'emerge vtk' fails with: ... -- Installing: /var/tmp/portage/sci-libs/vtk-5.8.0/image/usr/bin/vtkpython -- Installing: /var/tmp/portage/sci-libs/vtk-5.8.0/image/usr/bin/pvtkpython running cd "/var/tmp/portage/sci-libs/vtk-5.8.0/work/vtk-5.8.0_build/Wrapping/Python" && /usr/bin/python setup.py install --prefix="/usr" 2>&1 running install ACCESS DENIED open_wr: /usr/lib64/python2.7/site-packages/test-easy-install-29789.write-test error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 13] Permission denied: '/usr/lib64/python2.7/site-packages/test-easy-install-29789.write-test' The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /usr/lib64/python2.7/site-packages/ Perhaps your account does not have write access to this directory? If the installation directory is a system-owned directory, you may need to sign in as the administrator or "root" account. If you do not have administrative access to this machine, you may wish to choose a different installation directory, preferably one that is listed in your PYTHONPATH environment variable. For information on other options, you may wish to consult the documentation at: http://packages.python.org/distribute/easy_install.html Please make the appropriate changes for your system and try again. -- Installing: /var/tmp/portage/sci-libs/vtk-5.8.0/image/usr/lib64/vtk-5.8/java/vtk.jar -- Installing: /var/tmp/portage/sci-libs/vtk-5.8.0/image/usr/lib64/VTKTargets.cmake -- Installing: /var/tmp/portage/sci-libs/vtk-5.8.0/image/usr/lib64/VTKTargets-gentoo.cmake -- Installing: /var/tmp/portage/sci-libs/vtk-5.8.0/image/usr/lib64/vtk-5.8/VTKConfig.cmake -- Installing: /var/tmp/portage/sci-libs/vtk-5.8.0/image/usr/lib64/vtk-5.8/VTKConfigVersion.cmake `Examples' -> `examples' `/var/tmp/portage/sci-libs/vtk-5.8.0/work/VTKData' -> `/var/tmp/portage/sci-libs/vtk-5.8.0/work/data' * Installing API docs. This may take some time. >>> Completed installing vtk-5.8.0 into /var/tmp/portage/sci-libs/vtk-5.8.0/image/ --------------------------- ACCESS VIOLATION SUMMARY --------------------------- LOG FILE "/var/log/sandbox/sandbox-28851.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: open_wr S: deny P: /usr/lib64/python2.7/site-packages/test-easy-install-29789.write-test A: /usr/lib64/python2.7/site-packages/test-easy-install-29789.write-test R: /usr/lib64/python2.7/site-packages/test-easy-install-29789.write-test C: /usr/bin/python2.7 setup.py install --prefix=/usr -------------------------------------------------------------------------------- !!! When you file a bug report, please include the following information: GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.29" JAVACFLAGS="-source 1.5 -target 1.5" COMPILER="" and of course, the output of emerge --info >>> Failed to emerge sci-libs/vtk-5.8.0, Log file: >>> '/var/tmp/portage/sci-libs/vtk-5.8.0/temp/build.log' This bug seems to be similar with bug 396119. Reproducible: Always root@impala:/usr/local/portage/sci-biology(55)# emerge --info Portage 2.1.10.43 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.14.1-r1, 3.1.5-gentoo x86_64) ================================================================= System uname: Linux-3.1.5-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.1 Timestamp of tree: Wed, 28 Dec 2011 07:30:01 +0000 app-shells/bash: 4.2_p20 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r3::sage-on-gentoo, 3.2.2 dev-util/cmake: 2.8.6-r4 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1 sys-apps/openrc: 0.9.7 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-r1 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.5.3-r2 sys-devel/gcc-config: 1.5-r2 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.1 (virtual/os-headers) sys-libs/glibc: 2.14.1-r1 Repositories: gentoo x11 lordvan bicatali science sage-on-gentoo java-overlay sunrise x-portage x-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft Oracle-BCLA-JavaSE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=amdfam10 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /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/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="-march=amdfam10 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j5" 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/lordvan /var/lib/layman/bicatali /var/lib/layman/science /var/lib/layman/sage-on-gentoo /var/lib/layman/java-overlay /var/lib/layman/sunrise /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac abiword accessibility acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4a ssl subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter v4l2 vaapi video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file 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 log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="canon" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nouveau 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS root
Created attachment 297203 [details] bzip2ed /var/tmp/portage/sci-libs/vtk-5.8.0/temp/build.log
I get a different error when vtk-5.8.0 is compiled with the python USE flag: * ERROR: sci-libs/vtk-5.8.0 failed (configure phase): * cmake failed * * Call stack: * ebuild.sh, line 75: Called src_configure * environment, line 7250: Called cmake-utils_src_configure * environment, line 1483: Called _execute_optionaly 'src_configure' * environment, line 506: Called enable_cmake-utils_src_configure * environment, line 1971: Called die * The specific snippet of code: * "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed";
Created attachment 297207 [details] build log
Comment on attachment 297207 [details] build log For a different bug, file a new bug report.
(In reply to comment #3) > Created attachment 297207 [details] > build log That probably belongs to bug #396119 I was surprised it didn't seem to need patching.
Thanks for the nice build log Juergen we will probably be able to track the guilty cmake file with it.
I think we need to set VTK_INSTALL_PYTHON_USING_CMAKE otherwise "setup.py" in Wrapping/python is used and for that to install properly it would need to be done separately with the help of the python eclass. Actually looking at the various python install script I am not that would work.
A CMakeLists.txt file should call setup.py with "--root=${DESTDIR}" option instead of --prefix="/usr".
(In reply to comment #8) > A CMakeLists.txt file should call setup.py with "--root=${DESTDIR}" option > instead of --prefix="/usr". Ok that would bw Wrapping/python/CMakeLists.txt on line 543. It currently reads: SET(VTK_PYTHON_SETUP_ARGS "--prefix=\"${DOLLAR}{CMAKE_INSTALL_PREFIX}\"" you are suggesting it should be: SET(VTK_PYTHON_SETUP_ARGS "--root=\"${DOLLAR}{DESTDIR}\"" Is it correct?
(In reply to comment #9) Yes.
(In reply to comment #10) > (In reply to comment #9) > > Yes. I don't think it will work anyway because the setup.py doesn't use the root option. In fact the only mention of the root option is here: class my_install_data (install_data): def finalize_options (self): """Needed to make this thing work properly.""" self.set_undefined_options ('install', ('install_lib', 'install_dir'), ('root', 'root'), ('force', 'force'), ) So I am extremely doubtful it will work unless we do some extra work there.
(In reply to comment #11) distutils internally supports --root option.
(In reply to comment #12) > (In reply to comment #11) > > distutils internally supports --root option. Ah, should be OK then. Will experiment then.
Created attachment 297271 [details, diff] Proposed patch for the python install OK quick patch to add to the ebuild. I haven't really tried it yet.
I found the problem. But it should also have been a problem in 5.6.1. Anyways I do last testing and commit the fix.
29 Dec 2011; Justin Lecher <jlec@gentoo.org> vtk-5.8.0.ebuild: + Correct PYTHON_SETUP_ARGS to VTK_PYTHON_SETUP_ARGS, #396297 + Please test.
Repalcing PYTHON_SETUP_ARGS with VTK_PYTHON_SETUP_ARGS worked at the first system.
*** Bug 397339 has been marked as a duplicate of this bug. ***
(In reply to comment #15) > I found the problem. But it should also have been a problem in 5.6.1. Anyways I > do last testing and commit the fix. vtk-5.6.1 compiles fine, it only hits vtk-5.8.0 for me.
(In reply to comment #19) > (In reply to comment #15) > > I found the problem. But it should also have been a problem in 5.6.1. Anyways I > > do last testing and commit the fix. > > vtk-5.6.1 compiles fine, it only hits vtk-5.8.0 for me. Without a build.log we cannot help you.
(In reply to comment #20) > (In reply to comment #19) > > (In reply to comment #15) > > > I found the problem. But it should also have been a problem in 5.6.1. Anyways I > > > do last testing and commit the fix. > > > > vtk-5.6.1 compiles fine, it only hits vtk-5.8.0 for me. > > Without a build.log we cannot help you. The problem is exactly the same. My bug was correctly identified as a duplicate. I've just reacted on the comment, that it should also the same for 5.6.1. Although the section in the proposed diff file looks the same for both versions, 5.6.1 do not triggers the problem.
I suspect 5.6.1 was defaulting to VTK_INSTALL_PYTHON_USING_CMAKE being on and that setup.py was not used which is why it isn't affected. I am not in a position to check this right now but that would make sense.
