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Bug 471850 - dev-python/numexpr-2.1 - src_compile(): File "/usr/lib64/python3.2/site-packages/numpy/distutils/exec_command.py", line 197, in exec_command if _with_python and (0 or sys.__stdout__.fileno()==-1): ValueError: underlying buffer has been detached
Summary: dev-python/numexpr-2.1 - src_compile(): File "/usr/lib64/python3.2/site-packa...
Status: RESOLVED TEST-REQUEST
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Development (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Python Gentoo Team
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2013-05-30 22:28 UTC by Crayzee Wulf
Modified: 2013-07-20 16:47 UTC (History)
4 users (show)

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

Attachments
Outputs of commands mentioned in the description. (emerge_info.txt,141.63 KB, text/plain)
2013-05-30 22:28 UTC, Crayzee Wulf 		Details
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Description Crayzee Wulf 2013-05-30 22:28:38 UTC 
Created attachment 349688 [details]
Outputs of commands mentioned in the description.

Package dev-python/numexpr-2.1 fails to build on 64-bit platform. Outputs of the following commands are in the attachment:

    emerge --info '=dev-python/numexpr-2.1'
    emerge -pqv '=dev-python/numexpr-2.1'
    cat /var/tmp/portage/dev-python/numexpr-2.1/temp/build.log
    cat /var/tmp/portage/dev-python/numexpr-2.1/temp/environment
Comment 1 Crayzee Wulf 2013-05-30 23:21:10 UTC 
This appears to be a problem with the numexpr-2.1 source code as reported at:

https://code.google.com/p/numexpr/issues/detail?id=100
Comment 2 Jeroen Roovers (RETIRED) gentoo-dev 2013-05-31 14:15:00 UTC 
Assignee: 	timcera@earthlink.net did not match anything

Please fix metadata.xml
Comment 3 Justin Lecher (RETIRED) gentoo-dev 2013-05-31 14:21:31 UTC 
I cannot reproduce it. Lets wait for upstreams response.
Comment 4 Beetle B. 2013-06-11 02:16:04 UTC 
I have the same problem. Let me know if you need anything from me. 

Output of emerge --info:

Portage 2.1.11.62 (default/linux/amd64/13.0, gcc-4.5.4, glibc-2.15-r3, 2.6.32-gentoo-r7 x86_64)
=================================================================
System uname: Linux-2.6.32-gentoo-r7-x86_64-Intel-R-_Core-TM-_i7_CPU_870_@_2.93GHz-with-gentoo-2.1
KiB Mem:     8195964 total,   3327652 free
KiB Swap:    3903752 total,   2957868 free
Timestamp of tree: Mon, 06 May 2013 15:15:01 +0000
ld GNU ld (GNU Binutils) 2.22
app-shells/bash:          4.2_p37
dev-java/java-config:     2.1.12-r1
dev-lang/python:          2.6.8-r1, 2.7.3-r3, 3.1.5-r1, 3.2.3-r2
dev-util/cmake:           2.8.9
dev-util/pkgconfig:       0.27.1
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.11.5
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1, 1.12.6
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.4.5, 4.5.4, 4.6.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.4 (virtual/os-headers)
sys-libs/glibc:           2.15-r3
Repositories: gentoo multimedia xwing sage-on-gentoo kde-sunset interactive-fiction sunrise x-layman x-other
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native -ggdb"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/ext-active/ /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="-O2 -pipe -march=native -ggdb"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--autounmask=n"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.llarian.net/ ftp://gentoo.llarian.net/pub/gentoo http://gentoo.gossamerhost.com http://gentoo.mirrors.hoobly.com/ ftp://mirrors.tera-byte.com/pub/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
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"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/multimedia /var/lib/layman/xwing /var/lib/layman/sage-on-gentoo /var/lib/layman/kde-sunset /var/lib/layman/interactive-fiction /var/lib/layman/sunrise /var/lib/layman /var/lib/layman/other"
SYNC="rsync://rsync3.us.gentoo.org/gentoo-portage"
USE="X aac aalib acl alsa amd64 apache2 bash-completion berkdb bidi binfilter blas bzip2 cairo cdda cdr cleartype cli corefonts cracklib crypt css cups cxx dbus dga directfb djvu dri dvd dvdr emacs encode exif fbcon ffmpeg firefox fontconfig fortran ftp gdbm ggi gif gimp gnuplot gphoto2 gpm gtk handbook iconv imagemagick imap java javascript jpeg jpeg2k lapack latex lcms libcaca libmms libnotify lm_sensors lzma maildir matroska mbox midi mime mms mmx mng modules mozilla mp3 mp4 mpeg mudflap multilib ncurses nls nntp nptl nsplugin nvidia ofx ogg openexr opengl openmp pam pcre pdf png postscript python qt3support qt4 quicktime raw readline rss sasl scanner sdl seamonkey semantic-desktop session smp spell sse sse2 ssl startup-notification svg tcpd theora threads tiff truetype type1 unicode usb vcd vorbis wmf x264 xcomposite xine xmp xosd xscreensaver xulrunner xv xvid xvmc zlib zsh-completion" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" 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 keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia vesa" 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"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 5 bartoz 2013-07-04 23:36:59 UTC 
I see the same issue; are there any updates?

(In reply to Beetle B. from comment #4)
> I have the same problem. Let me know if you need anything from me. 
> 
> Output of emerge --info:
> 
> Portage 2.1.11.62 (default/linux/amd64/13.0, gcc-4.5.4, glibc-2.15-r3,
> 2.6.32-gentoo-r7 x86_64)
> =================================================================
> System uname:
> Linux-2.6.32-gentoo-r7-x86_64-Intel-R-_Core-TM-_i7_CPU_870_@_2.93GHz-with-
> gentoo-2.1
> KiB Mem:     8195964 total,   3327652 free
> KiB Swap:    3903752 total,   2957868 free
> Timestamp of tree: Mon, 06 May 2013 15:15:01 +0000
> ld GNU ld (GNU Binutils) 2.22
> app-shells/bash:          4.2_p37
> dev-java/java-config:     2.1.12-r1
> dev-lang/python:          2.6.8-r1, 2.7.3-r3, 3.1.5-r1, 3.2.3-r2
> dev-util/cmake:           2.8.9
> dev-util/pkgconfig:       0.27.1
> sys-apps/baselayout:      2.1-r1
> sys-apps/openrc:          0.11.5
> sys-apps/sandbox:         2.5
> sys-devel/autoconf:       2.13, 2.68
> sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1, 1.12.6
> sys-devel/binutils:       2.22-r1
> sys-devel/gcc:            4.4.5, 4.5.4, 4.6.3
> sys-devel/gcc-config:     1.7.3
> sys-devel/libtool:        2.4-r1
> sys-devel/make:           3.82-r4
> sys-kernel/linux-headers: 3.4 (virtual/os-headers)
> sys-libs/glibc:           2.15-r3
> Repositories: gentoo multimedia xwing sage-on-gentoo kde-sunset
> interactive-fiction sunrise x-layman x-other
> ACCEPT_KEYWORDS="amd64"
> ACCEPT_LICENSE="*"
> CBUILD="x86_64-pc-linux-gnu"
> CFLAGS="-O2 -pipe -march=native -ggdb"
> CHOST="x86_64-pc-linux-gnu"
> CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt
> /var/lib/hsqldb"
> CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/
> /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release
> /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/
> /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/
> /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/ext-active/
> /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="-O2 -pipe -march=native -ggdb"
> DISTDIR="/usr/portage/distfiles"
> EMERGE_DEFAULT_OPTS="--autounmask=n"
> FCFLAGS="-O2 -pipe"
> FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks
> ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox
> sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans
> userfetch"
> FFLAGS="-O2 -pipe"
> GENTOO_MIRRORS="http://gentoo.llarian.net/
> ftp://gentoo.llarian.net/pub/gentoo http://gentoo.gossamerhost.com
> http://gentoo.mirrors.hoobly.com/ ftp://mirrors.tera-byte.com/pub/gentoo"
> LANG="en_US.utf8"
> LDFLAGS="-Wl,-O1 -Wl,--as-needed"
> MAKEOPTS="-j9"
> PKGDIR="/usr/portage/packages"
> PORTAGE_CONFIGROOT="/"
> 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"
> PORTAGE_TMPDIR="/var/tmp"
> PORTDIR="/usr/portage"
> PORTDIR_OVERLAY="/var/lib/layman/multimedia /var/lib/layman/xwing
> /var/lib/layman/sage-on-gentoo /var/lib/layman/kde-sunset
> /var/lib/layman/interactive-fiction /var/lib/layman/sunrise /var/lib/layman
> /var/lib/layman/other"
> SYNC="rsync://rsync3.us.gentoo.org/gentoo-portage"
> USE="X aac aalib acl alsa amd64 apache2 bash-completion berkdb bidi
> binfilter blas bzip2 cairo cdda cdr cleartype cli corefonts cracklib crypt
> css cups cxx dbus dga directfb djvu dri dvd dvdr emacs encode exif fbcon
> ffmpeg firefox fontconfig fortran ftp gdbm ggi gif gimp gnuplot gphoto2 gpm
> gtk handbook iconv imagemagick imap java javascript jpeg jpeg2k lapack latex
> lcms libcaca libmms libnotify lm_sensors lzma maildir matroska mbox midi
> mime mms mmx mng modules mozilla mp3 mp4 mpeg mudflap multilib ncurses nls
> nntp nptl nsplugin nvidia ofx ogg openexr opengl openmp pam pcre pdf png
> postscript python qt3support qt4 quicktime raw readline rss sasl scanner sdl
> seamonkey semantic-desktop session smp spell sse sse2 ssl
> startup-notification svg tcpd theora threads tiff truetype type1 unicode usb
> vcd vorbis wmf x264 xcomposite xine xmp xosd xscreensaver xulrunner xv xvid
> xvmc zlib zsh-completion" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare
> dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter
> mmap_emul mulaw multi null plug rate route share shm softvol"
> 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 keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad
> cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text"
> LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer"
> OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3"
> PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2"
> RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia vesa"
> 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"
> Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND,
> PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS,
> USE_PYTHON
Comment 6 Ian Delaney (RETIRED) gentoo-dev 2013-07-20 16:47:28 UTC 
Hmm; Check your version of numpy.
Going off;

  File "/usr/lib64/python3.2/site-packages/numpy/distutils/exec_command.py", line 197, in exec_command
    if _with_python and (0 or sys.__stdout__.fileno()==-1):
ValueError: underlying buffer has been detached

My /usr/lib64/python3.2/site-packages/numpy/distutils/exec_command.py
line 197 reads
    oldenv = _preserve_environment( list(env.keys()) )

and 

numpy-1.6.2/numpy/distutils/exec_command.py
&&
numpy-1.7.0/numpy/distutils/exec_command.py

line 197 matches 
if _with_python and (0 or sys.__stdout__.fileno()==-1):

  20 Jul 2013; Ian Delaney <idella4@gentoo.org> numexpr-2.1.ebuild:
  update numpy in RDEPEND, fixes Bug #471850

Please test and verify