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Bug 366975 - [science overlay] sci-biology/gbrowse-2.33 fails to install, due to ACCESS VIOLATION
Summary: [science overlay] sci-biology/gbrowse-2.33 fails to install, due to ACCESS VI...
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard: Science overlay
Keywords:
Depends on:
Blocks:
 
Reported: 2011-05-12 10:44 UTC by Juergen Rose
Modified: 2012-01-04 08:07 UTC (History)
0 users

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


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Description Juergen Rose 2011-05-12 10:44:36 UTC
'emerge gbrowse' fails with:
...
Installing /var/tmp/portage/sci-biology/gbrowse-2.33/image/usr/bin/gbrowse_create_account.pl
Installing /var/tmp/portage/sci-biology/gbrowse-2.33/image/usr/bin/scan_gbrowse.pl
mkdir /var/lib/gbrowse2
ACCESS DENIED  mkdir:        /var/lib/gbrowse2
mkdir /var/lib/gbrowse2: Permission denied at /var/tmp/portage/sci-biology/gbrowse-2.33/work/GBrowse-2.33/install_util/GBrowseInstall.pm line 474
 * ERROR: sci-biology/gbrowse-2.33 failed (install phase):
 *   ./Build install failed
 * 
 * Call stack:
 *     ebuild.sh, line   56:  Called src_install
 *   environment, line 2893:  Called perl-module_src_install
 *   environment, line 2570:  Called die
 * The specific snippet of code:
 *           ./Build ${mytargets} || die "./Build ${mytargets} failed";
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/gbrowse-2.33',
 * the complete build log and the output of 'emerge -pqv =sci-biology/gbrowse-2.33'.
 * This ebuild is from an overlay named 'science': '/var/lib/layman/science/'
 * The complete build log is located at '/var/tmp/portage/sci-biology/gbrowse-2.33/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/gbrowse-2.33/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/gbrowse-2.33/work/GBrowse-2.33'
--------------------------- ACCESS VIOLATION SUMMARY ---------------------------
LOG FILE "/var/log/sandbox/sandbox-20080.log"

VERSION 1.0
FORMAT: F - Function called
FORMAT: S - Access Status
FORMAT: P - Path as passed to function
FORMAT: A - Absolute Path (not canonical)
FORMAT: R - Canonical Path
FORMAT: C - Command Line

F: mkdir
S: deny
P: /var/lib/gbrowse2
A: /var/lib/gbrowse2
R: /var/lib/gbrowse2
C: /usr/bin/perl5.12.3 ./Build install 
--------------------------------------------------------------------------------

>>> Failed to emerge sci-biology/gbrowse-2.33, Log file:


Reproducible: Always




root@orca:/usr/src(13)# emerge --info =sci-biology/gbrowse-2.33
Portage 2.1.9.48 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.13-r2, 2.6.38-gentoo-r5 x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.38-gentoo-r5-x86_64-Intel-R-_Xeon-R-_CPU_W3520_@_2.67GHz-with-gentoo-2.0.2
Timestamp of tree: Thu, 12 May 2011 06:00:01 +0000
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.1-r1, 3.1.3-r1
dev-util/cmake:           2.8.4-r1
sys-apps/baselayout:      2.0.2
sys-apps/openrc:          0.8.2-r1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21
sys-devel/gcc:            4.4.5, 4.5.2
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.13-r2
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe -ggdb"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/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="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe -ggdb"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news noclean parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j9"
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="/var/lib/layman/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/arcon /var/lib/layman/science /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile harness hddtemp hdf hdf5 hdri http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4 ssl startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thinkpad threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" ALSA_CARDS="intel8x0" 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="canon" 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" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nouveau vesa" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


root@orca:/usr/src(14)# emerge -pqv =sci-biology/gbrowse-2.33
[ebuild  N    ] sci-biology/gbrowse-2.33  USE="svg -minimal -test -vhosts"
Comment 1 Juergen Rose 2011-06-15 10:41:41 UTC
More than a month later. Any news?
Comment 2 Juergen Rose 2011-06-26 07:15:24 UTC
The file GBrowse-2.33.tar.gz seems to be disappeared from the CPAN mirrors. The current file is GBrowse-2.38.tar.gz. Perhaps the gentoo ebuild should be updated.
Comment 3 Juergen Rose 2011-07-05 08:23:46 UTC
Now is gbrowse-2.38 in the science overlay. But 'emerge gbrowse' fails with the same ACCESS VIOLATION as before:

Installing /var/tmp/portage/sci-biology/gbrowse-2.38/image/usr/bin/gbrowse_syn_load_alignment_database.pl
mkdir /var/lib/gbrowse2
ACCESS DENIED  mkdir:        /var/lib/gbrowse2
mkdir /var/lib/gbrowse2: Permission denied at /var/tmp/portage/sci-biology/gbrowse-2.38/work/GBrowse-2.38/install_util/GBrowseInstall.pm line 474
 * ERROR: sci-biology/gbrowse-2.38 failed (install phase):
 *   ./Build install failed


This problem exist at least for two month. Is there not any way to solve it?
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2011-07-05 08:46:42 UTC
How about you step up and contribute yourself to gentoo. We can give you commit access to the sci overlay and you can commit fixes there.
The reason why things don't get fixed isn't a matter of will but a matter of time and manpower. So what do you think?