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Bug 277226 - sci-biology/eugene fails tests
Summary: sci-biology/eugene fails tests
Status: RESOLVED CANTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Andrey Kislyuk (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2009-07-09 17:07 UTC by Diego Elio Pettenò (RETIRED)
Modified: 2009-09-09 21:56 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
Build log (eugene-3.5d:20090709-162554.log,89.45 KB, text/plain)
2009-07-09 17:07 UTC, Diego Elio Pettenò (RETIRED)
Details

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Description Diego Elio Pettenò (RETIRED) gentoo-dev 2009-07-09 17:07:33 UTC
Portage 2.1.6.13 (!../var/cache/portage/tree/profiles/default/linux/x86/2008.0, gcc-4.4.0-asneeded, glibc-2.10.1-r0, 2.6.30-gentoo-r1 i686)
=================================================================
System uname: Linux-2.6.30-gentoo-r1-i686-Quad-Core_AMD_Opteron-tm-_Processor_2350-with-gentoo-2.0.1
Timestamp of tree: Thu, 09 Jul 2009 11:30:01 +0000
ccache version 2.4 [enabled]
app-shells/bash:     4.0_p24
dev-java/java-config: 1.3.7-r1, 2.1.8-r1
dev-lang/python:     2.6.2-r1
dev-python/pycrypto: 2.0.1-r8
dev-util/ccache:     2.4-r8
dev-util/cmake:      2.6.4
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.4.3-r3
sys-apps/sandbox:    2.0
sys-devel/autoconf:  2.13, 2.63-r1
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils:  2.19.1-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.30
ACCEPT_KEYWORDS="x86 ~x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /opt/glftpd/etc /opt/glftpd/ftp-data /opt/openfire/resources/security/ /opt/openjms/config /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/bufrtables /usr/share/config /var/bind /var/lib/hsqldb /var/phxd /var/spool/torque /var/vpopmail/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -pipe"
DISTDIR="/var/cache/distfiles"
FEATURES="ccache distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict test test-fail-continue unmerge-orphans userfetch"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo"
INSTALL_MASK="  /usr/share/doc  /usr/share/man  /usr/share/info"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j14"
PKGDIR="/var/spool/portage/packages"
PORTAGE_COMPRESS=""
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="/var/cache/portage/tree-tinderbox"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl berkdb bzip2 cli cracklib crypt cups dri fortran gdbm gpm iconv ipv6 isdnlog java5 java6 midi mudflap ncurses nls nostatic nptl nptlonly openmp pam pcre perl pppd python qt3support readline reflection ruby session spl ssl sysfs tcpd unicode x86 xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 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" ELIBC="glibc" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Comment 1 Diego Elio Pettenò (RETIRED) gentoo-dev 2009-07-09 17:07:50 UTC
Created attachment 197366 [details]
Build log
Comment 2 Arttu Valo 2009-09-06 17:34:12 UTC
The error present in this build.log seemed to be fixed by just creating the directory which is missing from the sources: "${S}"/Test/TestTrace

But it won't help much further. Some data files from under /Annotations are apparently nowhere to be found (this is also once commented upon over at the stabilization bug #263041 ):

ERROR: tcl error sourcing tool-and-target-specific interface file Test/config/default.exp.
ls: cannot access /Annotation/Arabidopsis/araset/Genes: No such file or directory         
ls: cannot access /Annotation/Arabidopsis/araset/Genes: No such file or directory         
    while executing                                                                       
"exec ls /Annotation/Arabidopsis/araset/Genes"                                            
    ("eval" body line 1)                                                                  
    invoked from within                                                                   
"eval exec ls $SEQBASE_DIR"                                                               
    invoked from within
"set seq [eval exec ls $SEQBASE_DIR]"
    (file "Test/config/TestVar.tcl" line 98)
    invoked from within
"source Test/config/TestVar.tcl"
    (file "Test/config/default.exp" line 24)
    invoked from within
"source Test/config/default.exp"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 source Test/config/default.exp"
make[2]: *** [check-DEJAGNU] Error 1

So maybe this package should just RESTRICT="test"?

(And as a last point, also tried this with eugene-3.5g, which is available -- alas, no /Annotations data there either, so no luck, same problems.)
Comment 3 Andrey Kislyuk (RETIRED) gentoo-dev 2009-09-09 21:56:20 UTC
RESTRICT="test" committed, thanks