Bug 452672 – [science overlay] sci-mathematics/scilab-5.3.3-r1 - checking minimal version (1.8.4) of hdf5... configure: error: Wrong version of hdf5. Expected at least 1.8.4. Found 1.8.10

• Status: RESOLVED DUPLICATE of bug 452622
• Product: Gentoo Linux

[Description Juergen Rose 2013-01-17 14:26:08 UTC]

Created attachment 335914 [details]
/var/tmp/portage/sci-mathematics/scilab-5.3.3-r1/work/scilab-5.3.3/config.log

'emerge scilab' fails with:
...
checking jhdf5... /usr/share/hdf-java/lib//jhdf5.jar
checking for h5JNIFatalError in -ljhdf5... yes
checking minimal version (1.8.4) of hdf5... configure: error: Wrong version of hdf5. Expected at least 1.8.4. Found 1.8.10

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-mathematics/scilab-5.3.3-r1/work/scilab-5.3.3/config.log
 * ERROR: sci-mathematics/scilab-5.3.3-r1 failed (configure phase):


root@moose:/boot(45)# emerge --info '=sci-mathematics/scilab-5.3.3-r1'
Portage 2.1.11.43 (default/linux/amd64/10.0/desktop, gcc-4.6.3, glibc-2.16.0, 3.7.1-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.7.1-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.2
KiB Mem:     8167360 total,    853280 free
KiB Swap:   33575840 total,  33575752 free
Timestamp of tree: Wed, 16 Jan 2013 16:30:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p42
dev-java/java-config:     2.1.12-r1
dev-lang/python:          2.7.3-r3, 3.2.3-r2
dev-util/cmake:           2.8.10.2-r1
dev-util/pkgconfig:       0.27.1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.6
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.7 (virtual/os-headers)
sys-libs/glibc:           2.16.0
Repositories: gentoo x11 arcon bicatali sage-on-gentoo science lisp sunrise java-overlay 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-10.3 cadsoft Oracle-BCLA-JavaSE MakeMKV-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="${EPREFIX}/etc/gconf /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-php5.4/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="-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 protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr"
FFLAGS="-march=native -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/arcon /var/lib/layman/bicatali /var/lib/layman/sage-on-gentoo /var/lib/layman/science /var/lib/layman/lisp /var/lib/layman/sunrise /var/lib/layman/java-overlay /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba 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 fts3 fuse g3dvl garmin 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 harness 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 java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kqemu kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lm_sensors lua lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musepack musicbrainz mysql mysqli nautilus ncurses neXt 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 overview pae pam pango pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd 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 sse4 ssl ssse3 startup-notification 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 upower usb userlocales utempter v4l vaapi vala vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ALSA_CARDS="intel8x0" 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_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" 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 synaptics" 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" 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="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="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, USE_PYTHON

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

sci-mathematics/scilab-5.3.3-r1 was built with the following:
USE="bash-completion doc fftw gui hdf5 matio (multilib) nls openmp tk umfpack xcos -debug -static-libs -test" LINGUAS="de ru -ca_ES -es_ES -fr_FR -it -ja -pl -pt_BR -uk -zh_CN -zh_TW"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--no-as-needed"




root@moose:/boot(46)# emerge -pqv '=sci-mathematics/scilab-5.3.3-r1'
[ebuild   R   ] sci-mathematics/scilab-5.3.3-r1  USE="bash-completion doc fftw gui hdf5 matio nls openmp tk umfpack xcos -debug -static-libs {-test}" LINGUAS="de ru -ca_ES -es_ES -fr_FR -it -ja -pl -pt_BR -uk -zh_CN -zh_TW"

[Comment 1 Sébastien Fabbro (RETIRED) 2013-01-17 16:47:05 UTC]

*** This bug has been marked as a duplicate of bug 452622 ***

[Comment 2 Attila Tóth 2013-01-31 03:42:25 UTC]

(In reply to comment #1)
> 
> *** This bug has been marked as a duplicate of bug 452622 ***

I think this bug is not related to the duplicate.
This one has no relation to pytables. Pytables are not needed for scilab to install and this bug occures in the configure phase (GNU). I think python is not involved in failing to properly read the version number of hdf5.

However one might still come, that this scilab version is only accessible from the science overlay. However it's still a bug.

[Comment 3 Attila Tóth 2013-01-31 04:08:11 UTC]

(In reply to comment #1)
> 
> *** This bug has been marked as a duplicate of bug 452622 ***

But it's rather related to java detection routine, with some flaw in using minversion.compateto or the way the version string is prepared for comparison.