Bug 254157 – [science overlay] sci-biology/generic-genome-browser-1.68: cd: /var/tmp/portage/sci-biology/generic-genome-browser-1.68/image//usr/share/generic-genome-browser-1.68/scripts: No such file or directory

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Martin Mokrejš 2009-01-07 21:44:49 UTC]

Do I have some portage bug on my system? Anyway, this ebuild needs some cleanup.


>>> Emerging (1 of 1) sci-biology/generic-genome-browser-1.68
 * Generic-Genome-Browser--1.68.tar.gz RMD160 SHA1 SHA256 size ;-) ...                                                                                                                                                         [ ok ]
 * checking ebuild checksums ;-) ...                                                                                                                                                                                           [ ok ]
 * checking auxfile checksums ;-) ...                                                                                                                                                                                          [ ok ]
 * checking miscfile checksums ;-) ...                                                                                                                                                                                         [ ok ]
>>> Unpacking source...
>>> Unpacking Generic-Genome-Browser--1.68.tar.gz to /var/tmp/portage/sci-biology/generic-genome-browser-1.68/work
>>> Source unpacked.
>>> Compiling source in /var/tmp/portage/sci-biology/generic-genome-browser-1.68/work/Generic-Genome-Browser-1.68 ...
----------------------------------------------
                File Paths

   CONF /etc
 HTDOCS /var/www/localhost/htdocs
 CGIBIN /var/www/localhost/cgi-bin
    LIB 
    BIN 
  DO_XS 1
NONROOT 
SELINUX 

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------

Installed Bio::Graphics version 1.636 is less than desired version 1.654.
You need to update your BioPerl installation to version 1.5.2.

Died at Makefile.PL line 196.
>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/generic-genome-browser-1.68

>>> Install generic-genome-browser-1.68 into /var/tmp/portage/sci-biology/generic-genome-browser-1.68/image/ category sci-biology
/var/tmp/portage/sci-biology/generic-genome-browser-1.68/temp/environment: line 2435: cd: /var/tmp/portage/sci-biology/generic-genome-browser-1.68/image//usr/share/generic-genome-browser-1.68/scripts: No such file or directory
tar: ./figures/third_party1.gif: file changed as we read it
tar: ./figures/third_party2.gif: file changed as we read it
tar: ./figures: file changed as we read it
tar: ./data_files/volvox.gff3: file changed as we read it
tar: ./data_files/volvox_trace.scf: file changed as we read it
tar: ./data_files: file changed as we read it
tar: ./tutorial.html: file changed as we read it
tar: .: file changed as we read it
 * Cleaning out stray man files
>>> Completed installing generic-genome-browser-1.68 into /var/tmp/portage/sci-biology/generic-genome-browser-1.68/image/


>>> Installing sci-biology/generic-genome-browser-1.68
 * Man pages are not installed for most modules now.
 * Please use perldoc instead.

>>> Recording sci-biology/generic-genome-browser in "world" favorites file...


# equery files generic-genome-browser
[ Searching for packages matching generic-genome-browser... ]
* Contents of sci-biology/generic-genome-browser-1.68:
/etc
/usr
/usr/share
/usr/share/doc
/usr/share/doc/generic-genome-browser-1.68
/usr/share/doc/generic-genome-browser-1.68/Changes.bz2
/usr/share/doc/generic-genome-browser-1.68/History.bz2
/usr/share/doc/generic-genome-browser-1.68/INSTALL.bz2
/usr/share/doc/generic-genome-browser-1.68/MANIFEST.bz2
/usr/share/doc/generic-genome-browser-1.68/README.MacOSX.bz2
/usr/share/doc/generic-genome-browser-1.68/README.Ubuntu.bz2
/usr/share/doc/generic-genome-browser-1.68/README.berkeleydb.bz2
/usr/share/doc/generic-genome-browser-1.68/README.bz2
/usr/share/doc/generic-genome-browser-1.68/README.fedora.bz2
/usr/share/doc/generic-genome-browser-1.68/README.gff3.bz2
/usr/share/doc/generic-genome-browser-1.68/README.sessions.bz2
/usr/share/doc/generic-genome-browser-1.68/TODO.bz2
/usr/share/generic-genome-browser-1.68
/usr/share/generic-genome-browser-1.68/tutorial
/var
/var/www
/var/www/localhost
/var/www/localhost/cgi-bin
/var/www/localhost/htdocs
#

[Comment 1 Martin Mokrejš 2009-01-07 21:45:43 UTC]

# emerge --info
Portage 2.1.6.4 (default/linux/x86/2008.0/desktop, gcc-4.3.2, glibc-2.9_p20081201-r1, 2.6.27.7 i686)
=================================================================
System uname: Linux-2.6.27.7-i686-Mobile_Intel-R-_Pentium-R-_4_-_M_CPU_1.80GHz-with-glibc2.0
Timestamp of tree: Sat, 03 Jan 2009 12:20:01 +0000
distcc 3.1 i686-pc-linux-gnu [disabled]
app-shells/bash:     3.2_p48
dev-java/java-config: 1.3.7-r1, 2.1.6-r1
dev-lang/python:     2.5.2-r8
dev-python/pycrypto: 2.0.1-r6
dev-util/cmake:      2.6.2
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.4.1-r1
sys-apps/sandbox:    1.3.2
sys-devel/autoconf:  2.13, 2.63
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
sys-devel/binutils:  2.19
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.28-r1
ACCEPT_KEYWORDS="x86 ~x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /var/bind /var/qmail/alias /var/qmail/control /var/spool/torque /var/vpopmail/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz"
LDFLAGS="-Wl,-O1"
LINGUAS="en cs cz"
PKGDIR="/usr/portage/packages"
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/layman/sunrise /usr/local/portage/layman/science /usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="7zip R X Xaw3d a52 aac aalib ace acl acpi alsa amr amrnb amrwb apache2 audacious audiofile bash-completion bcmath berkdb blas bluetooth boost branding bzip2 cairo cblas cddb cdparanoia cdr clamav cli colordiff compress cpio cracklib crypt cscope css ctype cups curl curlwrappers cxx dbus dga dia directfb djbfft dri dts dv dvb dvd dvdr dvdread eds emacs emboss emf enblend encode enscript exif expat fam fame fat fbcon ffmpeg fftw firefox flac flash foomaticdb fortran fpx ftp gcj gd gdbm ggi gif gimp gimpprint glibc-compat20 glibc-omitfp glitz glut gmp gnuplot gnutls gpgme gphoto2 gpm graphviz gs gsl gstreamer gtk gtkhtml hal hdf hdf5 hp2xx i8x0 icc iconv icu id3 ieee1394 ifc imagemagick imlib inifile innodb isdnlog ithreads jack java javascript jbig jce jikes jpeg jpeg2k kdtree kerberos lame lapack laptop lcms leim libcaca libedit libnotify libwww live lzo lzw mad maildir matroska mhash midi mikmod mime ming mjpeg mmap mmx mng mod_python modperl modplug motif mozilla moznoirc mp2 mp3 mp4 mpeg mpi mpi_njtree mpich2 mplayer mudflap mule musepack mxdatetime mysql mysqli ncurses netcdf netpbm network nls nntp nptl nptlonly nsplugin ntfs numeric ogg opengl openmp pam pango pcmcia pcntl pcre pdf perl plotutils plugin png pnm postproc postscript ppds pppd procmail pymol python qt3 qt3support qt4 quicktime rar raw readline recode reflection reiserfs rpm samba sasl scanner scp seamonkey server session sftp sift slp smime sndfile soap sockets spell spl sqlite srt sse sse2 ssl startup-notification subtitles subversion svg svgz sysfs sysvipc t1lib tcl tcpd tetex theora threads tidy tiff tk transcode truetype unicode urandom usb userlocales uuencode v4l v4l2 vcd vhook vim-syntax vim-with-x vorbis wifi win32codecs wmf wxwindows x264 x86 xanim xcf xfs xft xinerama xinetd xml xorg xpm xprint xsl xslt xulrunner xv xvid xvmc yv12 zip zlib" ALSA_CARDS="intel-8x0m" 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 dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config mem_cache mime mime_magic rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" USERLAND="GNU" VIDEO_CARDS="radeon"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 2 Jeroen Roovers (RETIRED) 2009-01-08 15:38:11 UTC]

Please specify from which overlay you tried to emerge sci-biology/generic-genome-browser - it's not in the official tree.

[Comment 3 Martin Mokrejš 2009-01-08 16:18:47 UTC]

# head layman/science/sci-biology/generic-genome-browser/generic-genome-browser-1.68.ebuild 
# Copyright 1999-2007 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $

inherit perl-app

MY_PN="Generic-Genome-Browser"

# I don't know if the '--' is a typo... TODO contact somebody and find out.
MY_P="${MY_PN}--${PV}"

[Comment 4 Martin Mokrejš 2009-01-19 23:52:59 UTC]

Created attachment 179056 [details]
generic-genome-browser/generic-genome-browser-1.69.ebuild

Fix the typo and correct bioperl-1.5.2 requirement.

[Comment 5 Martin Mokrejš 2009-01-22 18:31:43 UTC]

(In reply to comment #2)
> Please specify from which overlay you tried to emerge
> sci-biology/generic-genome-browser - it's not in the official tree.
> 

I used the  "old" overlay:

The source of the overlay "science" seems to have changed. You currently sync
from "http://overlays.gentoo.org/svn/proj/science/overlay" while the global
layman list reports "git://git.overlays.gentoo.org/proj/sci.git" as correct
location. Please consider removing and readding the overlay!

[Comment 6 Andrey Kislyuk (RETIRED) 2009-10-11 23:28:30 UTC]

Please test with 1.70 and open new bugs as I rewrote it