'emerge scilab' fails with: >>> Preparing source in /var/tmp/portage/sci-mathematics/scilab-5.5.0_beta1/work/scilab-5.5.0-beta-1 ... * Applying scilab-5.5.0_beta1-followlinks.patch [ ok ] * Applying scilab-5.5.0_beta1-gluegen.patch ... [ ok ] * Applying scilab-5.5.0_beta1-fix-random-runtime-failure.patch ... [ ok ] * Applying scilab-5.5.0_beta1-disable-static-systemlib.patch ... [ ok ] * Applying scilab-5.5.0_beta1-always-use-dynamic-stack.patch ... [ ok ] * Applying scilab-5.5.0_beta1-accessviolation.patch ... [ ok ] * Applying scilab-5.5.0_beta1-java-heap.patch ... [ ok ] /var/tmp/portage/sci-mathematics/scilab-5.5.0_beta1/work/scilab-5.5.0-beta-1/jar /var/tmp/portage/sci-mathematics/scilab-5.5.0_beta1/work/scilab-5.5.0-beta-1 * ERROR: sci-mathematics/scilab-5.5.0_beta1::science failed (prepare phase): * Failed to find jogl-all.jar in jogl-2 ... !!! When you file a bug report, please include the following information: GENTOO_VM=icedtea-7 CLASSPATH="" JAVA_HOME="/usr/lib64/icedtea7" JAVACFLAGS="-source 1.5 -target 1.5" COMPILER="" There is not any jogl-all.jar in jogl-2.0_rc8-r1: root@lynx:/root(6)# qlist -Iv jogl dev-java/jogl-2.0_rc8-r1 root@lynx:/root(7)# qlist jogl | grep jar /usr/share/doc/jogl-2.0_rc8-r1/doc/deployment/lstjars/lstjars.linux_amd64-20100406.log.bz2 /usr/share/doc/jogl-2.0_rc8-r1/doc/deployment/lstjars/lstjars.linux_amd64-20100420.log.bz2 /usr/share/jogl-2/lib/jogl.all-mobile.jar /usr/share/jogl-2/lib/jogl.test.jar /usr/share/jogl-2/lib/jogl.all-noawt.jar /usr/share/jogl-2/lib/jogl-all-natives-linux-amd64.jar /usr/share/jogl-2/lib/jogl.all.jar root@lynx:/root(8)# root@lynx:/root(8)# emerge --info '=sci-mathematics/scilab-5.5.0_beta1::science' Portage 2.2.7 (default/linux/amd64/13.0/desktop, gcc-4.8.1, glibc-2.17, 3.11.6-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.11.6-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.2 KiB Mem: 3987400 total, 974908 free KiB Swap: 12582908 total, 12558416 free Timestamp of tree: Mon, 04 Nov 2013 06:30:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.5-r4, 3.2.5-r3, 3.3.2-r2 dev-util/cmake: 2.8.12 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 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: 4.7.3-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 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" 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 /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=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_lynx" 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 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 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 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 kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live 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 mudflap 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 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 sse4 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter v4l vaapi vala valgrind 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" 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 syslog" DVB_CARDS="usb-wt220u" 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 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, SYNC, USE_PYTHON root@lynx:/root(9)# emerge -pqv '=sci-mathematics/scilab-5.5.0_beta1::science' [ebuild U ] sci-mathematics/scilab-5.5.0_beta1 [5.4.1] USE="bash-completion doc fftw gui 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"
After unmasking dev-java/jogl-2.0.2 'emerge scilab' fails with: ... libtool: link: mpicxx -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/crtbeginS.o .libs/libscispecial_functions_la-sci_dlgamma.o .libs/libscispecial_functions_la-sci_bessely.o .libs/libscispecial_functions_la-sci_beta.o .libs/libscispecial_functions_la-sci_gamma.o .libs/libscispecial_functions_la-sci_legendre.o .libs/libscispecial_functions_la-sci_besselh.o .libs/libscispecial_functions_la-sci_besseli.o .libs/libscispecial_functions_la-sci_besselj.o .libs/libscispecial_functions_la-sci_besselk.o .libs/libscispecial_functions_la-gw_special_functions.o .libs/libscispecial_functions_la-sci_lgamma.o .libs/libscispecial_functions_la-sci_faddeeva.o -Wl,--whole-archive ./.libs/libscispecial_functions-algo.a -Wl,--no-whole-archive -Wl,--as-needed -Wl,--no-as-needed -lcurses -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/../../.. /usr/lib64/libmpi_cxx.so /usr/lib64/libmpi.so -lm -ldl -lrt -lnsl -lutil -lhwloc -ldl-lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/../../../../lib64/crtn.o -march=native -Wl,-O1 -pthread -Wl,-soname -Wl,libscispecial_functions.so.5 -o .libs/libscispecial_functions.so.5.5.0 /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.1/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -ldl-lm collect2: error: ld returned 1 exit status
(In reply to Juergen Rose from comment #1) > /usr/lib64/libmpi.so -lm -ldl -lrt -lnsl -lutil -lhwloc -ldl-lm -lpthread [...] > ld: cannot find -ldl-lm Looks like a typo in the makefile, or two strings concatenated together without space in between. If I were you, I'd try running the failing command manually from within the build directory where and when it fails, and just adding the missing space between -ldl and -lm. Then you can resume the build using 'ebuild <path and name of ebuild> install qmerge'. If that works then you know what you need to fix. Denis.
Looks like it's a bug in the configure file. Somehow the libtool file gets mangled. I need to investigate some more to figure out why. In the mean time it should compile fine if you reinstall hdf5 without the mpi useflag. USE="-mpi" emerge -1 hdf5
(In reply to Guillaume Horel from comment #3) > Looks like it's a bug in the configure file. Somehow the libtool file gets > mangled. I need to investigate some more to figure out why. > In the mean time it should compile fine if you reinstall hdf5 without the > mpi useflag. > USE="-mpi" emerge -1 hdf5 But there is a small problem with 'USE="-mpi" emerge -1 hdf5'. Several packages as hugin, flann and paraview depend on hdf5 with mpi flag, which have to reemerge too.
(In reply to Juergen Rose from comment #4) > (In reply to Guillaume Horel from comment #3) > > Looks like it's a bug in the configure file. Somehow the libtool file gets > > mangled. I need to investigate some more to figure out why. > > In the mean time it should compile fine if you reinstall hdf5 without the > > mpi useflag. > > USE="-mpi" emerge -1 hdf5 > > But there is a small problem with 'USE="-mpi" emerge -1 hdf5'. Several > packages as hugin, flann and paraview depend on hdf5 with mpi flag, which > have to reemerge too. If I have done this all and try to emerge scilab, it fails now with: ... -- Building documentation (en_US) -- LANG=C SCI_DISABLE_TK=1 SCI_JAVA_ENABLE_HEADLESS=1 ./bin/scilab-adv-cli -noatomsautoload -nb -nouserstartup -e "try xmltojar([],[],'en_US');catch disp(lasterror()); exit(-1);end;exit(0);" Building the Scilab manual master document for en_US. Building the scilab manual file [javaHelp] Info: Create image dae_1.png from line 572 in dae.xml Total files without example: 710 Total generated html files: 2795 Generate image ./dae_1.png from Scilab code from file dae.xml Generate a loader file Generate a Makefile ilib_gen_Make: configure : Generate Makefile. ilib_gen_Make: Copy compilation files (Makefile*, libtool...) to TMPDIR ilib_gen_Make: Copy t22.c to TMPDIR ilib_gen_Make: Modification of the Makefile in TMPDIR. Running the Makefile Generate a cleaner file Shared archive loaded. Link done. -- Building documentation (de_DE) -- LANG=C SCI_DISABLE_TK=1 SCI_JAVA_ENABLE_HEADLESS=1 ./bin/scilab-adv-cli -noatomsautoload -nb -nouserstartup -e "try xmltojar([],[],'de_DE');catch disp(lasterror()); exit(-1);end;exit(0);" setlanguage: Falscher Typ für Eingangsargument #1: Zeichenkette erwartet. Makefile:2027: recipe for target 'doc' failed make: *** [doc] Error 1 Should I file a separate bug?
'USE=-doc emerge -v scilab' worked.
Regarding the mpi flag: I changed the ebuild, so now I think it should build fine even if the mpi flag is set for hdf5. The other bug that you have seems to be doc related and specifically the german docs (I only tested with us and french). Can you please file a seperate bug for that. If you need it to work now, you can remove "de" from LINGUAS in your make.conf and it should build fine.
(In reply to Guillaume Horel from comment #7) > Regarding the mpi flag: I changed the ebuild, so now I think it should build > fine even if the mpi flag is set for hdf5. > > The other bug that you have seems to be doc related and specifically the > german docs (I only tested with us and french). Can you please file a > seperate bug for that. If you need it to work now, you can remove "de" from > LINGUAS in your make.conf and it should build fine. Is it possible to remove de LINGUA flag only for one package?
you should be able to do LINGUAS="en" emerge -1 scilab and it should only compile the english doc.
It should compile now with LINGUAS="de"
scilab-5.4.0 is not in the overlay anymore. The most recent version is scilab-5.5.2.
