Bug 488242 – sci-libs/vtk - File "/usr/lib64/python2.7/site-packages/vtk/__init__.py", line 43, in <module> from vtkIOPython import * ImportError: libpng15.so.15: cannot open shared object file: No such file or directory

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Juergen Rose 2013-10-16 15:30:08 UTC]

'emerge mayavi' fails with:
...
byte-compiling /var/tmp/portage/sci-visualization/mayavi-4.3.0/image//_python2.7/usr/lib64/python2.7/site-packages/mayavi/version.py to version.pyc
writing byte-compilation script '/var/tmp/portage/sci-visualization/mayavi-4.3.0/temp/python2.7/tmp4y5i4c.py'
/usr/bin/python2.7 -OO /var/tmp/portage/sci-visualization/mayavi-4.3.0/temp/python2.7/tmp4y5i4c.py
removing /var/tmp/portage/sci-visualization/mayavi-4.3.0/temp/python2.7/tmp4y5i4c.py
running install_data
Traceback (most recent call last):
  File "setup.py", line 498, in <module>
    **config
...
  File "/usr/lib64/python2.7/site-packages/vtk/__init__.py", line 43, in <module>
    from vtkIOPython import *
ImportError: libpng15.so.15: cannot open shared object file: No such file or directory
 * ERROR: sci-visualization/mayavi-4.3.0::gentoo failed (install phase):
...
>>> Failed to emerge sci-visualization/mayavi-4.3.0, Log file:




root@dog:/root(4)# emerge --info '=sci-visualization/mayavi-4.3.0::gentoo'
Portage 2.2.7 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.17, 3.11.1-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.11.1-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_E7300_@_2.66GHz-with-gentoo-2.2
KiB Mem:     4055104 total,   1178004 free
KiB Swap:   16777208 total,  16754068 free
Timestamp of tree: Wed, 16 Oct 2013 05:00:01 +0000
ld GNU ld (GNU Binutils) 2.23.2
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5-r2, 3.2.5-r2, 3.3.2-r2
dev-util/cmake:           2.8.11.2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.2
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, 1.13.4, 1.14
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.6.4, 4.7.3-r1, 4.8.1-r1
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.11 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo science sunrise voyageur x-portage g-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 NVIDIA-CUDA Nero-AAC-EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions /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-php5.5/ext-active/ /etc/php/cgi-php5.5/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=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="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
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_dog"
PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/voyageur /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 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 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 irda ithreads jabber jadetex java jbig 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 matrox media-library mercurial mikmod mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pae pam pango 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 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 ssse3 stlport subtitles subversion sudo suexec svg svm swig systemd 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 wifi win32codecs 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="hda-intel" 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" 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" 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



root@dog:/root(5)# emerge -pqv '=sci-visualization/mayavi-4.3.0::gentoo'
[ebuild     U ] sci-visualization/mayavi-4.3.0 [4.2.0] USE="doc examples {-test}" PYTHON_TARGETS="python2_7%*" 



root@dog:/root(6)# qlist -Iv libpng
media-libs/libpng-1.6.6



root@dog:/root(7)# ll /usr/lib/libpng*
lrwxrwxrwx 1 root root     18 Sep 25 16:37 /usr/lib/libpng16.so -> libpng16.so.16.6.0*
lrwxrwxrwx 1 root root     18 Sep 25 16:37 /usr/lib/libpng16.so.16 -> libpng16.so.16.6.0*
-rwxr-xr-x 1 root root 220192 Sep 25 16:37 /usr/lib/libpng16.so.16.6.0*
lrwxrwxrwx 1 root root     11 Sep 25 16:37 /usr/lib/libpng.so -> libpng16.so*



It looks if the installed grass and vtk depend on libpng15:

root@dog:/root(9)# for f in /usr/lib/*.so ; do if ldd $f | grep libpng15 ; then echo $f; fi ; done
ldd: /usr/lib/libcblas.so: No such file or directory
        libpng15.so.15 => not found
/usr/lib/libgrass_display.6.4.2.so
        libpng15.so.15 => not found
/usr/lib/libgrass_display.so
        libpng15.so.15 => not found
/usr/lib/libgrass_pngdriver.6.4.2.so
        libpng15.so.15 => not found
/usr/lib/libgrass_pngdriver.so
        libpng15.so.15 => not found
/usr/lib/libgrass_raster.6.4.2.so
        libpng15.so.15 => not found
/usr/lib/libgrass_raster.so
        libpng15.so.15 => not found
        libpng15.so.15 => not found
/usr/lib/libQVTK.so
        libpng15.so.15 => not found
        libpng15.so.15 => not found
/usr/lib/libvtkChartsJava.so
        libpng15.so.15 => not found
        libpng15.so.15 => not found
/usr/lib/libvtkChartsPythonD.so
        libpng15.so.15 => not found
        libpng15.so.15 => not found
/usr/lib/libvtkCharts.so
...
/usr/lib/libvtkWidgets.so
        libpng15.so.15 => not found
        libpng15.so.15 => not found
/usr/lib/libvtkWidgetsTCL.so
root@dog:/root(10)#

[Comment 1 Tom Wijsman (TomWij) (RETIRED) 2013-10-16 18:41:22 UTC]

Could you please try `revdep-rebuild` to ensure it is not broken linkage?

[Comment 2 Jeroen Roovers (RETIRED) 2013-10-18 14:45:31 UTC]

Either sci-libs/vtk doesn't work properly with media-libs/libpng-1.6, or you forgot to run `emerge @preserved-rebuild' (or indeed revdep-rebuild).

[Comment 3 Juergen Rose 2013-10-18 16:10:51 UTC]

I did revdep-rebuild, it fails only to reemerge vtk because.(In reply to Jeroen Roovers from comment #2)
> Either sci-libs/vtk doesn't work properly with media-libs/libpng-1.6, or you
> forgot to run `emerge @preserved-rebuild' (or indeed revdep-rebuild).

I did revdep-rebuild, but it fails to reemerge vtk because of bug https://bugs.gentoo.org/show_bug.cgi?id=477638. And the installed vtk depends on libpng15.so.15.