Bug 152292 - stabilization request for sci-biology/ncbi-tools-20060507
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Bug#:
152292
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Product: Gentoo Linux
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Version: 2006.1
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Platform: All
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OS/Version: Linux
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Status: RESOLVED
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Severity: normal
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Priority: P2
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Resolution: FIXED
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Assigned To: alpha@gentoo.org
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Reported By: je_fro@gentoo.org
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Component: Applications
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URL:
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Summary: stabilization request for sci-biology/ncbi-tools-20060507
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Keywords:
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Status Whiteboard:
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Opened: 2006-10-21 13:15 0000
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sci-biology/ncbi-tools-20060507 is ready for stabilization and will fix bug
152114.
please stabilize on amd64 and x86
thanks!
x86:
1) Emerged fine
2) Passed FEATURES="collision-protect"
3) GUI programs seemed to function as intended, couldn't perform extensive
tests as I have no idea what this program does or how to use it.
mark@rockley ~ $ emerge --info
Portage 2.1.1 (default-linux/x86/2006.1, gcc-4.1.1, glibc-2.4-r3,
2.6.17-gentoo-r4 i586)
=================================================================
System uname: 2.6.17-gentoo-r4 i586 AMD-K6(tm) 3D processor
Gentoo Base System version 1.12.5
Last Sync: Sun, 22 Oct 2006 00:50:01 +0000
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.3.7, 2.0.30
dev-lang/python: 2.3.5-r2, 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-r4
sys-devel/libtool: 1.5.22
virtual/os-headers: 2.6.17-r1
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i586-pc-linux-gnu"
CFLAGS="-O2 -march=k6-2 -pipe"
CHOST="i586-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 /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-O2 -march=k6-2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig collision-protect distlocks metadata-transfer
parallel-fetch sandbox sfperms strict test"
GENTOO_MIRRORS="ftp://ftp.swin.edu.au/gentoo http://ftp.swin.edu.au/gentoo "
LINGUAS=""
MAKEOPTS="-j2"
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://192.168.0.145/gentoo-portage"
USE="x86 3dnow X alsa berkdb bitmap-fonts cli cracklib crypt cups dlloader dri
elibc_glibc foomaticdb fortran gdbm gpm gtk gtk2 input_devices_keyboard
input_devices_mouse ipv6 isdnlog kernel_linux libg++ ncurses nls nptl nptlonly
pam pcre perl ppds pppd python readline reflection samba session spl ssl tcpd
test truetype-fonts type1-fonts udev unicode userland_GNU video_cards_nv xorg
zlib"
Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
PORTAGE_RSYNC_EXTRA_OPTS
[ebuild N ] sci-biology/ncbi-tools-20060507 USE="X -doc -mpi"
1) emerges fine
2) passes collision test
3) works
Portage 2.1.1 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r3,
2.6.17-gentoo-r8 i686)
=================================================================
System uname: 2.6.17-gentoo-r8 i686 AMD Athlon(tm) XP 2500+
Gentoo Base System version 1.12.5
Last Sync: Sun, 22 Oct 2006 05:50:01 +0000
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: [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-r4
sys-devel/libtool: 1.5.22
virtual/os-headers: 2.6.17-r1
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2"
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 /usr/share/config
/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/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-O2"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache collision-protect distlocks metadata-transfer
parallel-fetch sandbox sfperms strict test"
GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/"
LANG="de_DE@euro"
LC_ALL="de_DE@euro"
LINGUAS="de"
MAKEOPTS="-j2"
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.informatik.rwth-aachen.de/gentoo-portage"
USE="x86 3dnow 3dnowext X Xaw3d a52 aiglx alsa artworkextra asf audiofile
bash-completion beagle berkdb bidi bitmap-fonts bootsplash branding bzip2 cairo
cdda cddb cdparanoia cdr cli cracklib crypt css cups curl custom-cflags dbus
dga directfb divx4linux dlloader dri dts dvd dvdr dvdread dvi eds elibc_glibc
emacs emboss encode esd evo exif expat fam fat fbcon ffmpeg firefox fortran ftp
gb gcj gdbm gif gnome gpm gstreamer gtk gtk2 gtkhtml hal icq idn imagemagick
imap input_devices_keyboard input_devices_mouse ipv6 isdnlog java javascript
jikes jpeg jpeg2k kde kernel_linux ldap leim libg++ linguas_de lm_sensors mad
maildir matroska mbox mhash mikmod mime mmx mmxext mng mono mp3 mpeg mpeg2 mule
mysql nautilus ncurses nforce2 nls nocardbus nptl nptlonly nsplugin nvidia objc
ogg opengl pam pcre pdf perl plotutils pmu png ppds pppd preview-latex print
python qt3 qt4 quicktime readline reflection reiserfs samba sdk session slang
spell spl sse ssl svg svga t1lib tcltk tcpd tetex theora thunderbird tiff
truetype truetype-fonts type1-fonts udev usb userland_GNU vcd video_cards_fbdev
video_cards_radeon video_cards_vesa videos vorbis win32codecs wmf wxwindows
xine xml xorg xosd xv xvid zlib"
Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS,
PORTAGE_RSYNC_EXTRA_OPTS
1. emerges on x86
2. passes collision test
3. seems to work
sci-biology/ncbi-tools-20060507 USE="X -doc -mpi"
Portage 2.1.1 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r3,
2.6.18.1 i686)
=================================================================
System uname: 2.6.18.1 i686 Genuine Intel(R) CPU T2300 @ 1.66GHz
Gentoo Base System version 1.12.5
Last Sync: Sun, 22 Oct 2006 09:50:01 +0000
ccache version 2.3 [disabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.3.7, 2.0.30
dev-lang/python: 2.3.5-r3, 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, 2.59-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-r4
sys-devel/libtool: 1.5.22
virtual/os-headers: 2.6.17-r1
ACCEPT_KEYWORDS="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 /usr/share/config
/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/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"
EMERGE_DEFAULT_OPTS="--nospinner"
FEATURES="autoconfig collision-protect distlocks metadata-transfer
parallel-fetch sandbox sfperms strict test userfetch userpriv usersandbox"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LINGUAS="en de en_GB de_CH"
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"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="x86 X a52 aac acpi alsa apache2 asf berkdb bitmap-fonts cairo cdr cdrom
cli cracklib crypt cups dbus divx dlloader dri dts dvd dvdr dvdread eds
elibc_glibc emboss encode fam ffmpeg firefox flac fortran gdbm gif gnome gpm
gstreamer gtk hal input_devices_keyboard input_devices_mouse ipv6 isdnlog java
jpeg kde kernel_linux ldap libg++ linguas_de linguas_de_CH linguas_en
linguas_en_GB mad mikmod mmx mono mp3 mpeg ncurses nls nptl nptlonly ogg opengl
oss pam pcre perl png ppds pppd python qt3 qt4 quicktime readline reflection
rtsp samba sdl session smp spell spl sse sse2 sse3 ssl svg tcpd test tetex
theora threads truetype truetype-fonts type1-fonts udev unicode userland_GNU
vcd video_cards_fbdev video_cards_i810 video_cards_vesa vorbis win32codecs
wxwindows x264 xine xml xorg xprint xv xvid zlib"
Unset: CTARGET, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS,
PORTDIR_OVERLAY
CC'ing missing arches which might be interested in stabilising too.
Dropped ppc-macos, we don't have pmake
emerge --info @ http://diox.swords.be/at/emerge-info-diox
1) emerges fine
2) passes collision test
3) Haven't tested.
[ebuild R ] sys-devel/pmake-1.111.1 284 kB
[ebuild R ] sys-cluster/mpich-1.2.7_p1 USE="crypt -doc" 15,604 kB
[ebuild R ] virtual/mpi-1.0 0 kB
[ebuild R ] sci-biology/ncbi-tools-20060507 USE="X mpi -doc" 15,196 kB
grobian, ppc-macos:
Maybe you would like to stabilise 20050605-r2, then. Unlike the current stable
version on pcc-macos (20050605), it has a file collision fix for
dev-libs/libpcre (available on pcc-macos).
Looks like 20060507 tries to install outside of the build image:
>>> Install ncbi-tools-20060507 into /Library/Gentoo/var/tmp/portage/sci-biology/ncbi-tools-20060507/image/Library/Gentoo/ category sci-biology
install: cannot create directory `/usr/share/doc/ncbi-tools-20060507':
Permission denied
install: cannot create regular file
`/usr/share/doc/ncbi-tools-20060507/html///README.htm': No such file or
directory
install: cannot create directory `/usr/share/doc/ncbi-tools-20060507':
Permission denied
install: cannot create regular file
`/usr/share/doc/ncbi-tools-20060507/html///dispatcher.html': No such file or
directory
install: cannot create directory `/usr/share/doc/ncbi-tools-20060507':
Permission denied
install: cannot create regular file
`/usr/share/doc/ncbi-tools-20060507/html///firewall.html': No such file or
directory
install: cannot create directory `/usr/share/doc/ncbi-tools-20060507':
Permission denied
install: cannot create regular file
`/usr/share/doc/ncbi-tools-20060507/html///firedialog.gif': No such file or
directory
The rest of the install looks fine to me. I added this version to the prefix,
in which we do have pmake now. Hence, I dropped ppc-macos for ncbi-tools, it's
now in prefix.
Thanks a lot anyway!
alpha: Prod.
osx: See you in prefix, then. Removing CC.
alpha? you guys interested?
alpha stable, sorry for the delay.
Closing.
