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Bug 540314 - sci-libs/scipy-0.14.0-r1 with dev-python/cython-0.22 - python3_4: running distutils-r1_run_phase python_compile: Error compiling Cython file: ...
Summary: sci-libs/scipy-0.14.0-r1 with dev-python/cython-0.22 - python3_4: running dis...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Library (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords: PATCH
Depends on:
Blocks:
 
Reported: 2015-02-16 21:59 UTC by Denys Duchier
Modified: 2015-02-19 08:30 UTC (History)
2 users (show)

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


Attachments
fix for the problem (tell.patch,843 bytes, patch)
2015-02-16 21:59 UTC, Denys Duchier
Details | Diff
build.log (build.log,4.77 KB, text/plain)
2015-02-17 20:06 UTC, Denys Duchier
Details

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Description Denys Duchier 2015-02-16 21:59:01 UTC
Created attachment 396626 [details, diff]
fix for the problem

an incoherence in method tell profile/implementation causes a cython compilation error.
Comment 1 Jeroen Roovers (RETIRED) gentoo-dev 2015-02-17 08:12:31 UTC
1) Please post your `emerge --info' output in a comment.
2) Please attach the entire build log to this bug report.
Comment 2 Denys Duchier 2015-02-17 20:04:37 UTC
Portage 2.2.17 (python 2.7.9-final-0, default/linux/amd64/13.0/desktop/kde, gcc-4.9.2, glibc-2.20-r1, 3.19.0-gentoo x86_64)
=================================================================
System uname: Linux-3.19.0-gentoo-x86_64-Intel-R-_Core-TM-_i7-3520M_CPU_@_2.90GHz-with-gentoo-2.2
KiB Mem:     8038192 total,   4880652 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Tue, 17 Feb 2015 19:30:01 +0000
sh bash 4.3_p33-r1
ld GNU ld (Gentoo 2.25 p1.0) 2.25
app-shells/bash:          4.3_p33-r1::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.9-r2::gentoo, 3.4.2::gentoo
dev-util/cmake:           3.1.0::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.13.9::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.69::gentoo
sys-devel/automake:       1.11.6-r1::gentoo, 1.12.6::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25::gentoo
sys-devel/gcc:            4.7.4::gentoo, 4.9.2::gentoo
sys-devel/gcc-config:     1.8::gentoo
sys-devel/libtool:        2.4.6::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 3.19::gentoo (virtual/os-headers)
sys-libs/glibc:           2.20-r1::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

cvut-iut45
    location: /var/lib/layman/cvut-iut45
    masters: gentoo
    priority: 0

haskell
    location: /var/lib/layman/haskell
    masters: gentoo
    priority: 1

x11
    location: /var/lib/layman/x11
    masters: gentoo
    priority: 2

gamerlay
    location: /var/lib/layman/gamerlay
    masters: gentoo
    priority: 3

steam-overlay
    location: /var/lib/layman/steam
    masters: gentoo
    priority: 4

qt
    location: /var/lib/layman/qt
    masters: gentoo
    priority: 5

duchier
    location: /usr/local/portage
    masters: gentoo
    priority: 6

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.2/conf /usr/share/themes/oxygen-gtk/gtk-3.0"
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=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirrors.linuxant.fr/distfiles.gentoo.org/ http://gentoo.modulix.net/gentoo/ http://mirror.ovh.net/gentoo-distfiles/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi aes alsa amd64 avx berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli clucene consolekit cracklib crypt cups cxx dbus declarative device-mapper dri dts dvd dvdr emacs emboss encode excel exif expat extraengine fam farstream firefox flac fontconfig fortran gadu gbm gdbm gif glamor gmp gnuplot gnutls google gpm gtk gudev hscolour hwdb iconv icu imagemagick inotify ipv6 jpeg jpeg2k json kde kipi lcms ldap libav libkms libnotify libv4l libxml2 lzma mad matroska mmx mmxext mng modules mp3 mp4 mpeg msn multilib musicbrainz ncurses nls nptl nscd nsplugin odbc ogg opengl openmp oscar otr pam pango pcre pdf phonon plasma png policykit popcnt ppds qalculate qt3support qt4 qtwebkit readline sdl semantic-desktop session skype spell sqlite sse sse2 sse3 sse4 sse4_1 sse4_2 ssl ssse3 startup-notification svg tcpd telepathy theora threads tiff truetype udev udisks unicode upower usb uxa v4l vaapi vcd vdpau vorbis vpx webkit webpresence wxwidgets x264 xattr xcb xcomposite xinerama xml xorg xscreensaver xv xvid xvmc yahoo 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" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3 sse4" 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 ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en fr" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel" 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"
USE_PYTHON="2.7 3.4"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 3 Denys Duchier 2015-02-17 20:06:42 UTC
Created attachment 396746 [details]
build.log
Comment 4 Juergen Rose 2015-02-18 13:25:16 UTC
I have the same issue.
Comment 5 Juergen Rose 2015-02-18 23:19:19 UTC
The fix of the first posting solved also the problem for me.
Comment 6 Justin Lecher (RETIRED) gentoo-dev 2015-02-19 08:30:24 UTC
+*scipy-0.15.0 (19 Feb 2015)
+
+  19 Feb 2015; Justin Lecher <jlec@gentoo.org> +scipy-0.15.0.ebuild:
+  Version BUmp; fixes problems with newer cython, #540314
+