Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/i/intervalstorej/intervalstorej_1.2+dfsg-3_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/intervalstorej-1.2+dfsg-3_1jmhpx4/intervalstorej_1.2+dfsg-3_all.buildinfo Get source package info: intervalstorej=1.2+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/intervalstorej/1.2+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-3 binutils-common=2.35.1-3 binutils-x86-64-linux-gnu=2.35.1-3 bsdextrautils=2.36.1-1 bsdutils=1:2.36.1-1 build-essential=12.8 bzip2=1.0.8-4 ca-certificates=20200601 ca-certificates-java=20190909 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-17 dash=0.5.11+git20200708+dd9ef66-2 dctrl-tools=2.24-3+b1 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 default-jdk-headless=2:1.11-72 default-jre-headless=2:1.11-72 devscripts=2.20.4 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dirmngr=2.2.20-1 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 fakeroot=1.25.3-1.1 file=1:5.39-3 findutils=4.7.0+git20201010-2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.0-1 g++-10=10.2.0-17 gcc=4:10.2.0-1 gcc-10=10.2.0-17 gcc-10-base=10.2.0-17 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gnupg=2.2.20-1 gnupg-l10n=2.2.20-1 gnupg-utils=2.2.20-1 gpg=2.2.20-1 gpg-agent=2.2.20-1 gpg-wks-client=2.2.20-1 gpg-wks-server=2.2.20-1 gpgconf=2.2.20-1 gpgsm=2.2.20-1 gpgv=2.2.20-1 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 java-common=0.72 javahelper=0.77 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-17 libasound2=1.2.3.2-1+b1 libasound2-data=1.2.3.2-1 libassuan0=2.5.3-7.1 libatomic1=10.2.0-17 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libavahi-client3=0.8-3 libavahi-common-data=0.8-3 libavahi-common3=0.8-3 libb-hooks-op-check-perl=0.22-1+b3 libbinutils=2.35.1-3 libblkid1=2.36.1-1 libbrotli1=1.0.9-2+b1 libbsd0=0.10.0-1 libbsh-java=2.0b4-20 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-17 libclass-method-modifiers-perl=2.13-1 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-3 libctf0=2.35.1-3 libcups2=2.3.3-3 libdb5.3=5.3.28+dfsg1-0.6 libdbus-1-3=1.12.20-1 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdevel-callchecker-perl=0.008-1+b2 libdpkg-perl=1.20.5 libdynaloader-functions-perl=0.003-1 libelf1=0.182-1 libencode-locale-perl=1.05-1 libexpat1=2.2.10-1 libfakeroot=1.25.3-1.1 libffi7=3.3-5 libfile-homedir-perl=1.006-1 libfile-listing-perl=6.11-1 libfile-stripnondeterminism-perl=1.9.0-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.2+dfsg-4 libgcc-10-dev=10.2.0-17 libgcc-s1=10.2.0-17 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.3-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.6.15-4 libgomp1=10.2.0-17 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhogweed6=3.6-2 libhtml-parser-perl=3.75-1+b1 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.08-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.26-1 libhttp-negotiate-perl=6.01-1 libicu67=67.1-4 libidn2-0=2.3.0-4 libimport-into-perl=1.002005-1 libio-html-perl=1.001-1 libio-pty-perl=1:1.15-2 libio-socket-ssl-perl=2.068-1 libipc-run-perl=20200505.0-1 libisl22=0.22.1-1 libitm1=10.2.0-17 libjcommander-java=1.71-3 libjpeg62-turbo=1:2.0.5-1.1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libksba8=1.4.0-2 liblcms2-2=2.9-4+b1 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.0-17 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.09-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmodule-runtime-perl=0.016-1 libmoo-perl=2.004000-1 libmount1=2.36.1-1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-1 libnet-http-perl=6.19-1 libnet-ssleay-perl=1.88-3+b1 libnettle8=3.6-2 libnpth0=1.6-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.29-1 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libnss3=2:3.59-1 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libparams-classify-perl=0.015-1+b3 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libpcsclite1=1.9.0-1 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpng16-16=1.6.37-3 libpython3-stdlib=3.9.0-3 libpython3.9-minimal=3.9.0-5 libpython3.9-stdlib=3.9.0-5 libquadmath0=10.2.0-17 libreadline8=8.1~rc2-2 librole-tiny-perl=2.001004-1 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsemanage-common=3.1-1 libsemanage1=3.1-1+b1 libsepol1=3.1-1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-1 libsqlite3-0=3.33.0-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-17 libstdc++6=10.2.0-17 libstrictures-perl=2.000006-1 libsub-override-perl=0.09-2 libsub-quote-perl=2.006006-1 libsystemd0=246.6-3 libtasn1-6=4.16.0-2 libtimedate-perl=2.3300-1 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtry-tiny-perl=0.30-1 libtsan0=10.2.0-17 libubsan1=10.2.0-17 libuchardet0=0.0.7-1 libudev1=246.6-3 libunistring2=0.9.10-4 liburi-perl=5.05-1 libuuid1=2.36.1-1 libwww-perl=6.49-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxi6=2:1.7.10-1 libxml2=2.9.10+dfsg-6.2 libxrender1=1:0.9.10-1 libxtst6=2:1.2.3-1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 maven-repo-helper=1.9.4 mawk=1.3.4.20200120-2 media-types=1.0.1 mime-support=3.66 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 netbase=6.2 openjdk-11-jdk-headless=11.0.9.1+1-1 openjdk-11-jre-headless=11.0.9.1+1-1 openssl=1.1.1h-1 passwd=1:4.8.1-1 patch=2.7.6-6 patchutils=0.4.2-1 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 perl-openssl-defaults=5 pinentry-curses=1.1.0-4 po-debconf=1.0.21 python3=3.9.0-3 python3-minimal=3.9.0-3 python3.9=3.9.0-5 python3.9-minimal=3.9.0-5 readline-common=8.1~rc2-2 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 testng=6.9.12-4 ucf=3.0043 unzip=6.0-25 util-linux=2.36.1-1 wdiff=1.2.2-2+b1 x11-common=1:7.7+21 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201202T151734Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ 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 intervalstorej=1.2+dfsg-3 && mkdir -p /build/intervalstorej-lD28AE && dpkg-source --no-check -x /*.dsc /build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg && chown -R builduser:builduser /build/intervalstorej-lD28AE" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1606054951" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/intervalstorej-lD28AE /tmp/intervalstorej-1.2+dfsg-3_1jmhpx4 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201119T152556Z 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.RShNPRRgtj 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.RShNPRRgtj Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (828 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 ... 4690 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201202T151734Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.RShNPRRgtj Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 32s (1068 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.RShNPRRgtj I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d intervalstorej=1.2+dfsg-3 && mkdir -p /build/intervalstorej-lD28AE && dpkg-source --no-check -x /*.dsc /build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg && chown -R builduser:builduser /build/intervalstorej-lD28AE"' exec /tmp/mmdebstrap.RShNPRRgtj Reading package lists... NOTICE: 'intervalstorej' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/java-team/intervalstorej.git Please use: git clone https://salsa.debian.org/java-team/intervalstorej.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1584 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main intervalstorej 1.2+dfsg-3 (dsc) [2245 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main intervalstorej 1.2+dfsg-3 (tar) [1578 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main intervalstorej 1.2+dfsg-3 (diff) [4224 B] Fetched 1584 kB in 1s (1071 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'intervalstorej_1.2+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting intervalstorej in /build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg dpkg-source: info: unpacking intervalstorej_1.2+dfsg.orig.tar.xz dpkg-source: info: unpacking intervalstorej_1.2+dfsg-3.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1606054951" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.RShNPRRgtj dpkg-buildpackage: info: source package intervalstorej dpkg-buildpackage: info: source version 1.2+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . debian/rules clean dh clean --with javahelper --with maven-repo-helper jh_clean mh_clean dh_clean debian/rules binary-indep dh binary-indep --with javahelper --with maven-repo-helper dh_update_autotools_config -i dh_autoreconf -i jh_linkjars -i debian/rules override_jh_build make[1]: Entering directory '/build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg' # Specifying 1.8 because we need default methods. jh_build --no-javadoc --javacopts="-source 1.8 -target 1.8" warning: [options] bootstrap class path not set in conjunction with -source 8 Note: ./src/intervalstore/impl/IntervalStore.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 1 warning make[1]: Leaving directory '/build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg' # Running the tests manually in a temp folder. The classpath includes only # the built jar, the test sources and the jars of the test motor. # Two zip files inside the test sources, with data, have to be unzipped. SOURCEDIR=`pwd` && \ TESTDIR=`mktemp -d` && \ cp -r test/ $TESTDIR && \ export CLASSPATH=$TESTDIR/test:`readlink -f intervalstorej.jar`:/usr/share/java/testng.jar:/usr/share/java/jcommander.jar && \ cd $TESTDIR && \ find test -name "*.java" | xargs javac -source 1.8 -target 1.8 && \ for F in $(find test -name "*.zip"); do \ unzip $F -d ${F%/*}; \ done && \ java org.testng.TestNG $SOURCEDIR/debian/tests.xml warning: [options] bootstrap class path not set in conjunction with -source 8 Note: test/junit/extensions/PA.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 1 warning Archive: test/intervalstore/impl/brafVariants.csv.zip inflating: test/intervalstore/impl/brafVariants.csv Archive: test/intervalstore/impl/humanGenes.csv.zip inflating: test/intervalstore/impl/humanGenes.csv ... ... TestNG 6.9.10 by Cédric Beust (cedric@beust.com) ... [TestNG] Running: /build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg/debian/tests.xml testIntervalStoreDepth_genes: start chr1 size=5317, width=3709 (69.8%), nclSize = 1608, ncldepth=3 chr2 size=4006, width=2754 (68.7%), nclSize = 1252, ncldepth=7 chr3 size=3050, width=1943 (63.7%), nclSize = 1107, ncldepth=3 chr4 size=2510, width=1809 (72.1%), nclSize = 701, ncldepth=2 chr5 size=2878, width=1922 (66.8%), nclSize = 956, ncldepth=21 chr6 size=2907, width=2105 (72.4%), nclSize = 802, ncldepth=2 chr7 size=2917, width=2007 (68.8%), nclSize = 910, ncldepth=3 chr8 size=2386, width=1572 (65.9%), nclSize = 814, ncldepth=3 chr9 size=2275, width=1615 (71.0%), nclSize = 660, ncldepth=2 chr10 size=2240, width=1539 (68.7%), nclSize = 701, ncldepth=2 chr11 size=3285, width=2251 (68.5%), nclSize = 1034, ncldepth=3 chr12 size=2969, width=1897 (63.9%), nclSize = 1072, ncldepth=3 chr13 size=1335, width=899 (67.3%), nclSize = 436, ncldepth=2 chr14 size=2230, width=1495 (67.0%), nclSize = 735, ncldepth=3 chr15 size=2179, width=1272 (58.4%), nclSize = 907, ncldepth=2 chr16 size=2513, width=1580 (62.9%), nclSize = 933, ncldepth=3 chr17 size=3024, width=1910 (63.2%), nclSize = 1114, ncldepth=3 chr18 size=1183, width=725 (61.3%), nclSize = 458, ncldepth=3 chr19 size=2959, width=2089 (70.6%), nclSize = 870, ncldepth=2 chr20 size=1397, width=1006 (72.0%), nclSize = 391, ncldepth=2 chr21 size=833, width=579 (69.5%), nclSize = 254, ncldepth=2 chr22 size=1353, width=929 (68.7%), nclSize = 424, ncldepth=2 chrX size=2375, width=1794 (75.5%), nclSize = 581, ncldepth=3 chrY size=518, width=463 (89.4%), nclSize = 55, ncldepth=1 testIntervalStoreDepth_genes: end testIntervalStoreDepth_variants: start Found 46190 variants including 44016 SNVs and 1062 colocated Variants size=46190, width=43299 (93.7%), depth=28 testIntervalStoreDepth_variants: end testNclistDepth_genes: start chr1 NCList size=5317, width=3709 (69.8%), depth=4 chr2 NCList size=4006, width=2754 (68.7%), depth=8 chr3 NCList size=3050, width=1943 (63.7%), depth=4 chr4 NCList size=2510, width=1809 (72.1%), depth=3 chr5 NCList size=2878, width=1922 (66.8%), depth=22 chr6 NCList size=2907, width=2105 (72.4%), depth=3 chr7 NCList size=2917, width=2007 (68.8%), depth=4 chr8 NCList size=2386, width=1572 (65.9%), depth=4 chr9 NCList size=2275, width=1615 (71.0%), depth=3 chr10 NCList size=2240, width=1539 (68.7%), depth=3 chr11 NCList size=3285, width=2251 (68.5%), depth=4 chr12 NCList size=2969, width=1897 (63.9%), depth=4 chr13 NCList size=1335, width=899 (67.3%), depth=3 chr14 NCList size=2230, width=1495 (67.0%), depth=4 chr15 NCList size=2179, width=1272 (58.4%), depth=3 chr16 NCList size=2513, width=1580 (62.9%), depth=4 chr17 NCList size=3024, width=1910 (63.2%), depth=4 chr18 NCList size=1183, width=725 (61.3%), depth=4 chr19 NCList size=2959, width=2089 (70.6%), depth=3 chr20 NCList size=1397, width=1006 (72.0%), depth=3 chr21 NCList size=833, width=579 (69.5%), depth=3 chr22 NCList size=1353, width=929 (68.7%), depth=3 chrX NCList size=2375, width=1794 (75.5%), depth=4 chrY NCList size=518, width=463 (89.4%), depth=2 testNclistDepth_genes: end testNclistDepth_variants: start Found 46190 variants of which 44016 SNVs Variants NCList size=46190, width=43299 (93.7%), depth=28 testNclistDepth_variants: end WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by junit.extensions.PrivilegedAccessor (file:/tmp/tmp.hMK1BjDdxq/test/) to field java.lang.reflect.Field.modifiers WARNING: Please consider reporting this to the maintainers of junit.extensions.PrivilegedAccessor WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release error in NCList: range 42-44 [43-43] starts before 50 error in NCList: range 42-51 [43-43] ends after 50 error in NCList: range 41-48 starts before 42-44 [43-43] error in NCList: range 41-43 starts before 44 error in NCList: range 47-49 encloses preceding: 47-48 error in NCList: range 47-48 enclosed by preceding: 46-48 error in NCList: range 14-15 starts before 20 error in NCList: range 16-17 ends after 16 error in NCList: range 12-17 starts before 14-15 Duplicate feature generated 9:9:Pfam Duplicate feature generated 0:6:Cath Duplicate feature generated 4:10:Cath Duplicate feature generated 0:10:Cath Duplicate feature generated 0:9:Pfam Duplicate feature generated 0:5:Cath Duplicate feature generated 4:6:Pfam Covered all findOverlaps cases after 13 iterations for scale 10 Duplicate feature generated 0:65:Cath Duplicate feature generated 47:50:Pfam Covered all findOverlaps cases after 12 iterations for scale 100 nonNested invalid containment!: 20-30, 20-40 nonNested invalid containment!: 20-41, 20-40 nonNested wrong start order : 20-40, 15-35 error in NCList: range 26-29 ends after 28 [Utils] Attempting to create /tmp/tmp.hMK1BjDdxq/test-output/All/All.xml [Utils] Directory /tmp/tmp.hMK1BjDdxq/test-output/All exists: true PASSED: testContainsInterval PASSED: testEqualsInterval PASSED: testOverlapsInterval PASSED: testProperlyContainsInterval PASSED: testEquals_hashCode PASSED: testIntervalStoreDepth_genes PASSED: testIntervalStoreDepth_variants PASSED: testNclistDepth_genes PASSED: testNclistDepth_variants PASSED: testAdd_colocated PASSED: testAdd_enclosing PASSED: testAdd_inside PASSED: testAdd_onTheEnd PASSED: testAdd_onTheFront PASSED: testAdd_overlapping PASSED: testAdd_spanning PASSED: testConstructor PASSED: testContains PASSED: testFindFirstOverlap PASSED: testFindOverlaps PASSED: testGetDepth PASSED: testGetEntries PASSED: testIsValid PASSED: testIterator PASSED: testLoadOrder_alternates PASSED: testLoadOrder_treeBalance PASSED: testNestingDependsOnLoadOrder PASSED: testPrettyPrint PASSED: testPush PASSED: testRemove PASSED: testRemove_withPromotion PASSED: testRemove_withPromotionLeft PASSED: testRemove_withPromotionRight PASSED: testContainsInterval PASSED: testEqualsInterval PASSED: testOverlapsInterval PASSED: testProperlyContainsInterval PASSED: testAddNode PASSED: testAddNode_invalidRangeEnd PASSED: testAddNode_invalidRangeStart PASSED: testConstructor PASSED: testContainsInterval PASSED: testGetEntries PASSED: testIsValid PASSED: testIterator PASSED: testRemove PASSED: testCompare PASSED: test_pseudoRandom(10) PASSED: test_pseudoRandom(100) PASSED: testFindFirst PASSED: testAdd PASSED: testAddNonNestedInterval PASSED: testConstructor_nesting PASSED: testConstructor_noNesting PASSED: testContains PASSED: testFindOverlaps_colocatedNested PASSED: testFindOverlaps_colocatedNonNested PASSED: testFindOverlaps_mixed PASSED: testFindOverlaps_nested PASSED: testFindOverlaps_nonNested PASSED: testFindOverlaps_resultsArg_mixed PASSED: testFindOverlaps_resultsArg_nested PASSED: testFindOverlaps_resultsArg_nonNested PASSED: testGetDepth PASSED: testIsEmpty PASSED: testIsValid PASSED: testListContains PASSED: testPrettyPrint PASSED: testRemove PASSED: testRemoveNonNested PASSED: testRemove_readd PASSED: testToString PASSED: testNext =============================================== All Tests run: 73, Failures: 0, Skips: 0 =============================================== =============================================== All Total tests run: 73, Failures: 0, Skips: 0 =============================================== [TestNG] Time taken by org.testng.reporters.jq.Main@26f67b76: 2204 ms [TestNG] Time taken by org.testng.reporters.XMLReporter@2669b199: 309 ms [Utils] Attempting to create /tmp/tmp.hMK1BjDdxq/test-output/old/All/toc.html [Utils] Directory /tmp/tmp.hMK1BjDdxq/test-output/old/All exists: true [Utils] Attempting to create /tmp/tmp.hMK1BjDdxq/test-output/old/All/All.properties [Utils] Directory /tmp/tmp.hMK1BjDdxq/test-output/old/All exists: true [Utils] Attempting to create /tmp/tmp.hMK1BjDdxq/test-output/old/All/index.html [Utils] Directory /tmp/tmp.hMK1BjDdxq/test-output/old/All exists: 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[Utils] Directory test-output/old exists: true [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter@13c78c0b: 303 ms [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 1 ms [TestNG] Time taken by org.testng.reporters.EmailableReporter2@174d20a: 91 ms [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.NCNodeTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.RangeTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.NCListBuilderTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.api.IntervalITest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.NCListTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.BinarySearcherTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.IntervalStoreTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.LoadTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.IntervalIteratorTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.IntervalTest.xml [Utils] Directory test-output/junitreports exists: true [Utils] Attempting to create test-output/junitreports/TEST-intervalstore.impl.NCListRandomisedTest.xml [Utils] Directory test-output/junitreports exists: true [TestNG] Time taken by org.testng.reporters.JUnitReportReporter@4de8b406: 214 ms make[1]: Leaving directory '/build/intervalstorej-lD28AE/intervalstorej-1.2+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -i dh_prep -i mh_install -i jh_installjavadoc -i dh_installdocs -i dh_installchangelogs -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 'libintervalstorej-java' in '../libintervalstorej-java_1.2+dfsg-3_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../intervalstorej_1.2+dfsg-3_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/intervalstorej-lD28AE /tmp/intervalstorej-1.2+dfsg-3_1jmhpx4 I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_builduser W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: tmp.hMK1BjDdxq I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.RShNPRRgtj... I: success in 931.5793 seconds md5: libintervalstorej-java_1.2+dfsg-3_all.deb: OK sha1: libintervalstorej-java_1.2+dfsg-3_all.deb: OK sha256: libintervalstorej-java_1.2+dfsg-3_all.deb: OK Checksums: OK