| Summary: | sci-visualization/mayavi-4.0.0 fails to emerge building TVTK classes | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED DUPLICATE | ||
| Severity: | normal | CC: | Bernd.Feige, creffett, dominik.kriegner, grozin, jarausch, rei4dan |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | /var/tmp/portage/sci-visualization/mayavi-4.0.0/temp/build.log | ||
|
Description
Juergen Rose
2012-01-08 18:18:40 UTC
Created attachment 298335 [details]
/var/tmp/portage/sci-visualization/mayavi-4.0.0/temp/build.log
Same problem here.
Portage 2.1.10.44 (default/linux/amd64/10.0/desktop/gnome, gcc-4.6.2, glibc-2.14.1-r2, 3.2.0-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-3.2.0-gentoo-x86_64-Intel-R-_Core-TM-_i7-2630QM_CPU_@_2.00GHz-with-gentoo-2.1
Timestamp of tree: Tue, 10 Jan 2012 09:45:01 +0000
app-shells/bash: 4.2_p20
dev-java/java-config: 2.1.11-r3
dev-lang/python: 2.6.7-r2, 2.7.2-r3, 3.1.4-r3, 3.2.2
dev-util/cmake: 2.8.6-r4
dev-util/pkgconfig: 0.26
sys-apps/baselayout: 2.1
sys-apps/openrc: 0.9.8
sys-apps/sandbox: 2.5
sys-devel/autoconf: 2.13, 2.68
sys-devel/automake: 1.10.3, 1.11.2
sys-devel/binutils: 2.22-r1
sys-devel/gcc: 4.5.3-r2, 4.6.2
sys-devel/gcc-config: 1.5-r2
sys-devel/libtool: 2.4.2
sys-devel/make: 3.82-r3
sys-kernel/linux-headers: 3.2 (virtual/os-headers)
sys-libs/glibc: 2.14.1-r2
Repositories: gentoo x11 science local
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O3 -pipe -ggdb"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O3 -pipe -ggdb"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS=""
FEATURES="assume-digests binpkg-logs compress-build-logs distlocks ebuild-locks fixlafiles news parallel-fetch parallel-install protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-march=native -O3 -pipe -ggdb"
GENTOO_MIRRORS="ftp://trumpetti.atm.tut.fi/gentoo/ http://trumpetti.atm.tut.fi/gentoo/ http://gentoo.tups.lv/source/ "
LANG="lv_LV.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="lv en"
MAKEOPTS="-j9"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/science /usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 avx bash-completion berkdb bluetooth branding bzip2 cairo cdda cdio cdr cjk cleartype cli colord consolekit cracklib crypt cups cxx dbus dirac djvu dri dts dvd dvdr eds emboss encode evo exif fam ffmpeg fftw firefox flac fontconfig fortran gdbm gdu gif gnome gnome-keyring gnome-online-accounts gphoto2 gpm gsm gstreamer gtk gtk3 iconv idn ipv6 jpeg kate lcms ldap libcaca libnotify live mad matroska mmx mng modules mp3 mp4 mpeg mtp mudflap multilib musepack nautilus ncurses networkmanager nls nptl nptlonly ogg openexr opengl openmp pam pango pcre pdf png policykit ppds pppd pulseaudio qt3support qt4 raw readline schroedinger sdl session smp socialweb speex spell sse sse2 sse4_1 ssl ssse3 startup-notification svg sysfs system-sqlite tcpd theora tiff truetype udev unicode usb v4l v4l2 vaapi vorbis vpx wmf x264 xcb xetex xml xmp xorg xpm xulrunner xv xvid xvmc zlib" 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="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 stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" FOO2ZJS_DEVICES="hp1018" 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 synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="lv en" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev nvidia i965 intel 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
=================================================================
Package Settings
=================================================================
sci-visualization/mayavi-4.0.0 was built with the following:
USE="(multilib) -examples -test"
CFLAGS="-march=native -mtune=generic -mno-avx -O2 -pipe -ggdb"
CXXFLAGS="-march=native -mtune=generic -mno-avx -O2 -pipe -ggdb"
(In reply to comment #0) > 'emerge mayavi' fails with: > > ---------------------------------------------------------------------- > Building TVTK classes... vtkSimple3DCirclesStrategy: Ignoring method: > Get/SetMarkedValue > default: (invalid), range: None > vtkArrayNorm: Ignoring method: Get/SetWindow > default: [0, 9223372036854775807), range: None > vtkBoostRandomSparseArraySource: Ignoring method: Get/SetExtents > default: [0,2)x[0,2), range: None > vtkChart: Ignoring method: Get/SetSize > default: [0.0, 0.0, 0.0, 0.0], range: None > QWidget: Must construct a QApplication before a QPaintDevice Unfortunately I get the same error with the recent 4.1.0 version, Helmut. me too. Emerging of mayavi 4.0.0 and 4.1.0 fails with sci-libs/vtk-5.8.0 I'm restore sci-libs/vtk-5.6.1 and last mayavi is compiled correctly. mayavi-4.x doesn't like vtk-5.8.0 compiled with qt support that's what make the build fail. So either there are problem with qt4 binding in the vtk-5.8.0 ebuild or mayavi doesn't like them at all. The installation (compilation?) of mayavi-4.1.0 fails also, if the qt4 flag is removed for vtk: >>> Emerging (1 of 1) sci-visualization/mayavi-4.1.0 * mayavi-4.1.0.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking mayavi-4.1.0.tar.gz to /var/tmp/portage/sci-visualization/mayavi-4.1.0/work >>> Source unpacked in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work >>> Preparing source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... * Building of sci-visualization/mayavi-4.1.0 with CPython 2.7... python2.7 setup.py build -b build-2.7 running build /var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/environment: line 1442: 10234 Segmentation fault "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@" * ERROR: sci-visualization/mayavi-4.1.0 failed (compile phase): * Building failed with CPython 2.7 in distutils_building() function * * Call stack: * ebuild.sh, line 85: Called src_compile * environment, line 5240: Called distutils_src_compile * environment, line 1451: Called python_execute_function 'distutils_building' * environment, line 3587: Called die * The specific snippet of code: * die "${failure_message}"; * * If you need support, post the output of 'emerge --info =sci-visualization/mayavi-4.1.0', * the complete build log and the output of 'emerge -pqv =sci-visualization/mayavi-4.1.0'. * The complete build log is located at '/var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/environment'. * S: '/var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0' >>> Failed to emerge sci-visualization/mayavi-4.1.0, Log file: >>> '/var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/build.log' root@caiman:/usr/local/portage/sci-libs(32)# emerge -pvD vtk These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/vtk-5.8.0 USE="R X boost doc examples ffmpeg java mpi mysql odbc patented postgres python theora threads tk -cg -qt4" VIDEO_CARDS="-nvidia" 0 kB (In reply to comment #7) > The installation (compilation?) of mayavi-4.1.0 fails also, if the qt4 flag is > removed for vtk: > >>> Emerging (1 of 1) sci-visualization/mayavi-4.1.0 > * mayavi-4.1.0.tar.gz RMD160 SHA1 SHA256 size ;-) ... > > [ ok ] > >>> Unpacking source... > >>> Unpacking mayavi-4.1.0.tar.gz to /var/tmp/portage/sci-visualization/mayavi-4.1.0/work > >>> Source unpacked in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work > >>> Preparing source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... > >>> Source prepared. > >>> Configuring source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... > >>> Source configured. > >>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... > * Building of sci-visualization/mayavi-4.1.0 with CPython 2.7... > python2.7 setup.py build -b build-2.7 > running build > /var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/environment: line 1442: > 10234 Segmentation fault "$(PYTHON)" "${setup_file#*|}" > "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@" > * ERROR: sci-visualization/mayavi-4.1.0 failed (compile phase): > * Building failed with CPython 2.7 in distutils_building() function > * > * Call stack: > * ebuild.sh, line 85: Called src_compile > * environment, line 5240: Called distutils_src_compile > * environment, line 1451: Called python_execute_function > 'distutils_building' > * environment, line 3587: Called die > * The specific snippet of code: > * die "${failure_message}"; > * > * If you need support, post the output of 'emerge --info > =sci-visualization/mayavi-4.1.0', > * the complete build log and the output of 'emerge -pqv > =sci-visualization/mayavi-4.1.0'. > * The complete build log is located at > '/var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/build.log'. > * The ebuild environment file is located at > '/var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/environment'. > * S: '/var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0' > > >>> Failed to emerge sci-visualization/mayavi-4.1.0, Log file: > > >>> '/var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/build.log' > root@caiman:/usr/local/portage/sci-libs(32)# emerge -pvD vtk > > These are the packages that would be merged, in order: > > Calculating dependencies... done! > [ebuild R ] sci-libs/vtk-5.8.0 USE="R X boost doc examples ffmpeg java > mpi mysql odbc patented postgres python theora threads tk -cg -qt4" > VIDEO_CARDS="-nvidia" 0 kB Your error building mayavi is way different than the one in your original post, so this is a different failure altogether that occurs earlier. You don't even seem to start the build process anymore. I added at "caiman" where 'emerge mayavi' failed corresponding to comment 7 -qt4 to /etc/portage/packages.use: root@caiman:/usr/local/portage/net-nds(41)# grep sci-libs/vtk /etc/portage/package.use #sci-libs/vtk patented -ffmpeg sci-libs/vtk patented -qt4 Now some days later I see that mayavi-4.1.0 was emerged: root@caiman:/usr/local/portage/net-nds(42)# genlop -t mayavi | tail Thu Aug 4 07:49:26 2011 >>> sci-visualization/mayavi-4.0.0 merge time: 2 minutes and 9 seconds. Mon Sep 12 09:19:10 2011 >>> sci-visualization/mayavi-4.0.0 merge time: 44 seconds. Thu Feb 9 08:14:18 2012 >>> sci-visualization/mayavi-4.1.0 merge time: 1 minute and 18 seconds. But If I want to repeat this procedure at the next system, I get the old error: At "impala": root@impala:/usr/local/portage/net-nds(71)# USE=-qt4 emerge -pv1 vtk; emerge -uvDN mayavi These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/vtk-5.8.0 USE="R X boost cg doc examples ffmpeg java mpi mysql odbc patented postgres python theora threads tk -qt4*" VIDEO_CARDS="-nvidia" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] sci-visualization/mayavi-4.1.0 [4.0.0] USE="doc%* examples -test" 0 kB Total: 1 package (1 upgrade), Size of downloads: 0 kB WARNING: One or more updates have been skipped due to a dependency conflict: ... >>> Emerging (1 of 1) sci-visualization/mayavi-4.1.0 * mayavi-4.1.0.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking mayavi-4.1.0.tar.gz to /var/tmp/portage/sci-visualization/mayavi-4.1.0/work >>> Source unpacked in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work >>> Preparing source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... * Building of sci-visualization/mayavi-4.1.0 with CPython 2.7... python2.7 setup.py build -b build-2.7 running build /var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/environment: line 1433: 22586 Segmentation fault "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@" * ERROR: sci-visualization/mayavi-4.1.0 failed (compile phase): or at "lynx": root@lynx:/root(18)# USE=-qt4 emerge -pv1 vtk; emerge -uvN mayavi These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/vtk-5.8.0 USE="R X boost cg doc examples ffmpeg java mpi mysql odbc patented postgres python theora threads tk -qt4*" VIDEO_CARDS="-nvidia" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] sci-visualization/mayavi-4.1.0 [4.0.0] USE="doc%* examples -test" 0 kB ... >>> Emerging (1 of 1) sci-visualization/mayavi-4.1.0 * mayavi-4.1.0.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking mayavi-4.1.0.tar.gz to /var/tmp/portage/sci-visualization/mayavi-4.1.0/work >>> Source unpacked in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work >>> Preparing source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.1.0/work/mayavi-4.1.0 ... * Building of sci-visualization/mayavi-4.1.0 with CPython 2.7... python2.7 setup.py build -b build-2.7 running build /var/tmp/portage/sci-visualization/mayavi-4.1.0/temp/environment: line 1437: 13664 Segmentation fault "$(PYTHON)" "${setup_file#*|}" "${_DISTUTILS_GLOBAL_OPTIONS[@]}" build -b "$(_distutils_get_build_dir)" "$@" * ERROR: sci-visualization/mayavi-4.1.0 failed (compile phase): I think this bug is a duplicate of https://bugs.gentoo.org/show_bug.cgi?id=405099 . At least I could emerge mayavi-4.1.0 after masking >sci-libs/atlas-3.8.4 and reemerging atlas and numpy. No this is a different issue. AFAIK bug #399537 is duplicate of this bug, see comments there for reference to upstream one-liner patch for this. *** This bug has been marked as a duplicate of bug 399537 *** |
