Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/biojava4-live/biojava4-live_4.2.12+dfsg-6_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/biojava4-live-4.2.12+dfsg-663zkgovz/biojava4-live_4.2.12+dfsg-6_all.buildinfo Get source package info: biojava4-live=4.2.12+dfsg-6 Source URL: http://snapshot.notset.fr/mr/package/biojava4-live/4.2.12+dfsg-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 ant=1.10.11-1 ant-contrib=1.0~b3+svn177-12 ant-optional=1.10.11-1 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 ca-certificates-java=20190909 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 dctrl-tools=2.24-3+b1 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 default-jdk-doc=2:1.11-72 default-jdk-headless=2:1.11-72 default-jre-headless=2:1.11-72 devscripts=2.21.7 dh-autoreconf=20 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dirmngr=2.2.27-2 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 fakeroot=1.26-1 file=1:5.41-2 findutils=4.8.0-1 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 gnupg=2.2.27-2 gnupg-l10n=2.2.27-2 gnupg-utils=2.2.27-2 gpg=2.2.27-2 gpg-agent=2.2.27-2 gpg-wks-client=2.2.27-2 gpg-wks-server=2.2.27-2 gpgconf=2.2.27-2 gpgsm=2.2.27-2 gpgv=2.2.27-2 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 java-common=0.72 javahelper=0.78 junit=3.8.2-9 junit4=4.13.2-1 libacl1=2.3.1-1 libactivation-java=1.2.0-2 libaopalliance-java=20070526-6 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libargs4j-java=2.33-1.1 libasan6=11.2.0-12 libasm-java=9.2-1 libasound2=1.2.5.1-1 libasound2-data=1.2.5.1-1 libassuan0=2.5.5-1 libatinject-jsr330-api-java=1.0+ds1-5 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libavahi-client3=0.8-5 libavahi-common-data=0.8-5 libavahi-common3=0.8-5 libb-hooks-op-check-perl=0.22-1+b3 libbinutils=2.37-10 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b3 libbz2-1.0=1.0.8-5 libc-bin=2.32-5 libc-dev-bin=2.32-5 libc6=2.32-5 libc6-dev=2.32-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcdi-api-java=1.2-3 libclass-method-modifiers-perl=2.13-1 libclass-xsaccessor-perl=1.19-3+b7 libcodemodel-java=2.6+jaxb2.3.0.1-10 libcom-err2=1.46.4-1 libcommons-cli-java=1.4-2 libcommons-codec-java=1.15-1 libcommons-collections3-java=3.2.2-2 libcommons-compress-java=1.21-1 libcommons-dbcp-java=1.4-7 libcommons-exec-java=1.3-2 libcommons-io-java=2.11.0-2 libcommons-lang-java=2.6-9 libcommons-lang3-java=3.11-1 libcommons-logging-java=1.2-2 libcommons-math-java=2.2-8 libcommons-parent-java=43-1 libcommons-pool-java=1.6-4 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libcups2=2.3.3op2-7 libdb5.3=5.3.28+dfsg1-0.8 libdbus-1-3=1.12.20-3 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdevel-callchecker-perl=0.008-1+b2 libdom4j-java=2.1.3-1 libdpkg-perl=1.21.1 libdtd-parser-java=1.2-1 libdynaloader-functions-perl=0.003-1.1 libelf1=0.186-1 libencode-locale-perl=1.05-1.1 libexec-maven-plugin-java=1.6.0-4.1 libexpat1=2.4.1-3 libfakeroot=1.26-1 libfastinfoset-java=1.2.12-3 libffi8=3.4.2-3 libfile-dirlist-perl=0.05-2 libfile-homedir-perl=1.006-1 libfile-listing-perl=6.14-1 libfile-stripnondeterminism-perl=1.12.1-1 libfile-touch-perl=0.12-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.11.0+dfsg-1 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgeronimo-annotation-1.3-spec-java=1.3-1 libgeronimo-interceptor-3.0-spec-java=1.0.1-4 libglib2.0-0=2.70.2-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgoogle-gson-java=2.8.8-1 libgpg-error0=1.42-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 libguava-java=29.0-6 libguice-java=4.2.3-2 libhamcrest-java=1.3-9 libharfbuzz0b=2.7.4-1 libhogweed6=3.7.3-1 libhsqldb-java=2.6.1-1 libhtml-parser-perl=3.76-1 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.10-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.35-1 libhttp-negotiate-perl=6.01-1 libhttpclient-java=4.5.13-3 libhttpcore-java=4.4.14-2 libicu67=67.1-7 libidn2-0=2.3.2-2 libimport-into-perl=1.002005-1 libinchi1=1.03+dfsg-4+b1 libio-html-perl=1.004-2 libio-pty-perl=1:1.15-2 libio-socket-ssl-perl=2.072-1 libipc-run-perl=20200505.0-1 libisl23=0.24-2 libistack-commons-java=3.0.6-5 libitext5-java=5.5.13.2-1 libitm1=11.2.0-12 libjaxb-api-java=2.3.1-1 libjaxb-java=2.3.0.1-10 libjaxen-java=1.1.6-4 libjgraph-java=5.12.4.2+dfsg-5.1 libjgrapht0.8-java=0.8.3-5 libjmol-java=14.32.3+dfsg1-1 libjni-inchi-java=0.8+dfsg-6 libjni-inchi-jni=0.8+dfsg-6 libjpeg62-turbo=1:2.1.2-1 libjson-simple-java=2.3.0-1 libjsoup-java=1.14.3-1 libjsr305-java=0.1~+svn49-11 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libksba8=1.6.0-2 liblcms2-2=2.12~rc1-2 libldap-2.4-2=2.4.59+dfsg-1 liblightcouch-java=0.0.6-1.1 liblog4j1.2-java=1.2.17-10 liblog4j2-java=2.15.0-1 liblsan0=11.2.0-12 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.10-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmaven-compiler-plugin-java=3.8.1-4 libmaven-file-management-java=3.0.0-1 libmaven-parent-java=31-2 libmaven-resolver-java=1.4.2-3 libmaven-shared-incremental-java=1.1-3 libmaven-shared-io-java=3.0.0-3 libmaven-shared-utils-java=3.3.0-1 libmaven3-core-java=3.6.3-5 libmodule-runtime-perl=0.016-1 libmongodb-java=3.6.3-2 libmoo-perl=2.005004-3 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libnaga-java=3.0+svn80-4 libncursesw6=6.3-1 libnet-http-perl=6.21-1 libnet-ssleay-perl=1.90-1 libnettle8=3.7.3-1 libnetx-java=0.5-4 libnpth0=1.6-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.32-3 libnss3=2:3.73-1 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libparams-classify-perl=0.015-1+b3 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libpcsclite1=1.9.5-1 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libplexus-archiver-java=3.6.0-2 libplexus-cipher-java=1.8-2 libplexus-classworlds-java=2.6.0-1 libplexus-compiler-java=2.8.8-2 libplexus-component-annotations-java=2.1.0-1 libplexus-container-default-java=2.1.0-1 libplexus-interpolation-java=1.26-1 libplexus-io-java=3.2.0-1.1 libplexus-languages-java=0.9.10-2 libplexus-sec-dispatcher-java=1.4-4 libplexus-utils2-java=3.3.0-1 libpng16-16=1.6.37-3 libpython3-stdlib=3.9.8-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libqdox2-java=2.0.0-1 libquadmath0=11.2.0-12 libreadline8=8.1-2 librelaxng-datatype-java=1.0+ds1-3.1 librngom-java=2.3.0.1-10 librole-tiny-perl=2.002004-1 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsemanage-common=3.3-1 libsemanage2=3.3-1+b1 libsepol2=3.3-1 libservlet-api-java=4.0.1-2 libsigsegv2=2.13-1 libsisu-inject-java=0.3.4-2 libsisu-plexus-java=0.3.4-3 libslf4j-java=1.7.32-1 libsmartcols1=2.37.2-4 libsnappy-java=1.1.8.3-1 libsnappy-jni=1.1.8.3-1 libsnappy1v5=1.1.8-1 libsqlite3-0=3.36.0-2 libssl1.1=1.1.1l-1 libstax-ex-java=1.7.8-3 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libstreambuffer-java=1.5.4-1.1 libsub-override-perl=0.09-2 libsub-quote-perl=2.006006-1 libsystemd0=249.7-1 libtasn1-6=4.18.0-4 libtimedate-perl=2.3300-2 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtry-tiny-perl=0.31-1 libtsan0=11.2.0-12 libtxw2-java=2.3.0.1-10 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 liburi-perl=5.10-1 libuuid1=2.37.2-4 libvecmath-java=1.5.2-7 libwagon-http-java=3.3.4-1 libwagon-provider-api-java=3.3.4-1 libwww-perl=6.59-1 libwww-robotrules-perl=6.02-1 libxbean-reflect-java=4.5-8 libxml-commons-resolver1.1-java=1.2-11 libxml2=2.9.12+dfsg-5+b1 libxmlunit-java=1.6-2 libxsom-java=2.3.0.1-10 libxz-java=1.9-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.3-1 ncurses-bin=6.3-1 netbase=6.3 openjdk-11-doc=11.0.13+8-1 openjdk-11-jdk-headless=11.0.13+8-1 openjdk-11-jre-headless=11.0.13+8-1 openssl=1.1.1l-1 passwd=1:4.8.1-2 patch=2.7.6-7 patchutils=0.4.2-1 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 perl-openssl-defaults=5 pinentry-curses=1.1.0-4 po-debconf=1.0.21+nmu1 python3=3.9.8-1 python3-minimal=3.9.8-1 python3.9=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 ucf=3.0043 util-linux=2.37.2-4 wdiff=1.2.2-2+b1 xz-utils=5.2.5-2 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/20211218T031014Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211218T031014Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211218T150450Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211212T085436Z/ 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-6 && mkdir -p /build/biojava4-live-SRabQ6 && dpkg-source --no-check -x /*.dsc /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg && chown -R builduser:builduser /build/biojava4-live-SRabQ6" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1639343747" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/biojava4-live-SRabQ6 /tmp/biojava4-live-4.2.12+dfsg-663zkgovz bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211212T085436Z 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.KPlNY3thj6 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.KPlNY3thj6 Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211212T085436Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211212T085436Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (594 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 ... 4679 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-5) ... 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/20211218T031014Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211218T031014Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211218T150450Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211212T085436Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.KPlNY3thj6 Get:1 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211218T150450Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211212T085436Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main Sources [11.8 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211218T150450Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211218T150450Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211218T150450Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211218T150450Z unstable/main amd64 Packages [12.0 MB] Fetched 35.3 MB in 28s (1239 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.KPlNY3thj6 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-6 && mkdir -p /build/biojava4-live-SRabQ6 && dpkg-source --no-check -x /*.dsc /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg && chown -R builduser:builduser /build/biojava4-live-SRabQ6"' exec /tmp/mmdebstrap.KPlNY3thj6 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/20211218T031014Z bookworm/main biojava4-live 4.2.12+dfsg-6 (dsc) [2656 B] Get:2 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main biojava4-live 4.2.12+dfsg-6 (tar) [12.2 MB] Get:3 http://snapshot.notset.fr/archive/debian/20211218T031014Z bookworm/main biojava4-live 4.2.12+dfsg-6 (diff) [15.5 kB] Fetched 12.2 MB in 10s (1261 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'biojava4-live_4.2.12+dfsg-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting biojava4-live in /build/biojava4-live-SRabQ6/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-6.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-SRabQ6/biojava4-live-4.2.12+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1639343747" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.KPlNY3thj6 dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . 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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg' debian/rules binary-indep dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary-indep --with javahelper dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg' jh_linkjars -i debian/rules override_dh_auto_build make[1]: Entering directory '/build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-jcolorbrewer/classes [javac] Note: /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL Total time: 9 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-forester/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL Total time: 10 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-core/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL Total time: 4 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes [copy] Copying 2 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-phylo/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes [javac] Note: /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-alignment/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL Total time: 3 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes [javac] Creating empty /build/biojava4-live-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes [javac] Note: /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-genome/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL Total time: 3 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes [javac] Creating empty /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-sequencing/classes/org/biojava/nbio/sequencing/io/fastq/package-info.class [copy] Warning: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-sequencing/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL Total time: 9 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-structure-gui/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL Total time: 5 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes [javac] Note: /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-modfinder/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-ontology/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL Total time: 3 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes [javac] Creating empty /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes/org/biojava/nbio/ronn/package-info.class [javac] Creating empty /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-protein-disorder/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-protein-comparison-tool/classes [copy] Warning: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-ws/classes [copy] Warning: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-ws/src/main/resources does not exist. jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL Total time: 2 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml compile: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes [copy] Copying 1 file to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/build/biojava4-survival/classes jar: [jar] Building jar: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL Total time: 3 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-SRabQ6/biojava4-live-4.2.12+dfsg/biojavadoc/build.xml javadocs: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/javadoc [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/doc/biojava [javadoc] Generating Javadoc [javadoc] Debian build on Java 9+ detected: Adding the --ignore-source-errors option [javadoc] Debian build on Java 9+ detected: Adding the -Xdoclint:none option [javadoc] Javadoc execution [javadoc] Loading source files for package org.biojava.nbio.aaproperties... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.profeat... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... [javadoc] Loading source files for package org.biojava.nbio.aaproperties.xml... [javadoc] Loading source files for package org.biojava.nbio.alignment... [javadoc] Loading source files for package org.biojava.nbio.alignment.io... [javadoc] Loading source files for package org.biojava.nbio.alignment.routines... [javadoc] Loading source files for package org.biojava.nbio.alignment.template... [javadoc] Loading source files for package org.biojava.nbio.core.alignment... [javadoc] Loading source files for package org.biojava.nbio.core.alignment.matrices... [javadoc] Loading source files for package org.biojava.nbio.core.alignment.template... [javadoc] Loading source files for package org.biojava.nbio.core.exceptions... [javadoc] Loading source files for package org.biojava.nbio.core.search.io... [javadoc] Loading source files for package org.biojava.nbio.core.search.io.blast... [javadoc] Loading source files for package org.biojava.nbio.core.sequence... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.compound... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.edits... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.features... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.io.util... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.loader... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.location... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.location.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.storage... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.template... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.transcription... [javadoc] Loading source files for package org.biojava.nbio.core.sequence.views... [javadoc] Loading source files for package org.biojava.nbio.core.util... [javadoc] Loading source files for package org.biojava.nbio.data.sequence... [javadoc] Loading source files for package org.biojava.nbio.genome... [javadoc] Loading source files for package org.biojava.nbio.genome.homology... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.cytoband... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.geneid... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.genename... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.gff... [javadoc] Loading source files for package org.biojava.nbio.genome.parsers.twobit... [javadoc] Loading source files for package org.biojava.nbio.genome.query... [javadoc] Loading source files for package org.biojava.nbio.genome.uniprot... [javadoc] Loading source files for package org.biojava.nbio.genome.util... [javadoc] Loading source files for package org.biojava.nbio.ontology... [javadoc] Loading source files for package org.biojava.nbio.ontology.io... [javadoc] Loading source files for package org.biojava.nbio.ontology.obo... [javadoc] Loading source files for package org.biojava.nbio.ontology.utils... [javadoc] Loading source files for package org.biojava.nbio.phosphosite... [javadoc] Loading source files for package org.biojava.nbio.phylo... [javadoc] Loading source files for package org.biojava.nbio.proteincomparisontool... [javadoc] Loading source files for package org.biojava.nbio.protmod... [javadoc] Loading source files for package org.biojava.nbio.protmod.io... [javadoc] Loading source files for package org.biojava.nbio.protmod.structure... [javadoc] Loading source files for package org.biojava.nbio.ronn... [javadoc] Loading source files for package org.biojava.nbio.sequencing.io.fastq... [javadoc] Loading source files for package org.biojava.nbio.structure... [javadoc] Loading source files for package org.biojava.nbio.structure.align... [javadoc] Loading source files for package org.biojava.nbio.structure.align.ce... [javadoc] Loading source files for package org.biojava.nbio.structure.align.client... [javadoc] Loading source files for package org.biojava.nbio.structure.align.events... [javadoc] Loading source files for package org.biojava.nbio.structure.align.fatcat... [javadoc] Loading source files for package org.biojava.nbio.structure.align.fatcat.calc... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest... [javadoc] Loading source files for package org.biojava.nbio.structure.align.gui.jmol... [javadoc] Loading source files for package org.biojava.nbio.structure.align.helper... [javadoc] Loading source files for package org.biojava.nbio.structure.align.model... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple.mc... [javadoc] Loading source files for package org.biojava.nbio.structure.align.multiple.util... [javadoc] Loading source files for package org.biojava.nbio.structure.align.pairwise... [javadoc] Loading source files for package org.biojava.nbio.structure.align.seq... [javadoc] Loading source files for package org.biojava.nbio.structure.align.util... [javadoc] Loading source files for package org.biojava.nbio.structure.align.webstart... [javadoc] Loading source files for package org.biojava.nbio.structure.align.xml... [javadoc] Loading source files for package org.biojava.nbio.structure.asa... [javadoc] Loading source files for package org.biojava.nbio.structure.cath... [javadoc] Loading source files for package org.biojava.nbio.structure.contact... [javadoc] Loading source files for package org.biojava.nbio.structure.domain... [javadoc] Loading source files for package org.biojava.nbio.structure.domain.pdp... [javadoc] Loading source files for package org.biojava.nbio.structure.ecod... [javadoc] Loading source files for package org.biojava.nbio.structure.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.events... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.util... [javadoc] Loading source files for package org.biojava.nbio.structure.gui.util.color... [javadoc] Loading source files for package org.biojava.nbio.structure.io... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.chem... [javadoc] Loading source files for package org.biojava.nbio.structure.io.mmcif.model... [javadoc] Loading source files for package org.biojava.nbio.structure.io.sifts... [javadoc] Loading source files for package org.biojava.nbio.structure.io.util... [javadoc] Loading source files for package org.biojava.nbio.structure.jama... [javadoc] Loading source files for package org.biojava.nbio.structure.math... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary... [javadoc] Loading source files for package org.biojava.nbio.structure.quaternary.io... [javadoc] Loading source files for package org.biojava.nbio.structure.rcsb... [javadoc] Loading source files for package org.biojava.nbio.structure.scop... [javadoc] Loading source files for package org.biojava.nbio.structure.scop.server... [javadoc] Loading source files for package org.biojava.nbio.structure.secstruc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.analysis... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.core... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.geometry... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.gui... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.internal... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.misc... [javadoc] Loading source files for package org.biojava.nbio.structure.symmetry.utils... [javadoc] Loading source files for package org.biojava.nbio.structure.validation... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal... [javadoc] Loading source files for package org.biojava.nbio.structure.xtal.io... [javadoc] Loading source files for package org.biojava.nbio.survival.cox... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.comparators... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.matrix... [javadoc] Loading source files for package org.biojava.nbio.survival.cox.stats... [javadoc] Loading source files for package org.biojava.nbio.survival.data... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... [javadoc] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment... [javadoc] Loading source files for package org.biojava.nbio.ws.alignment.qblast... [javadoc] Loading source files for package org.biojava.nbio.ws.hmmer... [javadoc] Loading source files for package org.forester.analysis... [javadoc] Loading source files for package org.forester.application... [javadoc] Loading source files for package org.forester.applications... [javadoc] Loading source files for package org.forester.archaeopteryx... [javadoc] Loading source files for package org.forester.archaeopteryx.phylogeny.data... [javadoc] Loading source files for package org.forester.archaeopteryx.tools... [javadoc] Loading source files for package org.forester.archaeopteryx.webservices... [javadoc] Loading source files for package org.forester.datastructures... [javadoc] Loading source files for package org.forester.development... [javadoc] Loading source files for package org.forester.evoinference... [javadoc] Loading source files for package org.forester.evoinference.distance... [javadoc] Loading source files for package org.forester.evoinference.matrix.character... [javadoc] Loading source files for package org.forester.evoinference.matrix.distance... [javadoc] Loading source files for package org.forester.evoinference.parsimony... [javadoc] Loading source files for package org.forester.evoinference.tools... [javadoc] Loading source files for package org.forester.go... [javadoc] Loading source files for package org.forester.go.etc... [javadoc] Loading source files for package org.forester.io.parsers... [javadoc] Loading source files for package org.forester.io.parsers.nexus... [javadoc] Loading source files for package org.forester.io.parsers.nhx... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml... [javadoc] Loading source files for package org.forester.io.parsers.phyloxml.data... [javadoc] Loading source files for package org.forester.io.parsers.tol... [javadoc] Loading source files for package org.forester.io.parsers.util... [javadoc] Loading source files for package org.forester.io.writers... [javadoc] Loading source files for package org.forester.msa... [javadoc] Loading source files for package org.forester.msa_compactor... [javadoc] Loading source files for package org.forester.pccx... [javadoc] Loading source files for package org.forester.phylogeny... [javadoc] Loading source files for package org.forester.phylogeny.data... [javadoc] Loading source files for package org.forester.phylogeny.factories... [javadoc] Loading source files for package org.forester.phylogeny.iterators... [javadoc] Loading source files for package org.forester.protein... [javadoc] Loading source files for package org.forester.rio... [javadoc] Loading source files for package org.forester.sdi... [javadoc] Loading source files for package org.forester.sequence... [javadoc] Loading source files for package org.forester.species... [javadoc] Loading source files for package org.forester.surfacing... [javadoc] Loading source files for package org.forester.test... [javadoc] Loading source files for package org.forester.test.examples... [javadoc] Loading source files for package org.forester.tools... [javadoc] Loading source files for package org.forester.util... [javadoc] Loading source files for package org.forester.ws.hmmer... [javadoc] Loading source files for package org.forester.ws.seqdb... [javadoc] Loading source files for package org.forester.ws.wabi... [javadoc] Loading source files for package org.jcolorbrewer... [javadoc] Loading source files for package org.jcolorbrewer.ui... [javadoc] Constructing Javadoc information... [javadoc] Standard Doclet version 11.0.13 [javadoc] Building tree for all the packages and classes... [javadoc] /build/biojava4-live-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/doc/biojava/help-doc.html... [javadoc] 100 warnings BUILD SUCCESSFUL Total time: 25 seconds # rm -rf biojavadoc make[1]: Leaving directory '/build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-core/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes [copy] Copying 176 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes test: [echo] Using java version 11.0.13 [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: 3.618 sec [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.618 sec [junit] [junit] Testcase: testGetIndexOf took 0.045 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 0.001 sec [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0 sec [junit] Testcase: testGetSequenceIndexAt took 0.001 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 0.001 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 0.003 sec [junit] Testcase: testGetOriginalSequence took 0 sec [junit] Testcase: testGetCompoundAt took 0.001 sec [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetEnd took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0.001 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 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.003 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: 7.402 sec [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 7.402 sec [junit] [junit] Testcase: testGetIndexOf took 0.114 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.002 sec [junit] Testcase: testGetAlignedSequenceInt took 0.002 sec [junit] Testcase: testToStringInt took 0.012 sec [junit] Testcase: testToString took 0.002 sec [junit] Testcase: testToStringFormatted took 0.027 sec [junit] Testcase: testSimpleProfile took 0 sec [junit] Testcase: testGetSize took 0.001 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 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 0.004 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.003 sec [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetCompoundsAt took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.572 sec [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.572 sec [junit] [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.077 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.003 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumIdenticals took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumSimilars took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetAlignment took 0.098 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.356 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.356 sec [junit] ------------- Standard Error ----------------- [junit] Dec 19, 2021 11:36:24 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Dec 19, 2021 11:36:24 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testConstructorWithEvalueHspFilter took 0 sec [junit] SKIPPED: Attemps to use the network [junit] Testcase: testConstructorWithFactoryGuess took 0.218 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0 sec [junit] SKIPPED: Attemps to use the network [junit] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.048 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.048 sec [junit] ------------- Standard Output --------------- [junit] createObjects [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] ------------- Standard Error ----------------- [junit] Dec 19, 2021 11:36:30 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Dec 19, 2021 11:36:30 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 2 hits approximately in all results [junit] Dec 19, 2021 11:36:30 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits [junit] Dec 19, 2021 11:36:30 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 117713 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testCreateObjects took 1.513 sec [junit] Testcase: testGetFileExtensions took 0 sec [junit] Testcase: testSetFile took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.625 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.625 sec [junit] ------------- Standard Output --------------- [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testCreateObjects took 0 sec [junit] SKIPPED: Attempts to use the network [junit] Testcase: testStoreObjects took 0.005 sec [junit] Testcase: testSetDatabaseReferences took 0 sec [junit] SKIPPED [junit] Testcase: testGetFileExtensions took 0.029 sec [junit] Testcase: testSetQueryReferences took 0 sec [junit] SKIPPED [junit] Testcase: testSetFile took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.DNATest [junit] Testsuite: org.biojava.nbio.core.sequence.DNATest [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.883 sec [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.883 sec [junit] [junit] Testcase: sequenceEquality took 0.043 sec [junit] Testcase: subSequence took 0.007 sec [junit] Testcase: singleCompoundSequence took 0.008 sec [junit] Testcase: translateToRna took 0.066 sec [junit] Testcase: kmerNonOverlap took 0.005 sec [junit] Testcase: twoBit took 0.003 sec [junit] Testcase: composition took 0.002 sec [junit] Testcase: fourBit took 0.006 sec [junit] Testcase: complement took 0.003 sec [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.002 sec [junit] Testcase: at took 0.003 sec [junit] Testcase: gc took 0.002 sec [junit] Testcase: basesEqual took 0.002 sec [junit] Testcase: bogusSequence took 0.002 sec [junit] Testcase: kmerOverlap took 0.002 sec [junit] Testcase: reverseComplement took 0.004 sec [junit] Testcase: reverse took 0.002 sec [junit] Testcase: respectCase took 0.002 sec [junit] Testcase: basesEquivalent took 0.002 sec [junit] Testcase: badTwoBit took 0.003 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: 0.463 sec [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.463 sec [junit] [junit] Testcase: badSubstitute took 0.039 sec [junit] Testcase: delete took 0.004 sec [junit] Testcase: insert took 0.002 sec [junit] Testcase: substitute took 0.001 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: 0.43 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.43 sec [junit] [junit] Testcase: empty took 0.041 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: 0.33 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 sec [junit] [junit] Testcase: testGetCompoundsAt took 0.051 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: 0.503 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.503 sec [junit] [junit] Testcase: testLastIndexOf took 0.054 sec [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testInverse took 0.002 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: 2.262 sec [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.262 sec [junit] [junit] Testcase: translateN took 0.051 sec [junit] Testcase: basicTranslation took 0.001 sec [junit] Testcase: translateBrca2 took 0.553 sec [junit] Testcase: translateStopAtInternalStops took 0.005 sec [junit] Testcase: getUniversal took 0.001 sec [junit] Testcase: translateInternalStops took 0.004 sec [junit] Testcase: multiFrameTranslation took 0.011 sec [junit] Testcase: waitForStartCodon took 0.002 sec [junit] Testcase: translateInitMet took 0.002 sec [junit] Testcase: lowerCases took 0.001 sec [junit] Testcase: testHashCollision took 0.002 sec [junit] Testcase: translateBrca2ExonOne took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [junit] Testsuite: org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.331 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.331 sec [junit] [junit] Testcase: testAmbiguity took 0.037 sec [junit] Testcase: testBasicAmbiguity took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 sec [junit] [junit] Testcase: testConstructor took 0.049 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: 0.554 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.554 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.FastaReaderTest - process [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testSmallFasta2 took 0.028 sec [junit] Testcase: testProcess took 0.108 sec [junit] Testcase: testSmallFasta took 0.002 sec [junit] Running org.biojava.nbio.core.sequence.io.FastaWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.FastaWriterTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.409 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.409 sec [junit] [junit] Testcase: writeBasicFasta took 0.056 sec [junit] Testcase: writeFastaEqualToLineLength took 0 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: 0.372 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.372 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 0.131 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankReaderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.513 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.513 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 0.12 sec [junit] Testcase: CDStest took 0.015 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankWriterTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 sec [junit] [junit] Testcase: testProcess took 0.211 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: 0.269 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.269 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest - parseHeader [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testParseHeader took 0.028 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: 2.15 sec [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.15 sec [junit] [junit] Testcase: testProteinSequenceFactoring[0] took 0.006 sec [junit] Testcase: testFeatures[0] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[1] took 0 sec [junit] Testcase: testFeatures[1] took 0 sec [junit] Testcase: testProteinSequenceFactoring[2] took 0.001 sec [junit] Testcase: testFeatures[2] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[3] took 0.001 sec [junit] Testcase: testFeatures[3] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[4] took 0 sec [junit] Testcase: testFeatures[4] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[5] took 0 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 0.001 sec [junit] Testcase: testFeatures[7] took 0.005 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: 4.626 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.626 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest - test wrong sequence [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testWrongSequence took 4.364 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: 0.365 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.365 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 0.058 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: 0.055 sec [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.055 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: 0.781 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.781 sec [junit] [junit] Testcase: testWithStrandSwitch took 0.04 sec [junit] Testcase: modulateCircular took 0.001 sec [junit] Testcase: testStrandFlip took 0.001 sec [junit] Testcase: testBasicCircularLocation took 0.003 sec [junit] Testcase: badLocations took 0.001 sec [junit] Testcase: completePasses took 0 sec [junit] Testcase: testSubLocations took 0.004 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: 0.464 sec [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.464 sec [junit] [junit] Testcase: locationTest[0] took 0.03 sec [junit] Testcase: locationTest[1] took 0 sec [junit] Testcase: locationTest[2] took 0 sec [junit] Testcase: locationTest[3] took 0.001 sec BUILD SUCCESSFUL Total time: 1 minute 17 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 10 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes [copy] Copying 45 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-alignment/classes test: [echo] Using java version 11.0.13 [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: 0.872 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.872 sec [junit] [junit] Testcase: testGetQuery took 0.053 sec [junit] Testcase: testGetScore took 0.021 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 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: 1.187 sec [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.187 sec [junit] [junit] Testcase: testGetQuery took 0.056 sec [junit] Testcase: testGetScore took 0.03 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 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: 1.205 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.205 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 0.156 sec [junit] Testcase: testToString took 0.004 sec [junit] Testcase: testGetScoreMatrix took 0.006 sec [junit] Testcase: testGetRoot took 0.035 sec [junit] Testcase: testGetSequences took 0.003 sec [junit] Testcase: testGetDistanceMatrix took 0.003 sec [junit] Testcase: testGetAllPairsScores took 0.003 sec [junit] Testcase: testIterator took 0.002 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: 0.447 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.447 sec [junit] [junit] Testcase: shouldAllowZeroLengthMatches took 0.125 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: 2.99 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.99 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.075 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.03 sec [junit] Testcase: should_align_middle_anchor took 0.029 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec [junit] Testcase: should_align_all_anchored took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0 sec [junit] Testcase: testGetPair took 0.003 sec [junit] Testcase: should_align_multiple_anchors took 0.001 sec [junit] Testcase: testAnchoredDNAAlignment took 0.003 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_ending_anchor took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0.003 sec [junit] Testcase: testComplex took 0.012 sec [junit] Testcase: testGetScoreMatrixAsString took 0.018 sec [junit] Testcase: should_align_starting_anchor took 0.001 sec [junit] Testcase: anchors_should_not_change_score took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: testIntOverflowBug took 0.247 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: 0.931 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.931 sec [junit] [junit] Testcase: testOpenPenalty took 0.005 sec [junit] Testcase: testType took 0.001 sec [junit] Testcase: testExtensionPenalty took 0 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0.001 sec [junit] Testcase: testSimpleGapPenalty took 0.001 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 sec [junit] [junit] Testcase: testGetQuery took 0.071 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testSimpleProfilePair took 0.004 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.849 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.849 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.107 sec [junit] Testcase: testGetGapPenalty took 0.005 sec [junit] Testcase: testGetComputationTime took 0.004 sec [junit] Testcase: testGetQuery took 0.003 sec [junit] Testcase: testGetScore took 0.003 sec [junit] Testcase: testGetScoreMatrix took 0.003 sec [junit] Testcase: testGetPair took 0.009 sec [junit] Testcase: testGetProfile took 0.003 sec [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec [junit] Testcase: testGetScoreMatrixAsString took 0.032 sec [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.002 sec [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec [junit] Testcase: testGetTarget took 0.002 sec [junit] Testcase: testGetMaxScore took 0.001 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: 1.117 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.117 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.01 sec [junit] Testcase: testSetDescription took 0.025 sec [junit] Testcase: testToString took 0.039 sec [junit] Testcase: testCaseEquivalence took 0.001 sec [junit] Testcase: test took 0.012 sec [junit] Testcase: testSimpleSubstitutionMatrix took 0.011 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.004 sec [junit] Testcase: testSetName took 0.006 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: 2.106 sec [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.106 sec [junit] [junit] Testcase: testGetSubstitutionMatrix took 0.068 sec [junit] Testcase: testGetGapPenalty took 0 sec [junit] Testcase: testGetComputationTime took 0.024 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.002 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.006 sec [junit] Testcase: testSmithWaterman took 0.001 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec [junit] Testcase: testGetScoreMatrixAsString took 0.039 sec [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.465 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.465 sec [junit] [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.007 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.003 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 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.875 sec [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.875 sec [junit] [junit] Testcase: testGetComputationTime took 0.104 sec [junit] Testcase: testGuanUberbacher took 0.001 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetPair took 0.007 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: should_align_shorter_target took 0.027 sec [junit] Testcase: should_align_multiple_cuts took 0.002 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL Total time: 28 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [javac] Note: /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes [copy] Copying 32 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-aa-prop/classes test: [echo] Using java version 11.0.13 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.363 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.363 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 0.77 sec [junit] Testcase: testExample1 took 0.057 sec [junit] Testcase: testExample2 took 0.01 sec [junit] Testcase: testExample3 took 0.009 sec [junit] Testcase: testExample1WithCSV took 0.024 sec [junit] Testcase: testWithCases took 0.007 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.047 sec [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.047 sec [junit] [junit] Testcase: shortExample1 took 0.063 sec [junit] Testcase: shortExample2 took 0.568 sec [junit] Testcase: shortExample3 took 0.054 sec [junit] Testcase: shortExample4 took 0.001 sec [junit] Testcase: shortExample5 took 0.003 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.062 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.062 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 0.501 sec [junit] Testcase: testExample1 took 0.02 sec [junit] Testcase: testExample2 took 0.011 sec [junit] Testcase: testExample3 took 0.008 sec [junit] Testcase: testExample1WithCSV took 0.011 sec [junit] Testcase: testWithCases took 0.006 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.596 sec [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.596 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 0.061 sec [junit] Testcase: testMolecularWeightXMLSingleFile took 0.592 sec [junit] Testcase: testEnrichment took 0.013 sec [junit] Testcase: testApliphaticIndex took 0.002 sec [junit] Testcase: testMolecularWeightXMLNull took 0.006 sec [junit] Testcase: testApliphaticIndexNull took 0 sec [junit] Testcase: testIsoelectricPointExpasy took 0.003 sec [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0 sec [junit] Testcase: testAverageHydropathy took 0.002 sec [junit] Testcase: testExtinctionCoefficient took 0.002 sec [junit] Testcase: testAAComposition took 0.002 sec [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.044 sec [junit] Testcase: testMolecularWeight took 0.001 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.003 sec [junit] Testcase: testNetChargeNull took 0.001 sec [junit] Testcase: testExtinctionCoefficientNull took 0 sec [junit] Testcase: testNetCharge took 0.227 sec [junit] Testcase: testEnrichmentNull took 0.001 sec [junit] Testcase: testInstabilityIndexNull took 0 sec [junit] Testcase: testAverageHydropathyNull took 0 sec [junit] Testcase: testMolecularWeightXML took 0.055 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: 0.292 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.292 sec [junit] [junit] Testcase: testFake took 0.003 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: 0.131 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 sec [junit] [junit] Testcase: testFakeTest took 0.017 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.368 sec [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.368 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 0.476 sec [junit] Testcase: readWithIDXml took 0.202 sec [junit] Testcase: readMinXml took 0.079 sec [junit] Testcase: readAdvancedXml took 0.039 sec [junit] Testcase: generateXml took 0.065 sec [junit] Testcase: readXml took 0.063 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.354 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.354 sec [junit] [junit] Testcase: generateSchema took 0.703 sec [junit] Testcase: generateXml took 0.079 sec [junit] Testcase: readXml took 0.213 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: 0.245 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.245 sec [junit] [junit] Testcase: testFake took 0.023 sec BUILD SUCCESSFUL Total time: 19 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 2 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes [copy] Copying 8 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-phylo/classes test: [echo] Using java version 11.0.13 BUILD SUCCESSFUL Total time: 2 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 74 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes [copy] Copying 19 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-sequencing/classes test: [echo] Using java version 11.0.13 [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: 0.355 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.355 sec [junit] [junit] Testcase: testConvert took 0.15 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: 2.962 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.962 sec [junit] [junit] Testcase: testBuildAppendSequence took 0.006 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 sec [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0.001 sec [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0 sec [junit] Testcase: testBuildNullVariant took 0 sec [junit] Testcase: testBuildDefault took 0.001 sec [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0.001 sec [junit] Testcase: testBuildMultiple took 0 sec [junit] Testcase: testConstructor took 0 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: 0.997 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.997 sec [junit] [junit] Testcase: testImmutable took 0.003 sec [junit] Testcase: testBuilder took 0.004 sec [junit] Testcase: testVariant took 0 sec [junit] Testcase: testQuality took 0.004 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0.001 sec [junit] Testcase: testDescription took 0 sec [junit] Testcase: testConstructor took 0.001 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: 4.542 sec [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.542 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.004 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.001 sec [junit] Testcase: testConvertNullVariant took 0 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.002 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.077 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.001 sec [junit] Testcase: testQualityScoresNullIntArray took 0.001 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.002 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 0.001 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0.001 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0.001 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.003 sec [junit] Testcase: testConvertQualitiesNullVariant took 0.001 sec [junit] Testcase: testConvertSameVariant took 0 sec [junit] Testcase: testQualityScores took 0.008 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 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 0.001 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec [junit] Testcase: testErrorProbabilities took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.789 sec [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.789 sec [junit] [junit] Testcase: testParseFastqVariant took 0.005 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec [junit] Testcase: testIsSanger took 0.004 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0.001 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: 2.473 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.473 sec [junit] [junit] Testcase: testFullRangeAsIllumina took 0.037 sec [junit] Testcase: testWrappingAsIllumina took 0.002 sec [junit] Testcase: testValidateDescription took 0.014 sec [junit] Testcase: testValidateRepeatDescription took 0.004 sec [junit] Testcase: testMiscDnaAsIllumina took 0.003 sec [junit] Testcase: testMiscRnaAsIllumina took 0.003 sec [junit] Testcase: testLongReadsAsIllumina took 0.006 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.026 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.031 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.002 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 0.002 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec [junit] Testcase: testWrappedQuality took 0.002 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: 0.775 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.775 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.009 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec [junit] Testcase: testWriteFileIterable took 0.023 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.003 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: 4.719 sec [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.719 sec [junit] [junit] Testcase: testMiscRnaAsSanger took 0.057 sec [junit] Testcase: testFullRangeAsSanger took 0.004 sec [junit] Testcase: testWrappingOriginal took 0.003 sec [junit] Testcase: testLongReadsOriginal took 0.008 sec [junit] Testcase: testMiscDnaOriginal took 0.003 sec [junit] Testcase: testMiscRnaOriginal took 0.003 sec [junit] Testcase: testValidateDescription took 0.011 sec [junit] Testcase: testValidateRepeatDescription took 0.001 sec [junit] Testcase: testFullRangeOriginal took 0.002 sec [junit] Testcase: testWrappingAsSanger took 0.002 sec [junit] Testcase: testLongReadsAsSanger took 0.004 sec [junit] Testcase: testMiscDnaAsSanger took 0.001 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.03 sec [junit] Testcase: testReadEmptyFile took 0 sec [junit] Testcase: testErrorExamples took 0.029 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.002 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0.001 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 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 sec [junit] [junit] Testcase: testConvertNotSangerVariant took 0.013 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec [junit] Testcase: testWriteFileIterable took 0.024 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testWriteFileVararg took 0.003 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: 1.963 sec [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.963 sec [junit] [junit] Testcase: testMiscRnaAsSolexa took 0.057 sec [junit] Testcase: testFullRangeAsSolexa took 0.003 sec [junit] Testcase: testValidateDescription took 0.013 sec [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testWrappingAsSolexa took 0.002 sec [junit] Testcase: testLongReadsAsSolexa took 0.006 sec [junit] Testcase: testMiscDnaAsSolexa took 0.003 sec [junit] Testcase: testParseNullReadable took 0.001 sec [junit] Testcase: testReadRoundTripSingleFile took 0.029 sec [junit] Testcase: testReadEmptyFile took 0.001 sec [junit] Testcase: testErrorExamples took 0.028 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 0.002 sec [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0.001 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.SolexaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.587 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.587 sec [junit] [junit] Testcase: testConvertNotSolexaVariant took 0.009 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.003 sec [junit] Testcase: testWriteFileIterable took 0.019 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.003 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: 0.384 sec [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 sec [junit] [junit] Testcase: testStreamNullVariant took 0.004 sec [junit] Testcase: testStreamNullListener took 0.004 sec [junit] Testcase: testStreamNullReadable took 0.001 sec BUILD SUCCESSFUL Total time: 31 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-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes [copy] Warning: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-structure-gui/src/test/resources does not exist. [copy] Copying 141 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-structure-gui/classes test: [echo] Using java version 11.0.13 [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: 0.239 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.239 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: 0.147 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.147 sec [junit] [junit] Testcase: testSomeMethod took 0.001 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: 0.85 sec [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.85 sec [junit] [junit] Testcase: testGetColor took 0.003 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0.001 sec [junit] Testcase: testGetSelection took 0.004 sec [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec [junit] Testcase: testSetStyle took 0 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: 0.174 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.174 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL Total time: 6 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml compile-test: [mkdir] Created dir: /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [javac] /build/biojava4-live-SRabQ6/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-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 5 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes [copy] Copying 36 files to /build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg/buildtest/biojava4-ontology/classes test: [echo] Using java version 11.0.13 BUILD SUCCESSFUL Total time: 2 seconds make[1]: Leaving directory '/build/biojava4-live-SRabQ6/biojava4-live-4.2.12+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -i dh_install -i jh_installjavadoc -i 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-6_all.deb'. dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-6_all.deb'. dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-6_all.deb'. dpkg-genbuildinfo --build=all -O../biojava4-live_4.2.12+dfsg-6_all.buildinfo dpkg-genchanges --build=all -O../biojava4-live_4.2.12+dfsg-6_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-SRabQ6 /tmp/biojava4-live-4.2.12+dfsg-663zkgovz I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: hsperfdata_builduser W: deleting files in /tmp: convertTest1851706916629665226fastq W: deleting files in /tmp: convertTest11765153743782016135fastq W: deleting files in /tmp: convertTest13525712727605196721fastq W: deleting files in /tmp: convertTest3372597771133387587fastq W: deleting files in /tmp: convertTest13678391225762138098fastq W: deleting files in /tmp: convertTest7198236968178385228fastq W: deleting files in /tmp: convertTest17685093316411603761fastq W: deleting files in /tmp: convertTest3976543711527736246fastq W: deleting files in /tmp: convertTest17420758588801119274fastq W: deleting files in /tmp: abstractFastqReaderTest14987112077430608881.tmp W: deleting files in /tmp: abstractFastqReaderTest7368103877137990249.tmp W: deleting files in /tmp: abstractFastqReaderTest3834704765905914646.tmp W: deleting files in /tmp: abstractFastqWriterTest131770119771495386.tmp W: deleting files in /tmp: abstractFastqWriterTest1709359181910951218.tmp W: deleting files in /tmp: abstractFastqWriterTest16240271695097213045.tmp W: deleting files in /tmp: abstractFastqWriterTest6539935615450809280.tmp W: deleting files in /tmp: abstractFastqWriterTest15624074834014075658.tmp W: deleting files in /tmp: abstractFastqWriterTest16113928176634721009.tmp W: deleting files in /tmp: abstractFastqWriterTest7830553162545157050.tmp W: deleting files in /tmp: abstractFastqWriterTest3227994596864554692.tmp W: deleting files in /tmp: abstractFastqWriterTest14412105778363917888.tmp W: deleting files in /tmp: abstractFastqWriterTest1808776113065020604.tmp W: deleting files in /tmp: abstractFastqWriterTest8205443955825138163.tmp W: deleting files in /tmp: abstractFastqReaderTest1085524119129967479.tmp W: deleting files in /tmp: abstractFastqReaderTest8256094376525233470.tmp W: deleting files in /tmp: abstractFastqReaderTest8630636009825138117.tmp W: deleting files in /tmp: abstractFastqWriterTest7575350605721629786.tmp W: deleting files in /tmp: abstractFastqWriterTest5840022477914779132.tmp W: deleting files in /tmp: abstractFastqWriterTest14389566095357257770.tmp W: deleting files in /tmp: abstractFastqWriterTest16835766773545976435.tmp W: deleting files in /tmp: abstractFastqWriterTest3329571517274090661.tmp W: deleting files in /tmp: abstractFastqWriterTest17469814587167836212.tmp W: deleting files in /tmp: abstractFastqWriterTest7678830145527878539.tmp W: deleting files in /tmp: abstractFastqWriterTest2458712419313766372.tmp W: deleting files in /tmp: abstractFastqWriterTest11233018723457328320.tmp W: deleting files in /tmp: abstractFastqWriterTest2137842876846355420.tmp W: deleting files in /tmp: abstractFastqWriterTest8612917470212358933.tmp W: deleting files in /tmp: abstractFastqReaderTest2219274788585181685.tmp W: deleting files in /tmp: abstractFastqReaderTest17035179489142661648.tmp W: deleting files in /tmp: abstractFastqReaderTest2763322281362376494.tmp W: deleting files in /tmp: abstractFastqWriterTest9490143678484346622.tmp W: deleting files in /tmp: abstractFastqWriterTest7700409546616259067.tmp W: deleting files in /tmp: abstractFastqWriterTest6860376788299188104.tmp W: deleting files in /tmp: abstractFastqWriterTest5543509261303114010.tmp W: deleting files in /tmp: abstractFastqWriterTest16237759908223574560.tmp W: deleting files in /tmp: abstractFastqWriterTest5613583369618394612.tmp W: deleting files in /tmp: abstractFastqWriterTest10534957774201493537.tmp W: deleting files in /tmp: abstractFastqWriterTest14053476579642727036.tmp W: deleting files in /tmp: abstractFastqWriterTest7631868229834439109.tmp W: deleting files in /tmp: abstractFastqWriterTest17217821478300446819.tmp W: deleting files in /tmp: abstractFastqWriterTest4455052684686674617.tmp I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.KPlNY3thj6... I: success in 4930.3862 seconds md5: libbiojava4-java-doc_4.2.12+dfsg-6_all.deb: OK md5: libbiojava4-java_4.2.12+dfsg-6_all.deb: OK md5: libbiojava4.0-java_4.2.12+dfsg-6_all.deb: OK sha1: libbiojava4-java-doc_4.2.12+dfsg-6_all.deb: OK sha1: libbiojava4-java_4.2.12+dfsg-6_all.deb: OK sha1: libbiojava4.0-java_4.2.12+dfsg-6_all.deb: OK sha256: libbiojava4-java-doc_4.2.12+dfsg-6_all.deb: OK sha256: libbiojava4-java_4.2.12+dfsg-6_all.deb: OK sha256: libbiojava4.0-java_4.2.12+dfsg-6_all.deb: OK Checksums: OK