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Bug 353563

Summary: Please stabilize sci-biology/shrimp-2.0.1
Product: Gentoo Linux Reporter: Andrey Kislyuk (RETIRED) <weaver>
Component: New packagesAssignee: Andrey Kislyuk (RETIRED) <weaver>
Status: RESOLVED FIXED    
Severity: enhancement Keywords: STABLEREQ
Priority: High    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 331933    
Attachments: build.log

Description Andrey Kislyuk (RETIRED) gentoo-dev 2011-02-03 00:14:45 UTC
Please stabilize sci-biology/shrimp-2.0.1. 
 Note: Because of the complexity of science package testing, a compile test is sufficient from the arch teams
Comment 1 Agostino Sarubbo gentoo-dev 2011-02-04 12:58:48 UTC
amd64 ok
Comment 2 PaweĊ‚ Hajdan, Jr. (RETIRED) gentoo-dev 2011-02-07 13:29:50 UTC
Created attachment 261719 [details]
build.log

Portage 2.1.9.25 (default/linux/x86/10.0/developer, gcc-4.4.4, glibc-2.11.2-r3, 2.6.36-gentoo-r5 i686)
=================================================================
System uname: Linux-2.6.36-gentoo-r5-i686-Intel-R-_Core-TM-2_Duo_CPU_P8700_@_2.53GHz-with-gentoo-1.12.14
Timestamp of tree: Mon, 07 Feb 2011 06:30:01 +0000
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.6.6-r1, 3.1.2-r4
dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 1.12.14-r1
sys-apps/sandbox:    2.4
sys-devel/autoconf:  2.13, 2.65-r1
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.4-r2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
virtual/os-headers:  2.6.36.1 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="*"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=i686 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /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 -march=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs collision-protect distlocks fixlafiles fixpackages multilib-strict news parallel-fetch protect-owned sandbox sfperms splitdebug strict test test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa berkdb bzip2 cairo cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emacs emboss encode exif fam firefox flac fortran gdbm gdu gif gnutls gtk hal iconv jpeg lcms libnotify mad mbox mikmod mng modules mp3 mp4 mpeg mudflap ncurses nls nptl nptlonly nss ogg opengl openmp pam pango pcre pdf perl png policykit ppds pppd python qt3support readline sdl secure-delete session snmp spell sqlite ssl startup-notification subversion svg sysfs tcb tcpd tiff toolkit-scroll-bars truetype udev unicode usb vorbis x264 x86 xcb xft xinerama xml xorg xulrunner xv xvid zlib" ALSA_CARDS="ens1371" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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" 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 ubx" INPUT_DEVICES="evdev keyboard vmmouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vmware vesa vga" 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, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 3 Agostino Sarubbo gentoo-dev 2011-02-07 13:35:58 UTC
works here for me :)
Comment 4 David Abbott gentoo-dev 2011-02-08 21:35:54 UTC
Archtested on x86: Everything fine
Comment 5 blain 'Doc' Anderson 2011-02-11 01:07:39 UTC
amd64 VM


* QA Notice: Files built without respecting LDFLAGS have been detected
 *  Please include the following list of files in your report:
 * /usr/bin/md5sum-lite
 * /usr/bin/maq2sam-short
 * /usr/bin/samtools
 * /usr/bin/maq2sam-long
 * /usr/bin/wgsim
 * /usr/bin/md5fa


>>> Installing (1 of 1) sci-biology/samtools-0.1.12

>>> Recording sci-biology/samtools in "world" favorites file...
>>> Auto-cleaning packages...

>>> No outdated packages were found on your system.

 * GNU info directory index is up-to-date.


emerge --info
Portage 2.1.9.25 (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.11.2-r3, 2.6.36-gentoo-r5 x86_64)
=================================================================
System uname: Linux-2.6.36-gentoo-r5-x86_64-AMD_Phenom-tm-_9650_Quad-Core_Processor-with-gentoo-1.12.14
Timestamp of tree: Sat, 05 Feb 2011 15:00:01 +0000
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.6.6-r1, 3.1.2-r4
dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 1.12.14-r1
sys-apps/sandbox:    2.4
sys-devel/autoconf:  2.13, 2.65-r1
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.4-r2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
virtual/os-headers:  2.6.30-r1 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs collision-protect distlocks fixlafiles fixpackages multilib-strict news parallel-fetch protect-owned sandbox sfperms split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox"
GENTOO_MIRRORS="http://gentoo.lagis.at/ ftp://ftp.ing.umu.se/linux/gentoo/ ftp://chi-10g-1-mirror.fastsoft.net/pub/linux/gentoo/gentoo-distfiles/"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X acl amd64 apache2 berkdb bzip2 cairo cli cracklib crypt cups cxx dbus device-mapper dri extras fortran gdbm gdu gpm gt3support gtk iconv ipv6 kde mmx mng modules mudflap multilib mysql ncurses nls nptl nptlonly opengl openmp pam pcre perl png policykit pppd python qt3support qt4 readline session sql sqlite sse sse2 ssl svg sysfs tcpd threads unicode webkit xorg zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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" 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 ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia vesa fbdev" 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, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Comment 6 Markos Chandras (RETIRED) gentoo-dev 2011-02-27 20:15:06 UTC
amd64 done. I am ignoring the LDFLAGS problem for now. thank you guys
Comment 7 Thomas Kahle (RETIRED) gentoo-dev 2011-03-07 15:34:45 UTC
x86 done. Closing. Thanks everybody.