Bugzilla Bug 153774

I would appreciate if all supporting arches (alpha, ppc, sparc, x86) would
stabilise sci-biology/biopython-1.42. It has been in Portage for a while and
works well. (I use it in my daily work.)

amd64:

Biopython has never been marked stable on amd64. If you would rather not
support it in the stable branch, feel free to remove your team from CC.

SPARC Stable

Stable on ppc

Emerges fine on amd64, and the various .so modules import just fine.

Gentoo Base System version 1.12.5
Portage 2.1.1-r1 (default-linux/amd64/2006.1, gcc-4.1.1, glibc-2.4-r3,
2.6.15-gentoo-r72006040301 x86_64)
=================================================================
System uname: 2.6.15-gentoo-r72006040301 x86_64 AMD Athlon(tm) 64 Processor
3700+
Last Sync: Wed, 01 Nov 2006 21:50:01 +0000
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: [Not Present]
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, 2.60
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:  2.6.11-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig collision-protect confcache digest distlocks
metadata-transfer multilib-strict sandbox sfperms strict"
GENTOO_MIRRORS="http://gentoo.chem.wisc.edu/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"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.us.gentoo.org/gentoo-portage"
USE="amd64 berkdb bitmap-fonts cli cracklib crypt cups dlloader dri elibc_glibc
fortran gdbm gpm iconv input_devices_evdev input_devices_keyboard
input_devices_mouse ipv6 isdnlog kernel_linux libg++ ncurses nls nptl nptlonly
pam pcre perl ppds pppd python readline reflection session spl ssl tcpd
truetype-fonts type1-fonts udev unicode userland_GNU 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_i810 video_cards_mga video_cards_neomagic
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 xorg zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
LINGUAS, MAKEOPTS, PORTAGE_RSYNC_EXTRA_OPTS

1. emerges on x86
2. passes collision test
3. importing of these packages works fine, but don't know what to do with them

sci-biology/biopython-1.42

Portage 2.1.1-r1 (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 1.12.6
Last Sync: Thu, 02 Nov 2006 15:50:01 +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, 2.60
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://mirror.switch.ch/mirror/gentoo/ http://gentoo.inode.at/"
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 iconv 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

Emerges and works fine on amd64 with

FEATURES="sandbox cvs collision-protect digest multilib-strict strict maketest"

maketest has been deprecated long time ago, use FEATURES=test

keyworded amd64 nevertheless ;)

x86 always has love for poor animals without legs

*** mxTextTools *** is either not installed or out of date.

I get this error when building biopython. This should be in the dependency in
the ebuild.

Hi Saurabh,

The mxTextTools are already a dependency of BioPython (as
dev-python/egenix-mx-base). I guess you are using an outdated version of this
package. Please report whether updating egenix-mx-base solves your problem.
Also, please open a separate bug report if the issue persists (unless this is
related to stabilisation on the alpha architecture).

alpha stable, closing.