Bug 155780 – sci-biology/ucsc-genome-browser (new ebuild)

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description dawe 2006-11-20 08:49:43 UTC]

This is an ebuild to compile UCSC genome browser.

# emerge --info
Portage 2.1.1-r1 (default-linux/alpha/no-nptl/2.4, gcc-3.4.6, glibc-2.3.5-r3, 2.4.30 alpha)
=================================================================
System uname: 2.4.30 alpha EV68CB
Gentoo Base System version 1.6.15
Last Sync: Mon, 23 Oct 2006 12:30:01 +0000
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: [Not Present]
dev-lang/python:     2.3.5, 2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r7
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.13-r3
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.4.26-r1
ACCEPT_KEYWORDS="alpha"
AUTOCLEAN="yes"
CBUILD="alphaev67-unknown-linux-gnu"
CFLAGS="-mieee -mcpu=ev67 -Wa,-mev6 -O3 -pipe "
CHOST="alphaev67-unknown-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-mieee -mcpu=ev67 -Wa,-mev6 -O3 -pipe "
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
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"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="alpha apache2 arts berkdb bitmap-fonts cli cracklib crypt cups dlloader dri eds elibc_glibc encode esd foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 imlib input_devices_keyboard input_devices_mouse ipv6 isdnlog jpeg kde kernel_linux libg++ libwww mad mikmod motif mp3 mpeg mysql ncurses nls ogg opengl oss pam pcre perl png pppd python qt3 quicktime readline reflection sdl session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts userland_GNU video_cards_ati video_cards_cirrus video_cards_dummy video_cards_fbdev video_cards_glint video_cards_mga video_cards_nv video_cards_rendition video_cards_s3 video_cards_s3virge video_cards_savage video_cards_siliconmotion video_cards_sisusb video_cards_tdfx video_cards_tga video_cards_v4l video_cards_vga video_cards_voodoo vorbis xml xorg xv zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 dawe 2006-11-20 08:53:04 UTC]

Created attachment 102407 [details]
the ebuild for sci-biology/ucsc-genome-browser

I've added three USE variables:
minimal: to build only four executables, the minimum necessary
strict: since the flag -Werror in the makefile is pretty annoying, I've set to exclude unless specified
www: so that one can compile also cgi executables for complete mirroring of UCSC genome browser

The real problem is that the sources are released without versioning info. I've wrote to UCSC guys if they can add this to their zip files. The ebuild is for version 146 that is the latest released.

[Comment 2 dawe 2006-11-20 08:54:24 UTC]

*** Bug 155779 has been marked as a duplicate of this bug. ***

[Comment 3 dawe 2006-11-20 08:54:24 UTC]

*** Bug 155778 has been marked as a duplicate of this bug. ***

[Comment 4 dawe 2008-01-22 13:58:42 UTC]

app-arch/unzip should be added as DEPENDS

[Comment 5 Jeremy Olexa (darkside) (RETIRED) 2009-03-26 03:05:30 UTC]

(this is an automated message based on filtering criteria that matched this bug)
'EBUILD' is in the KEYWORDS which should mean that there is a ebuild attached 
to this bug.
This bug is assigned to maintainer-wanted which means that it is not in the 
main tree.
Heuristics show that no Gentoo developer has commented on your ebuild.

Hello, The Gentoo Team would like to firstly thank you for your ebuild 
submission. We also apologize for not being able to accommodate you in a timely
manner. There are simply too many new packages.

Allow me to use this opportunity to introduce you to Gentoo Sunrise. The 
sunrise overlay[1] is a overlay for Gentoo which we allow trusted users to 
commit to and all users can have ebuilds reviewed by Gentoo devs for entry 
into the overlay. So, the sunrise team is suggesting that you look into this 
and submit your ebuild to the overlay where even *you* can commit to. =)

Because this is a mass message, we are also asking you to be patient with us. 
We anticipate a large number of requests in a short time. 

Thanks,
On behalf of the Gentoo Sunrise Team,
Jeremy.

[1]: http://www.gentoo.org/proj/en/sunrise/
[2]: http://overlays.gentoo.org/proj/sunrise/wiki/SunriseFaq

[Comment 6 Andrey Kislyuk (RETIRED) 2009-10-24 03:32:31 UTC]

In Science overlay, please test

[Comment 7 Andrey Kislyuk (RETIRED) 2009-10-29 12:31:04 UTC]

In main tree

[Comment 8 Martin Mokrejš 2009-10-29 17:28:37 UTC]

(In reply to comment #6)
> In Science overlay, please test
> 

Sorry, will take me a while to test. But thanks for your effort! ;)

[Comment 9 Martin Mokrejš 2009-11-06 15:31:05 UTC]

On one amd64 machine it emerged for me virtual/httpd-cgi-0 although I had apache installed. Looks due to my USE=server flag.

[Comment 10 Andrey Kislyuk (RETIRED) 2009-11-06 16:49:18 UTC]

that's by design, it allows the use of other servers, although i haven't tested that part yet