* [gentoo-science] Failed emerge for sci-visualization/mayavi-4.4.2
@ 2016-05-20 13:34 marco restelli
2016-05-26 2:24 ` M. J. Everitt
0 siblings, 1 reply; 3+ messages in thread
From: marco restelli @ 2016-05-20 13:34 UTC (permalink / raw
To: gentoo-science
Hi,
I have a problem emerging sci-visualization/mayavi-4.4.2: here is
the error message:
>>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.4.2/work/mayavi-4.4.2 ...
* python2_7: running distutils-r1_run_phase distutils-r1_python_compile
/usr/bin/python2.7 setup.py build
running build
----------------------------------------------------------------------
Building TVTK classes.../var/tmp/portage/sci-visualization/mayavi-4.4.2/temp/environment:
line 1434: 13669 Segmentation fault "${@}"
* ERROR: sci-visualization/mayavi-4.4.2::science failed (compile phase):
* (no error message)
*
* Call stack:
* ebuild.sh, line 133: Called src_compile
* environment, line 3657: Called distutils-r1_src_compile
* environment, line 949: Called _distutils-r1_run_foreach_impl
'distutils-r1_python_compile'
* environment, line 370: Called python_foreach_impl
'distutils-r1_run_phase' 'distutils-r1_python_compile'
* environment, line 3189: Called multibuild_foreach_variant
'_python_multibuild_wrapper' 'distutils-r1_run_phase'
'distutils-r1_python_compile'
* environment, line 2291: Called _multibuild_run
'_python_multibuild_wrapper' 'distutils-r1_run_phase'
'distutils-r1_python_compile'
* environment, line 2289: Called _python_multibuild_wrapper
'distutils-r1_run_phase' 'distutils-r1_python_compile'
* environment, line 632: Called distutils-r1_run_phase
'distutils-r1_python_compile'
* environment, line 940: Called distutils-r1_python_compile
* environment, line 812: Called esetup.py 'build'
* environment, line 1440: Called die
* The specific snippet of code:
* "${@}" || die "${die_args[@]}" || return ${?}
I could open a bug, but first I would like to understand whether the
problem is with the mayavi ebuild, or mayavi itself, or some
dependency.
Thank you,
Marco
Here are some more details:
# emerge --info '=sci-visualization/mayavi-4.4.2::science'
/bin/sh: warning: setlocale: LC_ALL: cannot change locale (en)
setlocale: unsupported locale setting
setlocale: unsupported locale setting
Portage 2.2.28 (python 3.4.3-final-0,
default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.22-r4,
3.12.13-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-3.12.13-gentoo-x86_64-Intel-R-_Core-TM-_i3-2120_CPU_@_3.30GHz-with-gentoo-2.2
KiB Mem: 3926120 total, 739384 free
KiB Swap: 15999996 total, 15128780 free
Timestamp of repository gentoo: Fri, 20 May 2016 13:00:01 +0000
sh bash 4.3_p42-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash: 4.3_p42-r1::gentoo
dev-java/java-config: 2.2.0-r3::gentoo
dev-lang/perl: 5.20.2::gentoo
dev-lang/python: 2.7.10-r1::gentoo, 3.4.3-r1::gentoo
dev-util/cmake: 3.3.1-r1::gentoo
dev-util/pkgconfig: 0.28-r2::gentoo
sys-apps/baselayout: 2.2::gentoo
sys-apps/openrc: 0.19.1::gentoo
sys-apps/sandbox: 2.10-r1::gentoo
sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo
sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo,
1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils: 2.25.1-r1::gentoo
sys-devel/gcc: 4.9.3::gentoo
sys-devel/gcc-config: 1.7.3::gentoo
sys-devel/libtool: 2.4.6::gentoo
sys-devel/make: 4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc: 2.22-r4::gentoo
Repositories:
gentoo
location: /usr/portage
sync-type: rsync
sync-uri: rsync://rsync.gentoo.org/gentoo-portage
priority: -1000
science
location: /var/lib/layman/science
masters: gentoo
priority: 0
sage-on-gentoo
location: /var/lib/layman/sage-on-gentoo
masters: gentoo science
priority: 1
myebuild
location: /var/lib/myebuild
masters: gentoo
priority: 2
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
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"
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 splitdebug strict
unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv
usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en"
LC_ALL="en"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi afs alsa amd64 berkdb bluetooth branding bzip2
cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus djvu dri
dts dvd dvdr dvi emboss encode exif fam firefox flac fortran
fortran2003 gdbm gif glamor gpm gtk iconv icu ipv6 jpeg kerberos latex
lcms ldap libnotify lua luatex mad mate mmx mmxext mng modules mp3 mp4
mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf
png policykit ppds qt3support qt4 readline sdl seccomp session spell
sse sse2 ssl startup-notification svg tcpd tetex tiff truetype udev
udisks unicode upower usb vim vim-syntax vorbis wxwidgets x264 xattr
xcb xml xv xvid zlib" ABI_X86="32 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="avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2
ssse3" 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" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb
ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console
presenter-minimizer" LINGUAS="en en_US ar de eo es es_ES it af br da
cy fy he is nds nl oc yi el hr sr" OFFICE_IMPLEMENTATION="libreoffice"
PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7"
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"
Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK,
PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS,
PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [gentoo-science] Failed emerge for sci-visualization/mayavi-4.4.2
2016-05-20 13:34 [gentoo-science] Failed emerge for sci-visualization/mayavi-4.4.2 marco restelli
@ 2016-05-26 2:24 ` M. J. Everitt
2016-05-30 8:54 ` marco restelli
0 siblings, 1 reply; 3+ messages in thread
From: M. J. Everitt @ 2016-05-26 2:24 UTC (permalink / raw
To: gentoo-science
On 20/05/16 14:34, marco restelli wrote:
> Hi,
> I have a problem emerging sci-visualization/mayavi-4.4.2: here is
> the error message:
>
>>>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.4.2/work/mayavi-4.4.2 ...
> * python2_7: running distutils-r1_run_phase distutils-r1_python_compile
> /usr/bin/python2.7 setup.py build
> running build
> ----------------------------------------------------------------------
> Building TVTK classes.../var/tmp/portage/sci-visualization/mayavi-4.4.2/temp/environment:
> line 1434: 13669 Segmentation fault "${@}"
> * ERROR: sci-visualization/mayavi-4.4.2::science failed (compile phase):
> * (no error message)
> *
> * Call stack:
> * ebuild.sh, line 133: Called src_compile
> * environment, line 3657: Called distutils-r1_src_compile
> * environment, line 949: Called _distutils-r1_run_foreach_impl
> 'distutils-r1_python_compile'
> * environment, line 370: Called python_foreach_impl
> 'distutils-r1_run_phase' 'distutils-r1_python_compile'
> * environment, line 3189: Called multibuild_foreach_variant
> '_python_multibuild_wrapper' 'distutils-r1_run_phase'
> 'distutils-r1_python_compile'
> * environment, line 2291: Called _multibuild_run
> '_python_multibuild_wrapper' 'distutils-r1_run_phase'
> 'distutils-r1_python_compile'
> * environment, line 2289: Called _python_multibuild_wrapper
> 'distutils-r1_run_phase' 'distutils-r1_python_compile'
> * environment, line 632: Called distutils-r1_run_phase
> 'distutils-r1_python_compile'
> * environment, line 940: Called distutils-r1_python_compile
> * environment, line 812: Called esetup.py 'build'
> * environment, line 1440: Called die
> * The specific snippet of code:
> * "${@}" || die "${die_args[@]}" || return ${?}
>
>
> I could open a bug, but first I would like to understand whether the
> problem is with the mayavi ebuild, or mayavi itself, or some
> dependency.
>
> Thank you,
> Marco
>
>
> Here are some more details:
>
> # emerge --info '=sci-visualization/mayavi-4.4.2::science'
> /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en)
> setlocale: unsupported locale setting
> setlocale: unsupported locale setting
> Portage 2.2.28 (python 3.4.3-final-0,
> default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.22-r4,
> 3.12.13-gentoo x86_64)
> =================================================================
> System Settings
> =================================================================
> System uname: Linux-3.12.13-gentoo-x86_64-Intel-R-_Core-TM-_i3-2120_CPU_@_3.30GHz-with-gentoo-2.2
> KiB Mem: 3926120 total, 739384 free
> KiB Swap: 15999996 total, 15128780 free
> Timestamp of repository gentoo: Fri, 20 May 2016 13:00:01 +0000
> sh bash 4.3_p42-r1
> ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
> app-shells/bash: 4.3_p42-r1::gentoo
> dev-java/java-config: 2.2.0-r3::gentoo
> dev-lang/perl: 5.20.2::gentoo
> dev-lang/python: 2.7.10-r1::gentoo, 3.4.3-r1::gentoo
> dev-util/cmake: 3.3.1-r1::gentoo
> dev-util/pkgconfig: 0.28-r2::gentoo
> sys-apps/baselayout: 2.2::gentoo
> sys-apps/openrc: 0.19.1::gentoo
> sys-apps/sandbox: 2.10-r1::gentoo
> sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo
> sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo,
> 1.14.1::gentoo, 1.15::gentoo
> sys-devel/binutils: 2.25.1-r1::gentoo
> sys-devel/gcc: 4.9.3::gentoo
> sys-devel/gcc-config: 1.7.3::gentoo
> sys-devel/libtool: 2.4.6::gentoo
> sys-devel/make: 4.1-r1::gentoo
> sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
> sys-libs/glibc: 2.22-r4::gentoo
> Repositories:
>
> gentoo
> location: /usr/portage
> sync-type: rsync
> sync-uri: rsync://rsync.gentoo.org/gentoo-portage
> priority: -1000
>
> science
> location: /var/lib/layman/science
> masters: gentoo
> priority: 0
>
> sage-on-gentoo
> location: /var/lib/layman/sage-on-gentoo
> masters: gentoo science
> priority: 1
>
> myebuild
> location: /var/lib/myebuild
> masters: gentoo
> priority: 2
>
> ACCEPT_KEYWORDS="amd64"
> ACCEPT_LICENSE="* -@EULA"
> 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"
> 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 splitdebug strict
> unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv
> usersandbox usersync xattr"
> FFLAGS="-O2 -pipe"
> GENTOO_MIRRORS="http://distfiles.gentoo.org"
> LANG="en"
> LC_ALL="en"
> LDFLAGS="-Wl,-O1 -Wl,--as-needed"
> MAKEOPTS="-j1"
> 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 --exclude=/.git"
> PORTAGE_TMPDIR="/var/tmp"
> USE="X a52 aac acl acpi afs alsa amd64 berkdb bluetooth branding bzip2
> cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus djvu dri
> dts dvd dvdr dvi emboss encode exif fam firefox flac fortran
> fortran2003 gdbm gif glamor gpm gtk iconv icu ipv6 jpeg kerberos latex
> lcms ldap libnotify lua luatex mad mate mmx mmxext mng modules mp3 mp4
> mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf
> png policykit ppds qt3support qt4 readline sdl seccomp session spell
> sse sse2 ssl startup-notification svg tcpd tetex tiff truetype udev
> udisks unicode upower usb vim vim-syntax vorbis wxwidgets x264 xattr
> xcb xml xv xvid zlib" ABI_X86="32 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="avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2
> ssse3" 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" KERNEL="linux"
> LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb
> ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console
> presenter-minimizer" LINGUAS="en en_US ar de eo es es_ES it af br da
> cy fy he is nds nl oc yi el hr sr" OFFICE_IMPLEMENTATION="libreoffice"
> PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7"
> 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"
> Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK,
> PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS,
> PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
>
Segmentation fault .. nice....
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [gentoo-science] Failed emerge for sci-visualization/mayavi-4.4.2
2016-05-26 2:24 ` M. J. Everitt
@ 2016-05-30 8:54 ` marco restelli
0 siblings, 0 replies; 3+ messages in thread
From: marco restelli @ 2016-05-30 8:54 UTC (permalink / raw
To: gentoo-science
2016-05-26 4:24 GMT+0200, M. J. Everitt <m.j.everitt@iee.org>:
> On 20/05/16 14:34, marco restelli wrote:
>> Hi,
>> I have a problem emerging sci-visualization/mayavi-4.4.2: here is
>> the error message:
>>
>>>>> Compiling source in
>>>>> /var/tmp/portage/sci-visualization/mayavi-4.4.2/work/mayavi-4.4.2 ...
>> * python2_7: running distutils-r1_run_phase distutils-r1_python_compile
>> /usr/bin/python2.7 setup.py build
>> running build
>> ----------------------------------------------------------------------
>> Building TVTK
>> classes.../var/tmp/portage/sci-visualization/mayavi-4.4.2/temp/environment:
>> line 1434: 13669 Segmentation fault "${@}"
>>
> Segmentation fault .. nice....
Everitt, what do you mean?
^ permalink raw reply [flat|nested] 3+ messages in thread
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2016-05-20 13:34 [gentoo-science] Failed emerge for sci-visualization/mayavi-4.4.2 marco restelli
2016-05-26 2:24 ` M. J. Everitt
2016-05-30 8:54 ` marco restelli
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