Bug 153325

Summary:	sci-biology/generic-genome-browser removal request (was: 1.58 installed in ${D}/${D})
Product:	Gentoo Linux	Reporter:	Tao Zhang <forrest_zhang>
Component:	New packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	VERIFIED FIXED
Severity:	normal	CC:	jakub
Priority:	High	Keywords:	PMASKED
Version:	unspecified
Hardware:	x86
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Tao Zhang 2006-10-29 11:18:51 UTC

Portage 2.1.2_rc1-r1 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.5-r0, 2.6.17-gentoo-r8 i686)
=================================================================
System uname: 2.6.17-gentoo-r8 i686 Intel(R) Pentium(R) 4 CPU 2.40GHz
Gentoo Base System version 1.12.5
Last Sync: Sun, 29 Oct 2006 15:30:01 +0000
ccache version 2.3 [enabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.3.7, 2.0.30
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.3
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.60
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
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r1
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=prescott -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-O2 -march=prescott -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="ftp://ftp.sjtu.edu.cn/gentoo ftp://ftp.isu.edu.tw/pub/Linux/Gentoo "
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X alsa apache2 arts berkdb bitmap-fonts cairo cdr cli cracklib crypt cups dbus dlloader dri dvd dvdr eds elibc_glibc emacs emboss encode esd fam firefox fortran gdbm gif gnome gpm gstreamer hal iconv imap input_devices_evdev input_devices_keyboard input_devices_mouse isdnlog java jpeg kde kernel_linux ldap libg++ libwww mad maildir mikmod mmx mozilla mp3 mpeg mysql ncurses nls nptl nptlonly ogg opengl oss pam pcre perl php png postgres ppds pppd python qt qt3 qt4 quicktime readline reflection sasl sdl see2 server session spell spl sse ssl tcpd truetype truetype-fonts type1-fonts udev unicode userland_GNU vda video_cards_apm video_cards_ark video_cards_ati video_cards_chips video_cards_cirrus video_cards_cyrix video_cards_dummy video_cards_fbdev video_cards_glint video_cards_i128 video_cards_i740 video_cards_i810 video_cards_imstt video_cards_mga video_cards_neomagic video_cards_nsc video_cards_nv video_cards_rendition video_cards_s3 video_cards_s3virge video_cards_savage video_cards_siliconmotion video_cards_sis video_cards_sisusb video_cards_tdfx video_cards_tga video_cards_trident video_cards_tseng video_cards_v4l video_cards_vesa video_cards_vga video_cards_via video_cards_vmware video_cards_voodoo vorbis win32codecs xml xorg xv zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

Comment 1 Tao Zhang 2006-10-29 11:20:27 UTC

the error


QA Notice: //usr/share/man/man1/process_sgd.pl.1 installed in ${D}/${D}
QA Notice: //usr/share/man/man1/process_gadfly.pl.1 installed in ${D}/${D}
QA Notice: //usr/share/man/man3 installed in ${D}/${D}
QA Notice: //usr/bin installed in ${D}/${D}
QA Notice: //usr/bin/process_wormbase.pl installed in ${D}/${D}
QA Notice: //usr/bin/process_ncbi_human.pl installed in ${D}/${D}
QA Notice: //usr/bin/load_genbank.pl installed in ${D}/${D}
QA Notice: //usr/bin/process_sgd.pl installed in ${D}/${D}
QA Notice: //usr/bin/process_gadfly.pl installed in ${D}/${D}

!!! ERROR: sci-biology/generic-genome-browser-1.58 failed.
Call stack:
  misc-functions.sh, line 439:   Called install_qa_check
  misc-functions.sh, line 181:   Called die

!!! Aborting due to QA concerns: 78 files installed in /var/tmp/portage/sci-biology/generic-genome-browser-1.58/image///var/tmp/portage/sci-biology/generic-genome-browser-1.58/image/
!!! If you need support, post the topmost build error, and the call stack if relevant.

!!! install_qa_check failed; exiting.

Comment 2 Jakub Moc (RETIRED) gentoo-dev

2006-10-29 11:30:10 UTC

Not a portage bug.

Comment 3 Tao Zhang 2006-10-29 17:28:49 UTC

(In reply to comment #2)
> Not a portage bug.
> 

what kind of bug it is? Could you tell me something in detail.
Thank you.

Comment 4 Olivier Fisette (RETIRED) gentoo-dev

2006-10-30 06:18:02 UTC

Package masked until this and bug #54607 are fixed.

Hi Tao,

This is a bug in the Portage tree, so it falls under the Gentoo Linux category. The Portage category is for bugs in Portage itself (the package manager). Thanks for reporting this bug.

Comment 5 Jakub Moc (RETIRED) gentoo-dev

2008-02-03 03:18:10 UTC

# Olivier Fisette <ribosome@gentoo.org> (30 Oct 2006)
# Masked until bugs #153325 and #54607 are fixed.
sci-biology/generic-genome-browser

Well, please punt this bitrot from the tree, it's not like it'd be going anywhere.

Comment 6 Jeffrey Gardner (RETIRED) gentoo-dev

2008-02-03 04:39:17 UTC

Moved to the dungheap^H^H^H^H^H^H^H^H science overlay for some love.

Comment 7 Jakub Moc (RETIRED) gentoo-dev

2008-02-03 08:19:00 UTC

LOL... thanks.