Created attachment 394076 [details] build.log 'emerge h5py' fails with: ... writing manifest file '/var/tmp/portage/dev-python/h5py-2.4.0/work/h5py-2.4.0-python2_7/h5py.egg-info/SOURCES.txt' Copying /var/tmp/portage/dev-python/h5py-2.4.0/work/h5py-2.4.0-python2_7/h5py.egg-info to /var/tmp/portage/dev-python/h5py-2.4.0/image//_python2.7/usr/lib64/python2.7/site-packages/h5py-2.4.0-py2.7.egg-info running install_scripts * python2_7: running distutils-r1_run_phase python_install_all >>> Completed installing h5py-2.4.0 into /var/tmp/portage/dev-python/h5py-2.4.0/image/ * --------------------------- ACCESS VIOLATION SUMMARY --------------------------- * LOG FILE: "/var/log/sandbox/sandbox-25777.log" * VERSION 1.0 FORMAT: F - Function called FORMAT: S - Access Status FORMAT: P - Path as passed to function FORMAT: A - Absolute Path (not canonical) FORMAT: R - Canonical Path FORMAT: C - Command Line F: mkdir S: deny P: /usr/lib64/paraview-4.2/site-packages/mpi4py/__pycache__ A: /usr/lib64/paraview-4.2/site-packages/mpi4py/__pycache__ R: /usr/lib64/paraview-4.2/site-packages/mpi4py/__pycache__ C: /usr/bin/python3.3 setup.py install --root=/var/tmp/portage/dev-python/h5py-2.4.0/image//_python3.3 * -------------------------------------------------------------------------------- >>> Failed to emerge dev-python/h5py-2.4.0, Log file: root@condor:/root(31)# emerge --info Portage 2.2.15 (python 2.7.9-final-0, default/linux/amd64/13.0/desktop, gcc-4.8.4, glibc-2.20-r1, 3.18.2-gentoo x86_64) ================================================================= System uname: Linux-3.18.2-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_6600_@_2.40GHz-with-gentoo-2.2 KiB Mem: 7005712 total, 1051336 free KiB Swap: 50347696 total, 50276600 free Timestamp of tree: Fri, 16 Jan 2015 05:00:01 +0000 sh bash 4.3_p33 ld GNU ld (GNU Binutils) 2.24 app-shells/bash: 4.3_p33 dev-java/java-config: 2.2.0 dev-lang/perl: 5.20.1-r4 dev-lang/python: 2.7.9-r1, 3.3.5-r1, 3.4.2 dev-util/cmake: 3.0.2 dev-util/pkgconfig: 0.28-r2 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.13.7 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.10.3-r1, 1.11.6-r1, 1.12.6, 1.13.4, 1.15 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.4 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.4 sys-devel/make: 4.1-r1 sys-kernel/linux-headers: 3.18 (virtual/os-headers) sys-libs/glibc: 2.20-r1 Repositories: gentoo x11 science sunrise lordvan sage-on-gentoo local g-cpan g-octave Installed sets: @system ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS" 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 /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/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="-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="-march=native -O2 -pipe" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ " LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" 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" PORTDIR="/usr/portage_condor" PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/lordvan /var/lib/layman/sage-on-gentoo /usr/local/portage /var/lib/cpan /var/lib/g-octave" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java java6 jbig jit john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx vtk wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm mdraid syslog" DVB_CARDS="tda10045 tda10046lifeview" 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="keyboard mouse evdev void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
What's the output of: sudo -u portage python -c 'import mpi4py; print(mpi4py.__file__)' Looks like portage picks up alternative mpi4py you have installed...
root@condor:/root(32)# sudo -u portage python -c 'import mpi4py; print(mpi4py.__file__)' /usr/lib64/python2.7/site-packages/mpi4py/__init__.pyc root@condor:/root(33)#
(In reply to Juergen Rose from comment #2) > root@condor:/root(32)# sudo -u portage python -c 'import mpi4py; > print(mpi4py.__file__)' > /usr/lib64/python2.7/site-packages/mpi4py/__init__.pyc That's interesting... How about: sudo -u portage python -c 'import mpi4py; print(mpi4py.get_include())'
root@condor:/root(38)# sudo -u portage python -c 'import mpi4py; print(mpi4py.get_include())' /usr/lib64/python2.7/site-packages/mpi4py/include root@condor:/root(39)#
Still some more information. 'emerge h5py' fails on all of my systems with this sandbox error. The following python versions are installed: root@condor:/root(48)# qlist -Iv dev-lang/python dev-lang/python-2.7.9-r1 dev-lang/python-3.3.5-r1 dev-lang/python-3.4.2 dev-lang/python-exec-2.0.1-r1 The following mpi4py directories are found: root@condor:/root(49)# find /usr -name mpi4py /usr/portage_condor/dev-python/mpi4py /usr/lib64/python3.3/site-packages/mpi4py /usr/lib64/python3.3/site-packages/mpi4py/include/mpi4py /usr/lib64/paraview-4.2/site-packages/mpi4py /usr/lib64/paraview-4.2/site-packages/mpi4py/include/mpi4py /usr/lib64/python2.7/site-packages/mpi4py /usr/lib64/python2.7/site-packages/mpi4py/include/mpi4py There are installed by mpi4py-1.3.1 and paraview-4.2.0. root@condor:/root(50)# qfile -v /usr/lib64/python3.3/site-packages/mpi4py dev-python/mpi4py-1.3.1 (/usr/lib64/python3.3/site-packages/mpi4py) root@condor:/root(51)# qfile -v /usr/lib64/paraview-4.2/site-packages/mpi4py sci-visualization/paraview-4.2.0 (/usr/lib64/paraview-4.2/site-packages/mpi4py) root@condor:/root(52)# qfile -v /usr/lib64/python2.7/site-packages/mpi4py dev-python/mpi4py-1.3.1 (/usr/lib64/python2.7/site-packages/mpi4py) The last installation of mpi4py-1.3.1 was in Nov 24th 2014, the last installation of paraview was Dec 24th 2014, the last installation of python-2.7 and python-3.3 was in Jan 6th 2015. root@caiman:/root(33)# genlop -t mpi4py | tail Sun Dec 1 10:20:47 2013 >>> dev-python/mpi4py-1.3.1 merge time: 1 minute and 19 seconds. Tue Aug 12 05:27:25 2014 >>> dev-python/mpi4py-1.3.1 merge time: 53 seconds. Mon Nov 24 05:45:58 2014 >>> dev-python/mpi4py-1.3.1 merge time: 50 seconds. root@caiman:/root(34)# genlop -t python | tail Mon Jan 5 14:10:53 2015 >>> dev-lang/python-3.3.5-r1 merge time: 2 minutes and 9 seconds. Tue Jan 6 09:45:21 2015 >>> dev-lang/python-2.7.9-r1 merge time: 1 minute and 55 seconds. Tue Jan 6 09:47:30 2015 >>> dev-lang/python-3.3.5-r1 merge time: 2 minutes and 9 seconds. root@caiman:/root(35)# genlop -t paraview | tail Wed Nov 12 22:15:42 2014 >>> sci-visualization/paraview-4.1.0-r1 merge time: 38 minutes and 48 seconds. Wed Nov 26 11:49:36 2014 >>> sci-visualization/paraview-4.1.0-r1 merge time: 38 minutes and 25 seconds. Wed Dec 24 18:51:10 2014 >>> sci-visualization/paraview-4.2.0 merge time: 3 hours, 40 minutes and 24 seconds. 'python-updater' says "* No packages need to be reinstalled."
Reemerging of mpi4py and paraview does not improve anything.
It still fails. Maybe the following information is usefull: oot@gepard:/root(7)# sudo -u portage python3.3 -c 'import mpi4py; print(mpi4py.__file__)' /usr/lib64/python3.3/site-packages/mpi4py/__init__.py root@gepard:/root(8)# sudo -u portage python3.3 -c 'import mpi4py; print(mpi4py.get_include())' /usr/lib64/python3.3/site-packages/mpi4py/include
After deleting paraview-4.2.0 'emerge h5py' works. If I emerge paraview-4.2.0 again and try to emerge h5py-2.4.0 once more, it fails again with sandbox violation.
(In reply to Juergen Rose from comment #8) > After deleting paraview-4.2.0 'emerge h5py' works. If I emerge > paraview-4.2.0 again and try to emerge h5py-2.4.0 once more, it fails again > with sandbox violation. Could you try adding this: SANDBOX_PREDICT="/usr/lib64/paraview-4.2/site-packages/" to /etc/sandbox.d/40paraview and see if this fixes the issue?
19 Jan 2015; Matthias Maier <tamiko@gentoo.org> +paraview-4.0.1-r2.ebuild, +paraview-4.1.0-r2.ebuild, +paraview-4.2.0-r1.ebuild, -paraview-4.0.1-r1.ebuild, -paraview-4.1.0-r1.ebuild, -paraview-4.2.0.ebuild: do not set global PYTHONPATH environment variable, bug #499272
