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Bug 473530 - sci-libs/scikits_image USE=umfpack - circular dependency
Summary: sci-libs/scikits_image USE=umfpack - circular dependency
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Library (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2013-06-16 23:55 UTC by Horea Christian
Modified: 2013-06-19 15:43 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


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Description Horea Christian 2013-06-16 23:55:00 UTC
The umfpack USE flag does no longer exist for newer sci-libs/scipy versions (after 0.11.0-r1), but the newest sci-libs/scikits_image still requires it.

Here's a paste of my emerge attempt
Comment 1 Jeroen Roovers (RETIRED) gentoo-dev 2013-06-17 10:56:47 UTC
1) Please post your `emerge --info' output in a comment.
2) Please attach the entire build log to this bug report[1].

[1] And please do not use external paste sites. We have this bug tracker for that.
Comment 2 Horea Christian 2013-06-17 23:17:16 UTC
my emerge --info 

Portage (default/linux/amd64/13.0/desktop/gnome, gcc-4.7.3, glibc-2.17, 3.9.4-gentoo x86_64)
System uname: Linux-3.9.4-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_@_2.40GHz-with-gentoo-2.2
KiB Mem:     5094980 total,    191160 free
KiB Swap:    2097148 total,   1942676 free
Timestamp of tree: Sun, 16 Jun 2013 20:00:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5, 3.2.5, 3.3.2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.13.2
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.7.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo science
ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=nocona -O2 -pipe"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=nocona -O2 -pipe"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync metadata-transfer news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr eds emboss encode evo exif fam fat flac fortran gconf gdbm gif gimp gnome gnome-online-accounts gnutls gpm gstreamer gtk iconv imap ipv6 jpeg lcms libnotify libsecret mad mmkeys mmx mng modules mp3 mp4 mpeg mudflap multilib nautilus ncurses nls nptl ntfs ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio readline sdl session socialweb spell sse sse2 ssl startup-notification svg tcpd tiff trayicon truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xulrunner xv xvid zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en ru ro fr" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Comment 3 Horea Christian 2013-06-18 00:06:21 UTC
my full "emerge -av scikits_image" output:

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N     ] sci-libs/suitesparseconfig-4.0.2  USE="-static-libs" 0 kB
[ebuild  N     ] sci-libs/colamd-2.8.0  USE="-static-libs" 0 kB
[ebuild  N     ] sci-libs/amd-2.3.1  USE="fortran -doc -static-libs" 0 kB
[ebuild  N     ] sci-libs/cholmod-2.0.1  USE="-cuda -doc -lapack -metis -minimal -static-libs" 0 kB
[ebuild  N     ] sci-libs/umfpack-5.6.1-r1  USE="cholmod -doc -static-libs" 0 kB
[ebuild     UD ] sci-libs/scipy-0.11.0-r1 [0.12.0] USE="umfpack%* -doc {-test} (-sparse%)" PYTHON_TARGETS="python2_7 -python2_5 -python2_6 (-python3_2%*) (-python3_3%)" 0 kB
[ebuild  N     ] sci-libs/scikits_image-0.8.2  USE="gtk -doc -freeimage -qt4 {-test}" PYTHON_TARGETS="python2_7 -python2_6" 0 kB

Total: 7 packages (1 downgrade, 6 new), Size of downloads: 0 kB

!!! Multiple package instances within a single package slot have been pulled
!!! into the dependency graph, resulting in a slot conflict:


  (sci-libs/scipy-0.12.0::gentoo, installed) pulled in by
    sci-libs/scipy[python_targets_python2_6(-)?,python_targets_python2_7(-)?,python_targets_python3_2(-)?,-python_single_target_python2_6(-),-python_single_target_python2_7(-),-python_single_target_python3_2(-)] required by (dev-python/pandas-0.11.0::gentoo, installed)
    sci-libs/scipy[python_targets_python2_6(-)?,python_targets_python2_7(-)?,python_targets_python3_2(-)?,python_targets_python3_3(-)?,-python_single_target_python2_6(-),-python_single_target_python2_7(-),-python_single_target_python3_2(-),-python_single_target_python3_3(-)] required by (dev-python/bottleneck-0.6.0::gentoo, installed)
    sci-libs/scipy[python_targets_python2_6(-)?,python_targets_python2_7(-)?,python_targets_python3_2(-)?,python_targets_python3_3(-)?,-python_single_target_python2_6(-),-python_single_target_python2_7(-),-python_single_target_python3_2(-),-python_single_target_python3_3(-)] required by (sci-libs/scikits_learn-0.13.1::gentoo, installed)

  (sci-libs/scipy-0.11.0-r1::gentoo, ebuild scheduled for merge) pulled in by
    sci-libs/scipy[umfpack,python_targets_python2_6(-)?,python_targets_python2_7(-)?,-python_single_target_python2_6(-),-python_single_target_python2_7(-)] required by (sci-libs/scikits_image-0.8.2::gentoo, ebuild scheduled for merge)

It may be possible to solve this problem by using package.mask to
prevent one of those packages from being selected. However, it is also
possible that conflicting dependencies exist such that they are
impossible to satisfy simultaneously.  If such a conflict exists in
the dependencies of two different packages, then those packages can
not be installed simultaneously. You may want to try a larger value of
the --backtrack option, such as --backtrack=30, in order to see if
that will solve this conflict automatically.

For more information, see MASKED PACKAGES section in the emerge man
page or refer to the Gentoo Handbook.
Comment 4 Jeroen Roovers (RETIRED) gentoo-dev 2013-06-19 10:31:43 UTC
  17 Jun 2013; Sébastien Fabbro <>
  -scikits_image-0.7.2-r2.ebuild, scikits_image-0.8.2.ebuild:
  Call scipy with sparse flag instead of umfpack. Fixed python-2 only dependency
  for pygtk
Comment 5 Sébastien Fabbro (RETIRED) gentoo-dev 2013-06-19 15:43:28 UTC
it was probably fixed inbetween two syncs.
please try again and re-open if the bug persists.
thanks for the report