Bug 477638 – sci-libs/vtk-5.10.1 - ld: cannot find -lmysqlclient

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Juergen Rose 2013-07-21 13:52:02 UTC]

Created attachment 353774 [details]
bzip2ed  /var/tmp/portage/sci-libs/vtk-5.10.1/temp/build.log

'emerge vtk' fails to:
...
/usr/bin/x86_64-pc-linux-gnu-g++  -fPIC -march=amdfam10 -O2 -pipe   -Wno-deprecated  -Wl,-O1 -Wl,--as-needed  -shared -Wl,-soname,libvtkIO.so.5.10 -o ../bin/libvtkIO.so.5.10.1 CMakeFiles/vtkIO.dir/vtkAbstractParticleWriter.cxx.o CMakeFiles/vtkIO.dir/vtkASCIITextCodec.cxx.o CMakeFiles/vtkIO.dir/vtkAVSucdReader.cxx.o CMakeFiles/vtkIO.dir/vtkBMPReader.cxx.o CMakeFiles/vtkIO.dir/vtkBMPWriter.cxx.o CMakeFiles/vtkIO.dir/vtkBYUReader.cxx.o CMakeFiles/vtkIO.dir/vtkBYUWriter.cxx.o CMakeFiles/vtkIO.dir/vtkBase64InputStream.cxx.o CMakeFiles/vtkIO.dir/vtkBase64OutputStream.cxx.o CMakeFiles/vtkIO.dir/vtkBase64Utilities.cxx.o CMakeFiles/vtkIO.dir/vtkCGMWriter.cxx.o CMakeFiles/vtkIO.dir/vtkChacoReader.cxx.o CMakeFiles/vtkIO.dir/vtkCompositeDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkCompositeDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkDatabaseToTableReader.cxx.o CMakeFiles/vtkIO.dir/vtkDEMReader.cxx.o CMakeFiles/vtkIO.dir/vtkDICOMImageReader.cxx.o CMakeFiles/vtkIO.dir/vtkDataCompressor.cxx.o CMakeFiles/vtkIO.dir/vtkDataObjectReader.cxx.o CMakeFiles/vtkIO.dir/vtkDataObjectWriter.cxx.o CMakeFiles/vtkIO.dir/vtkDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkDataSetReader.cxx.o CMakeFiles/vtkIO.dir/vtkDataSetWriter.cxx.o CMakeFiles/vtkIO.dir/vtkDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkDelimitedTextWriter.cxx.o CMakeFiles/vtkIO.dir/vtkEnSight6BinaryReader.cxx.o CMakeFiles/vtkIO.dir/vtkEnSight6Reader.cxx.o CMakeFiles/vtkIO.dir/vtkEnSightGoldBinaryReader.cxx.o CMakeFiles/vtkIO.dir/vtkEnSightGoldReader.cxx.o CMakeFiles/vtkIO.dir/vtkEnSightMasterServerReader.cxx.o CMakeFiles/vtkIO.dir/vtkEnSightReader.cxx.o CMakeFiles/vtkIO.dir/vtkFLUENTReader.cxx.o CMakeFiles/vtkIO.dir/vtkFacetWriter.cxx.o CMakeFiles/vtkIO.dir/vtkGESignaReader.cxx.o CMakeFiles/vtkIO.dir/vtkGAMBITReader.cxx.o CMakeFiles/vtkIO.dir/vtkGaussianCubeReader.cxx.o CMakeFiles/vtkIO.dir/vtkGenericDataObjectReader.cxx.o CMakeFiles/vtkIO.dir/vtkGenericDataObjectWriter.cxx.o CMakeFiles/vtkIO.dir/vtkGenericEnSightReader.cxx.o CMakeFiles/vtkIO.dir/vtkGenericMovieWriter.cxx.o CMakeFiles/vtkIO.dir/vtkGlobFileNames.cxx.o CMakeFiles/vtkIO.dir/vtkGraphReader.cxx.o CMakeFiles/vtkIO.dir/vtkGraphWriter.cxx.o CMakeFiles/vtkIO.dir/vtkIVWriter.cxx.o CMakeFiles/vtkIO.dir/vtkImageReader.cxx.o CMakeFiles/vtkIO.dir/vtkImageReader2.cxx.o CMakeFiles/vtkIO.dir/vtkImageReader2Collection.cxx.o CMakeFiles/vtkIO.dir/vtkImageReader2Factory.cxx.o CMakeFiles/vtkIO.dir/vtkImageWriter.cxx.o CMakeFiles/vtkIO.dir/vtkInputStream.cxx.o CMakeFiles/vtkIO.dir/vtkJavaScriptDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkJPEGReader.cxx.o CMakeFiles/vtkIO.dir/vtkJPEGWriter.cxx.o CMakeFiles/vtkIO.dir/vtkLSDynaPart.cxx.o CMakeFiles/vtkIO.dir/vtkLSDynaPartCollection.cxx.o CMakeFiles/vtkIO.dir/vtkLSDynaReader.cxx.o CMakeFiles/vtkIO.dir/vtkLSDynaSummaryParser.cxx.o CMakeFiles/vtkIO.dir/vtkMFIXReader.cxx.o CMakeFiles/vtkIO.dir/vtkMaterialLibrary.cxx.o CMakeFiles/vtkIO.dir/vtkMCubesReader.cxx.o CMakeFiles/vtkIO.dir/vtkMCubesWriter.cxx.o CMakeFiles/vtkIO.dir/vtkMedicalImageProperties.cxx.o CMakeFiles/vtkIO.dir/vtkMedicalImageReader2.cxx.o CMakeFiles/vtkIO.dir/vtkMetaImageReader.cxx.o CMakeFiles/vtkIO.dir/vtkMetaImageWriter.cxx.o CMakeFiles/vtkIO.dir/vtkMINCImageAttributes.cxx.o CMakeFiles/vtkIO.dir/vtkMINCImageReader.cxx.o CMakeFiles/vtkIO.dir/vtkMINCImageWriter.cxx.o CMakeFiles/vtkIO.dir/vtkMPASReader.cxx.o CMakeFiles/vtkIO.dir/vtkMultiBlockPLOT3DReader.cxx.o CMakeFiles/vtkIO.dir/vtkMoleculeReaderBase.cxx.o CMakeFiles/vtkIO.dir/vtkNetCDFCAMReader.cxx.o CMakeFiles/vtkIO.dir/vtkNetCDFCFReader.cxx.o CMakeFiles/vtkIO.dir/vtkNetCDFPOPReader.cxx.o CMakeFiles/vtkIO.dir/vtkNetCDFReader.cxx.o CMakeFiles/vtkIO.dir/vtkOBJReader.cxx.o CMakeFiles/vtkIO.dir/vtkOggTheoraWriter.cxx.o CMakeFiles/vtkIO.dir/vtkOpenFOAMReader.cxx.o CMakeFiles/vtkIO.dir/vtkOutputStream.cxx.o CMakeFiles/vtkIO.dir/vtkPDBReader.cxx.o CMakeFiles/vtkIO.dir/vtkPLOT3DReader.cxx.o CMakeFiles/vtkIO.dir/vtkPLY.cxx.o CMakeFiles/vtkIO.dir/vtkPLYReader.cxx.o CMakeFiles/vtkIO.dir/vtkPLYWriter.cxx.o CMakeFiles/vtkIO.dir/vtkPNGReader.cxx.o CMakeFiles/vtkIO.dir/vtkPNGWriter.cxx.o CMakeFiles/vtkIO.dir/vtkPNMReader.cxx.o CMakeFiles/vtkIO.dir/vtkPNMWriter.cxx.o CMakeFiles/vtkIO.dir/vtkParticleReader.cxx.o CMakeFiles/vtkIO.dir/vtkPolyDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkPolyDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkPostScriptWriter.cxx.o CMakeFiles/vtkIO.dir/vtkProStarReader.cxx.o CMakeFiles/vtkIO.dir/vtkRectilinearGridReader.cxx.o CMakeFiles/vtkIO.dir/vtkRectilinearGridWriter.cxx.o CMakeFiles/vtkIO.dir/vtkRTXMLPolyDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkRowQuery.cxx.o CMakeFiles/vtkIO.dir/vtkSESAMEReader.cxx.o CMakeFiles/vtkIO.dir/vtkShaderCodeLibrary.cxx.o CMakeFiles/vtkIO.dir/vtkSLACParticleReader.cxx.o CMakeFiles/vtkIO.dir/vtkSLACReader.cxx.o CMakeFiles/vtkIO.dir/vtkSQLDatabase.cxx.o CMakeFiles/vtkIO.dir/vtkSQLDatabaseSchema.cxx.o CMakeFiles/vtkIO.dir/vtkSQLiteDatabase.cxx.o CMakeFiles/vtkIO.dir/vtkSQLiteToTableReader.cxx.o 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CMakeFiles/vtkIO.dir/vtkTreeWriter.cxx.o CMakeFiles/vtkIO.dir/vtkUGFacetReader.cxx.o CMakeFiles/vtkIO.dir/vtkUnstructuredGridReader.cxx.o CMakeFiles/vtkIO.dir/vtkUnstructuredGridWriter.cxx.o CMakeFiles/vtkIO.dir/vtkUTF8TextCodec.cxx.o CMakeFiles/vtkIO.dir/vtkUTF16TextCodec.cxx.o CMakeFiles/vtkIO.dir/vtkVolume16Reader.cxx.o CMakeFiles/vtkIO.dir/vtkVolumeReader.cxx.o CMakeFiles/vtkIO.dir/vtkWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLCompositeDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLDataParser.cxx.o CMakeFiles/vtkIO.dir/vtkXMLDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLDataSetWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLFileReadTester.cxx.o CMakeFiles/vtkIO.dir/vtkXMLGenericDataObjectReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLHierarchicalBoxDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLHierarchicalDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLImageDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLImageDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLHyperOctreeReader.cxx.o 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CMakeFiles/vtkIO.dir/vtkXMLPStructuredDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPStructuredGridReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPStructuredGridWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPUnstructuredDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPUnstructuredDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPUnstructuredGridReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPUnstructuredGridWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLParser.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPolyDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLPolyDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLRectilinearGridReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLRectilinearGridWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLShader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLStructuredDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLStructuredDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLStructuredGridReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLStructuredGridWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLUnstructuredDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLUnstructuredDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLUnstructuredGridReader.cxx.o CMakeFiles/vtkIO.dir/vtkXMLUnstructuredGridWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLUtilities.cxx.o CMakeFiles/vtkIO.dir/vtkXMLWriter.cxx.o CMakeFiles/vtkIO.dir/vtkXMLWriterC.cxx.o CMakeFiles/vtkIO.dir/vtkXYZMolReader.cxx.o CMakeFiles/vtkIO.dir/vtkZLibDataCompressor.cxx.o CMakeFiles/vtkIO.dir/vtkFFMPEGWriter.cxx.o CMakeFiles/vtkIO.dir/vtkPostgreSQLDatabase.cxx.o CMakeFiles/vtkIO.dir/vtkPostgreSQLQuery.cxx.o CMakeFiles/vtkIO.dir/vtkPostgreSQLToTableReader.cxx.o CMakeFiles/vtkIO.dir/vtkTableToPostgreSQLWriter.cxx.o CMakeFiles/vtkIO.dir/vtkMySQLDatabase.cxx.o CMakeFiles/vtkIO.dir/vtkMySQLQuery.cxx.o CMakeFiles/vtkIO.dir/vtkMySQLToTableReader.cxx.o CMakeFiles/vtkIO.dir/vtkTableToMySQLWriter.cxx.o CMakeFiles/vtkIO.dir/vtkODBCDatabase.cxx.o CMakeFiles/vtkIO.dir/vtkODBCQuery.cxx.o CMakeFiles/vtkIO.dir/vtkRowQueryToTable.cxx.o CMakeFiles/vtkIO.dir/vtkArrayReader.cxx.o CMakeFiles/vtkIO.dir/vtkArrayWriter.cxx.o CMakeFiles/vtkIO.dir/vtkArrayDataReader.cxx.o CMakeFiles/vtkIO.dir/vtkArrayDataWriter.cxx.o CMakeFiles/vtkIO.dir/vtkIOInstantiator.cxx.o  -L/usr/lib64/icedtea7/jre/lib/amd64/xawt  -L/usr/lib64/icedtea7/jre/lib/amd64/server -lpq -lmysqlclient -lz -liodbc ../bin/libvtkFiltering.so.5.10.1 ../bin/libvtkDICOMParser.so.5.10.1 ../bin/libvtkNetCDF.so.5.10.1 ../bin/libvtkNetCDF_cxx.so ../bin/libLSDyna.so.5.10.1 ../bin/libvtkmetaio.so.5.10.1 ../bin/libvtksqlite.so.5.10.1 -lpng -lz -lz -ljpeg -ltiff -lexpat -logg -ltheoraenc -ltheoradec ../bin/libvtksys.so.5.10.1 -lavformat -lavcodec -lavutil -lswscale ../bin/libvtkCommon.so.5.10.1 -lm ../bin/libvtkNetCDF.so.5.10.1 -lhdf5 -lhdf5_hl ../bin/libvtksys.so.5.10.1 -ldl -lpthread 
[34m[1mPython SIP Wrapping - generating for vtkImaging
[0mcd /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging && /usr/bin/sip -c /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging/vtkImagingPythonSIP.sip
sip: Deprecation warning: /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging/vtkImagingPythonSIP.sip:1: %Module version number should be specified using the 'version' argument
cd /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-libs/vtk-5.10.1/work/VTK5.10.1 /var/tmp/portage/sci-libs/vtk-5.10.1/work/VTK5.10.1/Imaging /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging /var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging/CMakeFiles/vtkImagingPythonSIP.dir/DependInfo.cmake --color=
Dependee "/var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging/CMakeFiles/vtkImagingPythonSIP.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging/CMakeFiles/vtkImagingPythonSIP.dir/depend.internal".
Dependee "/var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build/Imaging/CMakeFiles/vtkImagingPythonSIP.dir/depend.internal".
[35m[1mScanning dependencies of target vtkImagingPythonSIP
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmysqlclient
collect2: error: ld returned 1 exit status
make[2]: *** [bin/libvtkIO.so.5.10.1] Error 1


I think this bug is related to https://bugs.gentoo.org/show_bug.cgi?id=474952 .
I suppose that 'emerge vtk' fails, because it expects symlinks to libs in /usr/lib/mysql and does not use mysql_config. 



root@impala:/usr/local/portage/sci-geosciences(119)# emerge -pqv '=sci-libs/vtk-5.10.1'
[ebuild   R   ] sci-libs/vtk-5.10.1  USE="R X boost cg doc examples ffmpeg java mpi mysql odbc patented postgres python qt4 theora threads tk -chemistry" VIDEO_CARDS="-nvidia"

[Comment 1 Juergen Rose 2013-07-21 13:52:19 UTC]

root@impala:/usr/local/portage/sci-geosciences(118)# emerge --info '=sci-libs/vtk-5.10.1'
Portage 2.1.12.13 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.17, 3.10.0-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.10.0-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2
KiB Mem:     8165416 total,    876540 free
KiB Swap:   50347696 total,  48524964 free
Timestamp of tree: Sun, 21 Jul 2013 06:30:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5-r1, 3.2.5-r1, 3.3.2-r1
dev-util/cmake:           2.8.11.1
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.14
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.6.4, 4.7.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo x11 science sage-on-gentoo sunrise x-portage x-cpan g-octave
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"
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 /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-php5.3/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.5/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"
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 xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
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/x11 /var/lib/layman/science /var/lib/layman/sage-on-gentoo /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 accessibility 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 bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit cracklib crypt css cuda 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 gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade 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 id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate live lm_sensors lua 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 mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp pam pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline real reiserfs reports rhythmbox 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 stlport subtitles subversion sudo suexec svg svm swig szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" 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" 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" 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 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 ruby websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby18" 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, USE_PYTHON

=================================================================
                        Package Settings
=================================================================

sci-libs/vtk-5.10.1 was built with the following:
USE="R X boost cg doc examples ffmpeg java mpi (multilib) mysql odbc patented postgres python qt4 theora threads tk -chemistry" ABI_X86="64" VIDEO_CARDS="-nvidia"

[Comment 2 Justin Lecher (RETIRED) 2013-07-21 14:26:20 UTC]

I am currently üpreparing the bump to version 6. I will test it for mariadb.

[Comment 3 Juergen Rose 2013-08-04 07:26:32 UTC]

(In reply to Justin Lecher from comment #2)
> I am currently üpreparing the bump to version 6. I will test it for mariadb.

Any news?

[Comment 4 Justin Lecher (RETIRED) 2013-08-07 15:14:43 UTC]

(In reply to Juergen Rose from comment #3)
> (In reply to Justin Lecher from comment #2)
> > I am currently üpreparing the bump to version 6. I will test it for mariadb.
> 
> Any news?

Yeah, vtk changed build system and I have less time. Perhaps I will make it at the weekend. The ebuild is nearly ready, but some modules do not get installed.

[Comment 5 Juergen Rose 2013-10-18 15:22:00 UTC]

Now it fails on the next system with the same error.

[Comment 6 Justin Lecher (RETIRED) 2013-10-21 04:18:57 UTC]

(In reply to Juergen Rose from comment #5)
> Now it fails on the next system with the same error.

There is a branch in the sci overlay with the version bump. Currently I don't have the time to really work on it. The last problem with the ebuild is that not all vtk modules get build.

[Comment 7 Justin Lecher (RETIRED) 2014-01-11 17:04:31 UTC]

Please test version 6.0.0

[Comment 8 Juergen Rose 2014-01-13 14:07:43 UTC]

(In reply to Justin Lecher from comment #7)
> Please test version 6.0.0

How can I do this? I unmasked vtk, set the keywords and I am using the science overlay, but 'emerge -vD vtk' wants to emerge vtk-5.10.1:

root@lynx:/root(15)# grep vtk /etc/portage/package.*
/etc/portage/package.keywords:sci-libs/vtk ~* *
/etc/portage/package.unmask:sci-libs/vtk
/etc/portage/package.use:#sci-libs/vtk patented -qt4
/etc/portage/package.use:sci-libs/vtk patented rendering
root@lynx:/root(16)# layman -l

 * dlan                      [Git       ] (git://github.com/dlanx/dlan-overlay.git                                                                                                                                     )
 * sage-on-gentoo            [Git       ] (http://github.com/cschwan/sage-on-gentoo.git                                                                                                                                )
 * science                   [Git       ] (http://git.overlays.gentoo.org/gitroot/proj/sci.git                                                                                                                         )
 * sunrise                   [Git       ] (http://git.overlays.gentoo.org/gitroot/proj/sunrise-reviewed.git                                                                                                            )
 * x11                       [Git       ] (http://git.overlays.gentoo.org/gitroot/proj/x11.git                                                                                                                         )

root@lynx:/root(17)# emerge -pvD vtk

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] sci-libs/vtk-5.10.1  USE="R X boost cg doc examples ffmpeg java mpi mysql odbc patented postgres python qt4 theora threads tk -chemistry" VIDEO_CARDS="-nvidia" 0 kB

Total: 1 package (1 reinstall), Size of downloads: 0 kB

WARNING: One or more updates have been skipped due to a dependency conflict:

sci-libs/netcdf:0

  (sci-libs/netcdf-4.3.0::gentoo, ebuild scheduled for merge) conflicts with
    ~sci-libs/netcdf-4.1.3[cxx,hdf5] required by (sci-visualization/paraview-4.0.1-r1::gentoo, installed)


!!! The following update(s) have been skipped due to unsatisfied dependencies
!!! triggered by backtracking:

sci-libs/vtk:0

[Comment 9 Juergen Rose 2014-01-13 14:17:24 UTC]

'emerge -pvD --backtrack=30 vtk' did not changed anything.

[Comment 10 Justin Lecher (RETIRED) 2014-01-13 14:24:17 UTC]

(In reply to Juergen Rose from comment #8)
> How can I do this? I unmasked vtk, set the keywords and I am using the
> science overlay, but 'emerge -vD vtk' wants to emerge vtk-5.10.1:

The version is in the tree. PLease check it there.

[Comment 11 Juergen Rose 2014-01-13 15:14:30 UTC]

(In reply to Justin Lecher from comment #10)
> (In reply to Juergen Rose from comment #8)
> > How can I do this? I unmasked vtk, set the keywords and I am using the
> > science overlay, but 'emerge -vD vtk' wants to emerge vtk-5.10.1:
> 
> The version is in the tree. PLease check it there.

How can I check this? At several hosts I observed the following behaviour. If the USE flag rendering is not set for vtk, 'emerge -vD vtk' wants to emerge 
vtk-6.0.0, but if I set this USE flag, only vtk-5.10.1 is to emerge:

root@orca:/root(12)# emerge -pvD vtk

These are the packages that would be merged, in order:

Calculating dependencies |

!!! Problem resolving dependencies for sci-libs/vtk
... done!

!!! The ebuild selected to satisfy "vtk" has unmet requirements.
- sci-libs/vtk-6.0.0::gentoo USE="R X boost cg doc examples ffmpeg java mpi mysql odbc postgres python qt4 tcl theora tk (-aqua) -imaging -offscreen -rendering -test -views" PYTHON_SINGLE_TARGET="python2_7 -python2_6" PYTHON_TARGETS="python2_7 -python2_6" VIDEO_CARDS="-nvidia"

  The following REQUIRED_USE flag constraints are unsatisfied:
    tcl? ( rendering )

  The above constraints are a subset of the following complete expression:
    java? ( qt4 ) python? ( python_single_target_python2_6? ( python_targets_python2_6 ) python_single_target_python2_7? ( python_targets_python2_7 ) exactly-one-of ( python_single_target_python2_6 python_single_target_python2_7 ) ) tcl? ( rendering ) test? ( python ) tk? ( tcl ) exactly-one-of ( X aqua offscreen )

root@orca:/root(13)# we /etc/portage/package.use 
[1] 24963
root@orca:/root(14)# 
** (package_use:24963): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-ZoAyXjjd6e: Connection refused

[1]+  Done                    emacs -i $GEOMETRY $NO_DOS_CONV -name "$BASENAME" "$*"
root@orca:/root(14)# emerge -pvD vtk

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] sci-libs/vtk-5.10.1  USE="R X boost cg doc examples ffmpeg java mpi mysql odbc patented postgres python qt4 theora threads tk -chemistry" VIDEO_CARDS="-nvidia" 0 kB

Total: 1 package (1 reinstall), Size of downloads: 0 kB




Could it be that is reason that vtk-6.0.0 is not found, is the same as the reason in Bug 497860, that prevents the updating of remaining packages?

[Comment 12 Justin Lecher (RETIRED) 2014-01-13 15:19:52 UTC]

(In reply to Juergen Rose from comment #11)
>   The following REQUIRED_USE flag constraints are unsatisfied:
>     tcl? ( rendering )

if you enable USE=tcl you also need to enable USE=rendering

> Could it be that is reason that vtk-6.0.0 is not found, is the same as the
> reason in Bug 497860, that prevents the updating of remaining packages?

No that is different.

[Comment 13 Juergen Rose 2014-01-13 15:43:17 UTC]

(In reply to Justin Lecher from comment #12)
> (In reply to Juergen Rose from comment #11)
> >   The following REQUIRED_USE flag constraints are unsatisfied:
> >     tcl? ( rendering )
> 
> if you enable USE=tcl you also need to enable USE=rendering

That I understand. But why 'emerge -pvD vtk' says, that emerge want to install vtk-5.10.1, if this USE flag is set?


> > Could it be that is reason that vtk-6.0.0 is not found, is the same as the
> > reason in Bug 497860, that prevents the updating of remaining packages?
> 
> No that is different.

[Comment 14 Justin Lecher (RETIRED) 2014-12-26 12:23:09 UTC]

+*vtk-6.1.0 (26 Dec 2014)
+
+  26 Dec 2014; Justin Lecher <[e-mail]> -vtk-5.10.0.ebuild,
+  -vtk-5.10.1.ebuild, vtk-6.0.0.ebuild, +vtk-6.1.0.ebuild,
+  +files/vtk-6.1.0-freetype.patch, +files/vtk-6.1.0-glext.patch,
+  +files/vtk-6.1.0-install.patch, +files/vtk-6.1.0-netcdf.patch,
+  +files/vtk-6.1.0-system.patch, +files/vtk-6.1.0-web.patch, metadata.xml:
+  Version BUmp, #500814; fixes GLintptr declaration problems, #523786; Add slot
+  operators to dependencies, #531040; drop old which obsoletes, #477638,
+  #497224, #520310
+