Bug 581818 – sci-biology/gatk-2.4 : /.../build.xml:276: Execute failed: java.io.IOException: Cannot run program git : error=2, No such file or directory

• Product: Gentoo Linux
• Status: RESOLVED DUPLICATE

[Description Toralf Förster 2016-05-02 08:07:55 UTC]

Total time: 0 seconds
 * ERROR: sci-biology/gatk-2.4::gentoo failed (compile phase):
 *   eant failed
 * 
 * Call stack:


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-gnome-unstable_20160423-225856) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------

  make.conf: USE="mmx sse sse2 pax_kernel xtpax -cdinstall -oci8 -bindist aes-ni -alsa cairo cdda cgoups csc curl dec_av2 -declarative designer drmkms gles2 graphtft gtk3 inifile ipv6 mdnsresponder-compat mng mysqli obj openmpi pdo pwquality python qemu qt5 sdl spice -sql sqlite -sqlite3 sse4_2 system-cairo system-icu szip uml -usb usbredir xmp xslt xcb gles2 egl pcre16"

  -----------------------------------------------------------------
Portage 2.2.28 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/gnome, gcc-5.3.0, glibc-2.23-r2, 4.5.2-hardened-r1 x86_64)
=================================================================
System uname: Linux-4.5.2-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16157888 total,   4273212 free
KiB Swap:   16777212 total,  16644764 free
Timestamp of repository gentoo: Mon, 02 May 2016 01:04:08 +0000
sh bash 4.3_p42-r2
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p42-r2::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.22.1::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.3-r7::gentoo
dev-util/cmake:           3.5.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.20.5::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.3.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.5::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage/
    priority: 1

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/entropy /etc/omega.conf /etc/stunnel/stunnel.conf /usr/lib64/tomoyo/conf /usr/share/config /usr/share/easy-rsa /var/lib/hsqldb /var/lib/i2pd/certificates /var/yp/Makefile"
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"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose-conflicts --color=n --nospinner --tree --quiet-build --accept-properties=-interactive --accept-restrict=-fetch"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi aes-ni amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cgoups cli colord consolekit cracklib crypt csc cups curl cxx dbus dec_av2 designer dri drmkms dts dvd dvdr eds egl emboss encode evo exif fam firefox flac fortran gdbm gif glamor gles2 gnome gnome-keyring gnome-online-accounts gpm graphtft gstreamer gtk gtk3 iconv inifile introspection ipv6 jpeg lcms ldap libnotify libsecret mad mdnsresponder-compat mmx mmxext mng modules mp3 mp4 mpeg multilib mysqli nautilus ncurses nls nptl obj ogg opengl openmp openmpi pam pango pax_kernel pcre pcre16 pdf pdo png policykit ppds pulseaudio pwquality python qemu qt3support qt4 qt5 readline sdl seccomp session spell spice sqlite sse sse2 sse4_2 ssl startup-notification svg system-cairo system-icu szip tcpd tiff tracker truetype udev udisks uml unicode upower usbredir vorbis wxwidgets x264 xattr xcb xml xmp xslt xtpax xv 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" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Toralf Förster 2016-05-02 08:07:58 UTC]

Created attachment 432942 [details]
emerge-history.txt

[Comment 2 Toralf Förster 2016-05-02 08:08:01 UTC]

Created attachment 432944 [details]
environment

[Comment 3 Toralf Förster 2016-05-02 08:08:03 UTC]

Created attachment 432946 [details]
sci-biology:gatk-2.4:20160502-040241.log

[Comment 4 Toralf Förster 2016-05-02 09:29:03 UTC]

disclaimer: might be an issue caused by the hardened-4.5.2-r1 kernel

[Comment 5 Toralf Förster 2016-09-04 14:29:15 UTC]

(In reply to Toralf Förster from comment #4)
>disclaimer: might be an issue caused by the hardened-4.5.2-r1 kernel

nope, don't think so in the mean while

[Comment 6 Toralf Förster 2020-07-25 14:02:08 UTC]

*** This bug has been marked as a duplicate of bug 515816 ***