenceFactoring[3] took 0 sec [junit] Testcase: testFeatures[3] took 0 sec [junit] Testcase: testProteinSequenceFactoring[4] took 0 sec [junit] Testcase: testFeatures[4] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[5] took 0.007 sec [junit] Testcase: testFeatures[5] took 0 sec [junit] Testcase: testProteinSequenceFactoring[6] took 0 sec [junit] Testcase: testFeatures[6] took 0 sec [junit] Testcase: testProteinSequenceFactoring[7] took 0 sec [junit] Testcase: testFeatures[7] took 0 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: 4.01 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.01 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest - test wrong sequence [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testWrongSequence took 3.714 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: 0.324 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 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 0.091 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: 0.305 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.305 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: 0.478 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.478 sec [junit] [junit] Testcase: testWithStrandSwitch took 0.196 sec [junit] Testcase: modulateCircular took 0.001 sec [junit] Testcase: testStrandFlip took 0.002 sec [junit] Testcase: testBasicCircularLocation took 0.087 sec [junit] Testcase: badLocations took 0.001 sec [junit] Testcase: completePasses took 0.001 sec [junit] Testcase: testSubLocations took 0.079 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: 0.284 sec [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 sec [junit] [junit] Testcase: locationTest[0] took 0.102 sec [junit] Testcase: locationTest[1] took 0.077 sec [junit] Testcase: locationTest[2] took 0.001 sec [junit] Testcase: locationTest[3] took 0.001 sec BUILD SUCCESSFUL Total time: 2 minutes 27 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 10 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 45 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes test: [echo] Using java version 11.0.8 [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: 0.725 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.725 sec [junit] [junit] Testcase: testGetQuery took 0.308 sec [junit] Testcase: testGetScore took 0.199 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.081 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: 0.679 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.679 sec [junit] [junit] Testcase: testGetQuery took 0.313 sec [junit] Testcase: testGetScore took 0.099 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 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: 1.187 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.187 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 0.868 sec [junit] Testcase: testToString took 0.004 sec [junit] Testcase: testGetScoreMatrix took 0.008 sec [junit] Testcase: testGetRoot took 0.122 sec [junit] Testcase: testGetSequences took 0.062 sec [junit] Testcase: testGetDistanceMatrix took 0.003 sec [junit] Testcase: testGetAllPairsScores took 0.012 sec [junit] Testcase: testIterator took 0.003 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: 0.784 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.784 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.69 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: 2.044 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.044 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.314 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.284 sec [junit] Testcase: should_align_middle_anchor took 0.205 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testNeedlemanWunsch took 0 sec [junit] Testcase: should_align_all_anchored took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0 sec [junit] Testcase: testGetPair took 0.001 sec [junit] Testcase: should_align_multiple_anchors took 0.001 sec [junit] Testcase: testAnchoredDNAAlignment took 0.004 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_ending_anchor took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec [junit] Testcase: testComplex took 0.078 sec [junit] Testcase: testGetScoreMatrixAsString took 0.024 sec [junit] Testcase: should_align_starting_anchor took 0 sec [junit] Testcase: anchors_should_not_change_score took 0.058 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 sec [junit] Testcase: testIntOverflowBug took 0.845 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: 0.196 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 sec [junit] [junit] Testcase: testOpenPenalty took 0.079 sec [junit] Testcase: testType took 0 sec [junit] Testcase: testExtensionPenalty took 0 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec [junit] Testcase: testSimpleGapPenalty took 0 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: 0.619 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.619 sec [junit] [junit] Testcase: testGetQuery took 0.48 sec [junit] Testcase: testGetTarget took 0.005 sec [junit] Testcase: testSimpleProfilePair took 0.007 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: 0.806 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.806 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.401 sec [junit] Testcase: testGetGapPenalty took 0.088 sec [junit] Testcase: testGetComputationTime took 0.005 sec [junit] Testcase: testGetQuery took 0.002 sec [junit] Testcase: testGetScore took 0.002 sec [junit] Testcase: testGetScoreMatrix took 0.004 sec [junit] Testcase: testGetPair took 0.004 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetScoreMatrixAsString took 0.175 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.006 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.003 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0 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: 0.492 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.492 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.005 sec [junit] Testcase: testSetDescription took 0.089 sec [junit] Testcase: testToString took 0.105 sec [junit] Testcase: testCaseEquivalence took 0.001 sec [junit] Testcase: test took 0.086 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.093 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.003 sec [junit] Testcase: testSetName took 0.007 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.003 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: 1.019 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.019 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.384 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.101 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.096 sec [junit] Testcase: testSmithWaterman took 0.001 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.303 sec [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.002 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: 0.183 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.004 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.067 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.001 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 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: 0.886 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.886 sec [junit] [junit] Testcase: testGetComputationTime took 0.416 sec [junit] Testcase: testGuanUberbacher took 0.077 sec [junit] Testcase: testGetScore took 0 sec [junit] Testcase: testGetPair took 0.009 sec [junit] Testcase: testGetProfile took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_shorter_target took 0.165 sec [junit] Testcase: should_align_multiple_cuts took 0.003 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL Total time: 1 minute 4 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] Note: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [copy] Copying 7 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [copy] Copying 32 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes test: [echo] Using java version 11.0.8 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.081 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.081 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 2.423 sec [junit] Testcase: testExample1 took 0.116 sec [junit] Testcase: testExample2 took 0.01 sec [junit] Testcase: testExample3 took 0.025 sec [junit] Testcase: testExample1WithCSV took 0.108 sec [junit] Testcase: testWithCases took 0.013 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.386 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.386 sec [junit] [junit] Testcase: shortExample1 took 0.089 sec [junit] Testcase: shortExample2 took 1.785 sec [junit] Testcase: shortExample3 took 0.288 sec [junit] Testcase: shortExample4 took 0.002 sec [junit] Testcase: shortExample5 took 0.004 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.702 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.702 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 2.184 sec [junit] Testcase: testExample1 took 0.097 sec [junit] Testcase: testExample2 took 0.123 sec [junit] Testcase: testExample3 took 0.091 sec [junit] Testcase: testExample1WithCSV took 0.082 sec [junit] Testcase: testWithCases took 0.018 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.604 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.604 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 0.173 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 2.59 sec [junit] Testcase: testEnrichment took 0.019 sec [junit] Testcase: testApliphaticIndex took 0.001 sec [junit] Testcase: testMolecularWeightXMLNull took 0.085 sec [junit] Testcase: testApliphaticIndexNull took 0 sec [junit] Testcase: testIsoelectricPointExpasy took 0.002 sec [junit] Testcase: testAbsorbanceNull took 0.001 sec [junit] Testcase: testIsoelectricPointNull took 0 sec [junit] Testcase: testAverageHydropathy took 0.001 sec [junit] Testcase: testExtinctionCoefficient took 0.002 sec [junit] Testcase: testAAComposition took 0.001 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.273 sec [junit] Testcase: testMolecularWeight took 0.011 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.006 sec [junit] Testcase: testNetChargeNull took 0 sec [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec [junit] Testcase: testNetCharge took 0.597 sec [junit] Testcase: testEnrichmentNull took 0.099 sec [junit] Testcase: testInstabilityIndexNull took 0 sec [junit] Testcase: testAverageHydropathyNull took 0.001 sec [junit] Testcase: testMolecularWeightXML took 0.586 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: 0.087 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec [junit] [junit] Testcase: testFake took 0.001 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: 0.181 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 sec [junit] [junit] Testcase: testFakeTest took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.394 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.394 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 1.795 sec [junit] Testcase: readWithIDXml took 0.823 sec [junit] Testcase: readMinXml took 0.204 sec [junit] Testcase: readAdvancedXml took 0.107 sec [junit] Testcase: generateXml took 0.091 sec [junit] Testcase: readXml took 0.188 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest [junit] WARNING: An illegal reflective access operation has occurred [junit] WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/usr/share/java/jaxb-runtime.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.758 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.758 sec [junit] [junit] Testcase: generateSchema took 1.586 sec [junit] Testcase: generateXml took 0.209 sec [junit] Testcase: readXml took 0.779 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: 0.194 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec [junit] [junit] Testcase: testFake took 0.002 sec BUILD SUCCESSFUL Total time: 1 minute 2 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 2 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 8 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes test: [echo] Using java version 11.0.8 BUILD SUCCESSFUL Total time: 11 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 74 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 19 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes test: [echo] Using java version 11.0.8 [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: 0.399 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.399 sec [junit] [junit] Testcase: testConvert took 0.309 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: 0.093 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] [junit] Testcase: testBuildAppendSequence took 0.004 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0.001 sec [junit] Testcase: testBuild took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0.056 sec [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0 sec [junit] Testcase: testBuildNullVariant took 0.004 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: 0.104 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec [junit] [junit] Testcase: testImmutable took 0.003 sec [junit] Testcase: testBuilder took 0.002 sec [junit] Testcase: testVariant took 0 sec [junit] Testcase: testQuality took 0.004 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: 0.393 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.393 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 0.192 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0.001 sec [junit] Testcase: testCreateQualityScores took 0.067 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0.001 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.002 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec [junit] Testcase: testQualityScores took 0.013 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 sec [junit] Testcase: testToList took 0 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: 0.129 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 sec [junit] [junit] Testcase: testParseFastqVariant took 0.009 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.001 sec [junit] Testcase: testIsSanger took 0.004 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec [junit] Testcase: testIsSolexa took 0 sec [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0 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: 0.481 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.481 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.113 sec [junit] Testcase: testWrappingAsIllumina took 0.002 sec [junit] Testcase: testValidateDescription took 0.066 sec [junit] Testcase: testValidateRepeatDescription took 0.004 sec [junit] Testcase: testMiscDnaAsIllumina took 0.007 sec [junit] Testcase: testMiscRnaAsIllumina took 0.003 sec [junit] Testcase: testLongReadsAsIllumina took 0.005 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.074 sec [junit] Testcase: testReadEmptyFile took 0.001 sec [junit] Testcase: testErrorExamples took 0.104 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 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 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.005 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 0.066 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: 0.206 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.008 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec [junit] Testcase: testWriteFileIterable took 0.074 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.013 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: 0.699 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.699 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.192 sec [junit] Testcase: testFullRangeAsSanger took 0.005 sec [junit] Testcase: testWrappingOriginal took 0.008 sec [junit] Testcase: testLongReadsOriginal took 0.01 sec [junit] Testcase: testMiscDnaOriginal took 0.072 sec [junit] Testcase: testMiscRnaOriginal took 0.003 sec [junit] Testcase: testValidateDescription took 0.072 sec [junit] Testcase: testValidateRepeatDescription took 0.012 sec [junit] Testcase: testFullRangeOriginal took 0.002 sec [junit] Testcase: testWrappingAsSanger took 0.003 sec [junit] Testcase: testLongReadsAsSanger took 0.011 sec [junit] Testcase: testMiscDnaAsSanger took 0.001 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.014 sec [junit] Testcase: testReadEmptyFile took 0.001 sec [junit] Testcase: testErrorExamples took 0.021 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 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 0.001 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 0.001 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: 0.123 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.007 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.003 sec [junit] Testcase: testWriteFileIterable took 0.087 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.002 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: 0.562 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.562 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.115 sec [junit] Testcase: testFullRangeAsSolexa took 0.003 sec [junit] Testcase: testValidateDescription took 0.067 sec [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testWrappingAsSolexa took 0.004 sec [junit] Testcase: testLongReadsAsSolexa took 0.008 sec [junit] Testcase: testMiscDnaAsSolexa took 0.002 sec [junit] Testcase: testParseNullReadable took 0.002 sec [junit] Testcase: testReadRoundTripSingleFile took 0.09 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.097 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.002 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.001 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: 0.21 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.21 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.085 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec [junit] Testcase: testWriteFileIterable took 0.024 sec [junit] Testcase: testWriteOutputStreamIterable took 0 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testWriteFileVararg took 0.016 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: 0.092 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec [junit] [junit] Testcase: testStreamNullVariant took 0.002 sec [junit] Testcase: testStreamNullListener took 0.002 sec [junit] Testcase: testStreamNullReadable took 0 sec BUILD SUCCESSFUL Total time: 55 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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [copy] Warning: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-structure-gui/src/test/resources does not exist. [copy] Copying 141 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes test: [echo] Using java version 11.0.8 [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: 0.099 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec [junit] [junit] Testcase: testMe took 0.001 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: 0.098 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec [junit] [junit] Testcase: testSomeMethod took 0.002 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: 0.111 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec [junit] [junit] Testcase: testGetColor took 0.008 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.008 sec [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0.001 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 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: 0.022 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL Total time: 24 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [javac] /build/biojava4-live-bkYa0a/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/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 5 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 36 files to /build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes test: [echo] Using java version 11.0.8 BUILD SUCCESSFUL Total time: 13 seconds make[1]: Leaving directory '/build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-indep dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary-indep --with javahelper dh_testroot -i dh_prep -i dh_install -i debian/rules override_jh_installjavadoc make[1]: Entering directory '/build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg' dpkg: warning: --compare-versions used with obsolete relation operator '>' jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ $(dpkg -L $(apt-cache show default-jdk-doc | grep Depends | awk '{print $2}') | grep /usr/share/doc/ | head -n1) \ debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/ Now scanning "/usr/share/doc/openjdk-11-doc", found 10332 files. Now scanning "debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java", found 1874 files. Now have 12206 files in total. Removed 1 files due to nonunique device and inode. Total size is 323208893 bytes or 308 MiB Removed 7299 files due to unique sizes from list.4906 files left. Now eliminating candidates based on first bytes:removed 746 files from list.4160 files left. Now eliminating candidates based on last bytes:removed 19 files from list.4141 files left. Now eliminating candidates based on sha1 checksum:removed 4101 files from list.40 files left. It seems like you have 40 files that are not unique Totally, 1 MiB can be reduced. Now making results file results.txt Now making symbolic links. creating Failed moving /usr/share/doc/openjdk-11-doc/api/jquery/external/jquery/jquery.js to a temporary file Failed to make symlink /usr/share/doc/openjdk-11-doc/api/jquery/external/jquery/jquery.js to /usr/share/doc/openjdk-11-doc/api/jquery/jquery-3.3.1.js Making 20 links. make[1]: Leaving directory '/build/biojava4-live-bkYa0a/biojava4-live-4.2.12+dfsg' dh_installdocs -i dh_installchangelogs -i dh_lintian -i dh_perl -i dh_link -i jh_installlibs -i jh_classpath -i jh_manifest -i jh_depends -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb'. dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-3.1_all.deb'. dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../biojava4-live_4.2.12+dfsg-3.1_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/biojava4-live-bkYa0a /tmp/biojava4-live-4.2.12+dfsg-3.1d61rk52o I: cleaning package lists and apt cache... W: deleting files in /tmp: abstractFastqWriterTest10506959453729636969.tmp W: deleting files in /tmp: abstractFastqWriterTest13506628412136679628.tmp W: deleting files in /tmp: abstractFastqWriterTest3227669446588923815.tmp W: deleting files in /tmp: abstractFastqWriterTest1854133474651268460.tmp W: deleting files in /tmp: abstractFastqWriterTest6390105128084413760.tmp W: deleting files in /tmp: abstractFastqWriterTest17073779113682194736.tmp W: deleting files in /tmp: convertTest5440192904720216468fastq W: deleting files in /tmp: hsperfdata_builduser W: deleting files in /tmp: abstractFastqWriterTest15870233949541764137.tmp W: deleting files in /tmp: abstractFastqReaderTest6475543013677584623.tmp W: deleting files in /tmp: abstractFastqWriterTest8514467997414936168.tmp W: deleting files in /tmp: abstractFastqWriterTest15544836080879206367.tmp W: deleting files in /tmp: convertTest2990225904676574242fastq W: deleting files in /tmp: convertTest8603960004134391114fastq W: deleting files in /tmp: abstractFastqReaderTest5496741149252034046.tmp W: deleting files in /tmp: abstractFastqWriterTest16095793949343839129.tmp W: deleting files in /tmp: abstractFastqWriterTest8667389183478895880.tmp W: deleting files in /tmp: abstractFastqReaderTest18342310625327819086.tmp W: deleting files in /tmp: abstractFastqWriterTest16163782974716370987.tmp W: deleting files in /tmp: abstractFastqWriterTest16033376669733172712.tmp W: deleting files in /tmp: convertTest5215282224834671973fastq W: deleting files in /tmp: abstractFastqWriterTest5871394472112991980.tmp W: deleting files in /tmp: abstractFastqWriterTest3942199526439500981.tmp W: deleting files in /tmp: abstractFastqReaderTest4872261041115169217.tmp W: deleting files in /tmp: abstractFastqWriterTest14579019537962021925.tmp W: deleting files in /tmp: abstractFastqWriterTest5074921124862622458.tmp W: deleting files in /tmp: abstractFastqWriterTest13596146095753104365.tmp W: deleting files in /tmp: abstractFastqWriterTest8207804727165376061.tmp W: deleting files in /tmp: abstractFastqWriterTest1284017077690772629.tmp W: deleting files in /tmp: abstractFastqWriterTest15527984064477939843.tmp W: deleting files in /tmp: abstractFastqReaderTest7386025435589762779.tmp W: deleting files in /tmp: convertTest12298637580286093597fastq W: deleting files in /tmp: abstractFastqWriterTest474123752450547886.tmp W: deleting files in /tmp: abstractFastqWriterTest12841281791083472150.tmp W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: abstractFastqWriterTest9176108872025061860.tmp W: deleting files in /tmp: abstractFastqWriterTest4592776679042123058.tmp W: deleting files in /tmp: convertTest10053685563042916651fastq W: deleting files in /tmp: abstractFastqReaderTest16982651668548213771.tmp W: deleting files in /tmp: abstractFastqWriterTest12495369101249712812.tmp W: deleting files in /tmp: abstractFastqWriterTest5961747381693656258.tmp W: deleting files in /tmp: convertTest2017812635692558754fastq W: deleting files in /tmp: abstractFastqReaderTest1030927013766801822.tmp W: deleting files in /tmp: abstractFastqWriterTest13361810076035113310.tmp W: deleting files in /tmp: abstractFastqReaderTest9608584146822963580.tmp W: deleting files in /tmp: abstractFastqWriterTest1067444318500045659.tmp W: deleting files in /tmp: abstractFastqWriterTest10991413086497800010.tmp W: deleting files in /tmp: convertTest7151786985760390720fastq W: deleting files in /tmp: abstractFastqWriterTest233743284995332032.tmp W: deleting files in /tmp: abstractFastqWriterTest8054137710519090403.tmp W: deleting files in /tmp: convertTest2987484658431255654fastq W: deleting files in /tmp: abstractFastqWriterTest2095424192430337665.tmp W: deleting files in /tmp: abstractFastqReaderTest7268819622066251569.tmp I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.EEB_CeeJGh... I: success in 2172.7770 seconds md5: libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb: OK md5: libbiojava4-java_4.2.12+dfsg-3.1_all.deb: OK md5: libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb: OK sha1: libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb: OK sha1: libbiojava4-java_4.2.12+dfsg-3.1_all.deb: OK sha1: libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb: OK sha256: libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb: OK sha256: libbiojava4-java_4.2.12+dfsg-3.1_all.deb: OK sha256: libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb: OK Checksums: OK