* Package: sci-biology/gatk-2.4 * Repository: gentoo * Maintainer: sci-biology * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox * Using: icedtea-bin-7 >>> Unpacking source... >>> Source unpacked in /var/tmp/portage/sci-biology/gatk-2.4/work >>> Preparing source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ... Rewriting attributes Rewriting ./build.xml >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4 ... * Disabling all optional ANT_TASKS Buildfile: /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build.xml [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found. git.describe: BUILD FAILED /var/tmp/portage/sci-biology/gatk-2.4/work/gatk-2.4/build.xml:276: Execute failed: java.io.IOException: Cannot run program "git": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1041) at java.lang.Runtime.exec(Runtime.java:617) at org.apache.tools.ant.taskdefs.launcher.Java13CommandLauncher.exec(Java13CommandLauncher.java:41) at org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:428) at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:442) at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:628) at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:669) at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:495) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292) at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:435) at org.apache.tools.ant.Target.performTasks(Target.java:456) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393) at org.apache.tools.ant.Project.executeTarget(Project.java:1364) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) at org.apache.tools.ant.Project.executeTargets(Project.java:1248) at org.apache.tools.ant.Main.runBuild(Main.java:851) at org.apache.tools.ant.Main.startAnt(Main.java:235) at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.<init>(UNIXProcess.java:135) at java.lang.ProcessImpl.start(ProcessImpl.java:130) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1022) ... 23 more Total time: 0 seconds * ERROR: sci-biology/gatk-2.4::gentoo failed (compile phase): * eant failed Portage 2.2.10 (default/linux/amd64/13.0/desktop/kde, gcc-4.8.3, glibc-2.19-r1, 3.15.0-gentoo x86_64) ================================================================= System uname: Linux-3.15.0-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2 KiB Mem: 7919000 total, 800852 free KiB Swap: 25165812 total, 25159952 free Timestamp of tree: Unknown ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.2_p47 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.7, 3.2.5-r4, 3.3.5, 3.4.1 dev-util/cmake: 2.8.12.2-r1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.69 sys-devel/automake: 1.14.1 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2-r1 sys-devel/make: 4.0-r1 sys-kernel/linux-headers: 3.15 (virtual/os-headers) sys-libs/glibc: 2.19-r1 Repositories: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="-j2" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync parallel-fetch preserve-libs protect-owned sandbox sfperms split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirrors.163.com/gentoo/ ftp://ftp.kaist.ac.kr/gentoo/ http://ftp.kaist.ac.kr/pub/gentoo/ http://gentoo.mirrors.hoobly.com/ http://gentoo.mirrors.easynews.com/linux/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j4" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam ffmpeg firefox flac fortran gbm gd gdbm gif glade gpm gtk iconv icu ipv6 java jpeg kde kipi lapack lcms ldap libkms libnotify mad mmx mng modules mp3 mp4 mpeg multilib ncurses nls nptl objc ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds python qt3support qt4 readline sdl semantic-desktop session spell sqlite sse sse2 ssl startup-notification svg tcpd threads tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xa xcb xcomposite xinerama xml xscreensaver xv xvfb xvid zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3 php5-4" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2 pypy python3_3 python3_4" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
Same here.
*** Bug 581818 has been marked as a duplicate of this bug. ***
ping
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=07bea2652d449ecfd5bae8ca97e28e66272d902d commit 07bea2652d449ecfd5bae8ca97e28e66272d902d Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-04-05 16:48:21 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-04-05 16:48:21 +0000 package.mask: last-rite sci-biology/gatk Bug: https://bugs.gentoo.org/418625 Bug: https://bugs.gentoo.org/431644 Bug: https://bugs.gentoo.org/515816 Bug: https://bugs.gentoo.org/542940 Bug: https://bugs.gentoo.org/574632 Bug: https://bugs.gentoo.org/780396 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 ++++++ 1 file changed, 6 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92cb6e9daf7c9865bfc003d4968b56501d5d00c6 commit 92cb6e9daf7c9865bfc003d4968b56501d5d00c6 Author: Jakov Smolic <jakov.smolic@sartura.hr> AuthorDate: 2021-05-04 21:57:13 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-05-04 22:29:36 +0000 sci-biology/gatk: Remove last-rited pkg Closes: https://bugs.gentoo.org/780396 Closes: https://bugs.gentoo.org/574632 Closes: https://bugs.gentoo.org/542940 Closes: https://bugs.gentoo.org/515816 Closes: https://bugs.gentoo.org/431644 Closes: https://bugs.gentoo.org/418625 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Closes: https://github.com/gentoo/gentoo/pull/20667 Signed-off-by: Sam James <sam@gentoo.org> profiles/package.mask | 6 ------ sci-biology/gatk/Manifest | 1 - sci-biology/gatk/gatk-2.4.ebuild | 32 -------------------------------- sci-biology/gatk/metadata.xml | 11 ----------- 4 files changed, 50 deletions(-)
