'emerge scilab' fails now with: ... libtool: link: mpif77 -shared .libs/libscicore_la-inffic.o .libs/libscicore_la-cs2st.o .libs/libscicore_la-tmpdir.o .libs/libscicore_la-intmacr2tree.o .libs/libscicore_la-run.o .libs/libscicore_la-InitScilab.o .libs/libscicore_la-getval.o .libs/libscicore_la-md5.o .libs/libscicore_la-inisci-c.o .libs/libscicore_la-IsAScalar.o .libs/libscicore_la-texmacs.o .libs/libscicore_la-sciquit.o .libs/libscicore_la-stack1.o .libs/libscicore_la-realmain.o .libs/libscicore_la-stack3.o .libs/libscicore_la-str2sci.o .libs/libscicore_la-getmodules.o .libs/libscicore_la-setgetSCIpath.o .libs/libscicore_la-getmemory.o .libs/libscicore_la-Funtab.o .libs/libscicore_la-csignal.o .libs/libscicore_la-callinterf.o .libs/libscicore_la-scimem.o .libs/libscicore_la-banier.o .libs/libscicore_la-isanan.o .libs/libscicore_la-parse.o .libs/libscicore_la-timer.o .libs/libscicore_la-stack2.o .libs/libscicore_la-xscion.o .libs/libscicore_la-SetScilabEnvironment.o .libs/libscicore_la-hashtable_core.o .libs/libscicore_la-returnanan.o .libs/libscicore_la-LoadFunctionsTab.o .libs/libscicore_la-with_module.o .libs/libscicore_la-loadversion.o .libs/libscicore_la-version.o .libs/libscicore_la-stackinfo.o .libs/libscicore_la-scirun.o .libs/libscicore_la-SCIHOME.o .libs/libscicore_la-warningmode.o .libs/libscicore_la-InitializeCore.o .libs/libscicore_la-TerminateCore.o .libs/libscicore_la-coretable.o .libs/libscicore_la-returnProperty.o .libs/libscicore_la-returnPropertyList.o .libs/libscicore_la-scilabmode.o .libs/libscicore_la-GetXmlFileEncoding.o .libs/libscicore_la-islittleendian.o .libs/libscicore_la-terme.o .libs/libscicore_la-ifexpr.o .libs/libscicore_la-expr.o .libs/libscicore_la-getcommandlineargs.o .libs/libscicore_la-syncexec.o .libs/libscicore_la-callFunctionFromGateway.o .libs/libscicore_la-getvariablesname.o .libs/libscicore_la-commandwords.o .libs/libscicore_la-freeArrayOfString.o .libs/libscicore_la-getstaticdebuginfo.o .libs/libscicore_la-getdynamicdebuginfo.o .libs/libscicore_la-callDynamicGateway.o .libs/libscicore_la-gw_dynamic_generic.o .libs/libscicore_la-dynamic_gateways.o .libs/libscicore_la-readGateway.o .libs/libscicore_la-comparehandles.o .libs/libscicore_la-setPrecisionFPU.o .libs/libscicore_la-LaunchScilabSignal.o .libs/libscicore_la-getos.o .libs/libscicore_la-mode_exec.o .libs/libscicore_la-predef.o .libs/libscicore_la-transposeMatrix.o .libs/libscicore_la-recursionFunction.o .libs/libscicore_la-typename.o .libs/libscicore_la-inittypenames.o .libs/libscicore_la-funcprot.o .libs/libscicore_la-scimem64.o .libs/clunit.o .libs/getlin.o .libs/allowptr.o .libs/isany.o .libs/hmcreate.o .libs/nextj.o .libs/setgetmode.o .libs/showstack.o .libs/misops.o .libs/iseye.o .libs/chkvar.o .libs/setippty.o .libs/compil.o .libs/funnam.o .libs/isnum.o .libs/cmdstr.o .libs/logops.o .libs/atome.o .libs/hndlops.o .libs/cmplxt.o .libs/skpins.o .libs/folhp.o .libs/cvname.o .libs/funs.o .libs/fact.o .libs/inibrk.o .libs/typ2cod.o .libs/prompt.o .libs/intstr.o .libs/createref.o .libs/btof.o .libs/matzs.o .libs/getnum.o .libs/btofm.o .libs/getsym.o .libs/findequal.o .libs/stackg.o .libs/find.o .libs/israt.o .libs/setlnb.o .libs/mrknmd.o .libs/stackgl.o .libs/allops.o .libs/mname.o .libs/command.o .libs/ref2val.o .libs/namstr.o .libs/stack.o .libs/isbrk.o .libs/majmin.o .libs/xerbla.o .libs/dtosci.o .libs/bexec.o .libs/varfunptr.o .libs/getfun.o .libs/savlod.o .libs/error.o .libs/cvdm.o .libs/tradsl.o .libs/mkindx.o .libs/whatln.o .libs/errmgr.o .libs/defmat.o .libs/mklist.o .libs/sigbas.o .libs/indxg.o .libs/matz.o .libs/istrue.o .libs/inisci.o .libs/ptover.o .libs/getfunction.o .libs/stackp.o .libs/dbasin.o .libs/macro.o .libs/extlarg.o .libs/getstr.o .libs/cvwm.o .libs/storeglobal.o .libs/lst2vars.o .libs/basnms.o .libs/matc.o .libs/ptrback.o .libs/getch.o .libs/ftob.o .libs/seteol.o .libs/basin.o .libs/clause.o .libs/compcl.o .libs/termf.o .libs/expsum.o .libs/eqid.o .libs/copyvar.o .libs/putid.o .libs/itosci.o .libs/stackr2d.o .libs/stacki2d.o .libs/stackc2i.o .libs/isinstring.o .libs/relocstack.o .libs/libscicore_la-sci_stacksize.o .libs/libscicore_la-sci_resume.o .libs/libscicore_la-sci_mtlb_mode.o .libs/libscicore_la-sci_banner.o .libs/libscicore_la-sci_where.o .libs/libscicore_la-sci_errcatch.o .libs/libscicore_la-sci_getos.o .libs/libscicore_la-sci_format.o .libs/libscicore_la-sci_getmemory.o .libs/libscicore_la-sci_havewindow.o .libs/libscicore_la-sci_delbpt.o .libs/libscicore_la-sci_macr2lst.o .libs/libscicore_la-sci_isdef.o .libs/libscicore_la-sci_isglobal.o .libs/libscicore_la-sci_who.o .libs/libscicore_la-sci_errclear.o .libs/libscicore_la-sci_global.o .libs/libscicore_la-sci_funcprot.o .libs/libscicore_la-sci_newfun.o .libs/libscicore_la-sci_warning.o .libs/libscicore_la-sci_dispbpt.o .libs/libscicore_la-sci_intppty.o .libs/libscicore_la-sci_ieee.o .libs/libscicore_la-sci_gstacksize.o .libs/libscicore_la-sci_lasterror.o .libs/libscicore_la-sci_funptr.o .libs/libscicore_la-sci_return.o .libs/libscicore_la-sci_exists.o .libs/libscicore_la-sci_getmd5.o .libs/libscicore_la-sci_clear.o .libs/libscicore_la-sci_clearfun.o .libs/libscicore_la-sci_setbpt.o .libs/libscicore_la-sci_getmodules.o .libs/libscicore_la-sci_what.o .libs/libscicore_la-sci_predef.o .libs/libscicore_la-sci_clearglobal.o .libs/libscicore_la-sci_arg.o .libs/libscicore_la-sci_type.o .libs/libscicore_la-sci_typename.o .libs/libscicore_la-sci_mode.o .libs/libscicore_la-sci_macr2tree.o .libs/libscicore_la-sci_iserror.o .libs/libscicore_la-sci_getversion.o .libs/libscicore_la-sci_getdebuginfo.o .libs/libscicore_la-sci_debug.o .libs/libscicore_la-gw_core.o .libs/libscicore_la-gw_user.o .libs/libscicore_la-gw_user2.o .libs/libscicore_la-sci_error.o .libs/libscicore_la-sci_sciargs.o .libs/libscicore_la-sci_with_module.o .libs/libscicore_la-sci_islittleendian.o .libs/libscicore_la-sci_getscilabmode.o .libs/libscicore_la-sci_getvariablesonstack.o .libs/libscicore_la-sci_readgateway.o .libs/libscicore_la-sci_comp.o .libs/libscicore_la-sci_exit.o .libs/sci_errclear.o .libs/sci_global.o .libs/sci_mtlb_mode.o .libs/sci_resume.o .libs/sci_dispbpt.o .libs/sci_useascommand.o .libs/sci_intppty.o .libs/sci_ieee.o .libs/sci_macrovar.o .libs/sci_exists.o .libs/sci_errcatch.o .libs/sci_clear.o .libs/sci_argn.o .libs/sci_setbpt.o .libs/sci_clearglobal.o .libs/sci_delbpt.o .libs/where.o .libs/sci_iserror.o .libs/sci_debug.o .libs/sci_comp.o .libs/sci_isglobal.o /usr/lib64/libxml2.so -lz -ldl -lcurses -lm -march=nocona -m64 -O1 -soname libscicore.so.5 -o .libs/libscicore.so.5.0.2 x86_64-pc-linux-gnu-gfortran: libscicore.so.5: No such file or directory x86_64-pc-linux-gnu-gfortran: unrecognized option '-soname' make[2]: *** [libscicore.la] Error 1 Reproducible: Always root@moose:/root(11)# emerge --info =sci-mathematics/scilab-5.2.1 Portage 2.1.8.3 (default/linux/amd64/10.0/desktop, gcc-4.4.3, glibc-2.11.1-r0, 2.6.33-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.33-gentoo-r1-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.0.1 Timestamp of tree: Wed, 26 May 2010 10:00:01 +0000 app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11 dev-lang/python: 2.6.5-r2, 3.1.2-r3 dev-python/pycrypto: 2.1.0 dev-util/cmake: 2.8.1-r1 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.1-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.3-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.7b virtual/os-headers: 2.6.33 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" GENTOO_MIRRORS="http://distfiles.gentoo.org" LC_ALL="C" LDFLAGS="-Wl,-O1" LINGUAS="de fr" MAKEOPTS="-j3" 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/science /var/lib/layman/x11 /var/lib/layman/n4g /var/lib/layman/java-overlay /var/lib/layman/zugaina /var/lib/layman/sunrise /var/lib/layman/arcon /usr/local/portage /var/lib/cpan" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit X Xaw3d a52 aac abiword acl acpi afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth 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 dbase dbi dbm dbus designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi eds elf emacs emboss empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm gedit geoip geolocation geos gif gimp ginac git glade glib glitz gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings qemu qhull qt3support qt4 quicktime readline reflection reiserfs rle romio rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc 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_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache 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" CAMERAS="canon" ELIBC="glibc" 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" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="nv nvidia 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, LANG, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS root@moose:/root(12)# emerge -pqv =sci-mathematics/scilab-5.2.1 [ebuild N ] sci-mathematics/scilab-5.2.1 USE="doc fftw gui hdf5 matio nls tk umfpack -xcos"
Created attachment 232979 [details] /var/tmp/portage/sci-mathematics/scilab-5.2.1/temp/build.log
I get the same error on i686 systems: ... la-sci_comp.o .libs/libscicore_la-sci_exit.o .libs/sci_errclear.o .libs/sci_global.o .libs/sci_mtlb_mode.o .libs/sci_resume.o .libs/sci_dispbpt.o .libs/sci_useascommand.o .libs/sci_intppty.o .libs/sci_ieee.o .libs/sci_macrovar.o .libs/sci_exists.o .libs/sci_errcatch.o .libs/sci_clear.o .libs/sci_argn.o .libs/sci_setbpt.o .libs/sci_clearglobal.o .libs/sci_delbpt.o .libs/where.o .libs/sci_iserror.o .libs/sci_debug.o .libs/sci_comp.o .libs/sci_isglobal.o /usr/lib/libxml2.so -lz -ldl -lcurses -lm -march=pentium-m -O1 -soname libscicore.so.5 -o .libs/libscicore.so.5.0.2 i686-pc-linux-gnu-gfortran: libscicore.so.5: No such file or directory i686-pc-linux-gnu-gfortran: unrecognized option '-soname' make[2]: *** [libscicore.la] Error 1
Almost two weeks later: any news?
One month later: anybody here?
(In reply to comment #4) > One month later: anybody here? Dear Jürgen, thank you for reporting this bug. We at sci-math are heavily overworked, not to mention we are all volunteers. You could take a more active stance and try to investigate this issue yourself. For instance, if you unpack the tarball and try to build independent of portage. Does the problem persist? If yes, you could contact the developers and ask them for help. If not, then it is a Gentoo issue and you could look at the ebuild and try to figure the reason there. Any additional information you can provide will speed up the process of getting this fixed. No offense, thanks for flying Gentoo.
Could you please comment on that, cp-cluster?
(In reply to comment #6) > Could you please comment on that, cp-cluster? > 1. The buildsystem is calling the fortran compiler incorrectly, i.e. directly passing linker flags to it. 2. 5.2.1 isn't in the main tree, what overlay are you using?
Hi Thomas, I am prepared to support you, but I need some suggestions. I unpacked the tarball /usr/src and did a './configure --prefix=/usr', but it failed with: configure: error: Could not find or use the Java package/jar jgraphx used by Diagram design (looking for package com.mxgraph.model.mxCell) I tried to find some jgraphx specific configure options: orca scilab-5.2.1 # ./configure --help | grep -ie "java\|jgraphx" --enable-debug-java Print warning messages and line numbers (Java code) --enable-build-swig Regenerate Java => C wrappers produces by Swig (A Java Development Kit (JDK) is mandatory for this --enable-build-giws Regenerate C/C++ => Java wrappers produces by Giws (A Java Development Kit (JDK) is mandatory for this --without-javasci Disable the Java/Scilab interface (javasci) I don't see anything helpful. I was looking for jgraphx specific patches in scilab-5.2.1.ebuild: orca scilab-5.2.1 # grep -i -A4 jgraphx /var/lib/layman/science/sci-mathematics/scilab/scilab-5.2.1.ebuild >=dev-java/jgraphx-1.2.0.7 dev-java/jogl dev-java/jgoodies-looks dev-java/skinlf dev-java/jrosetta -- # fix for jgraphx epatch "${FILESDIR}"/${P}-scilib-fix.patch epatch "${FILESDIR}"/${P}-nojavacheckversion.patch # apply blindly some debian patches I don't know, how to apply the scilab-5.2.1-scilib-fix.patch to my source tree. And it seems me, that it has nothing to do with my problem. orca scilab-5.2.1 # cat /var/lib/layman/science/sci-mathematics/scilab/files/scilab-5.2.1-scilib-fix.patch ... -SCILIB=$SCI/bin:$SCI/lib/scilab/:$SCI/lib64/scilab/ +SCILIB=$SCI/bin:$SCI/lib/scilab/:$SCI/lib64/scilab/:/usr/lib64/scilab:/usr/lib /scilab ... /usr/lib64/scilab and /usr/lib/scilab does not yet exist. I applied the scilab-nojavacheckversion.patch manually: orca scilab-5.2.1 # cat /var/lib/layman/science/sci-mathematics/scilab/files/scilab-5.2.1-nojavacheckversion.patch ... - AC_JAVA_CHECK_VERSION_PACKAGE([jgraphx],[import com.mxgraph.view.mxGraph;],$JGRAPHX,[1.2.0.7],[mxGraph.VERSION]) + #AC_JAVA_CHECK_VERSION_PACKAGE([jgraphx],[import com.mxgraph.view.mxGraph;],$JGRAPHX,[1.2.0.7],[mxGraph.VERSION]) ... But I still get the same error. Any further suggestion?
Hi Justin, it is in the science overlay: orca scilab-5.2.1 # emerge -pvuDN scilab These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] sci-mathematics/scilab-5.2.1 USE="doc fftw gui hdf5 matio nls tk umfpack -xcos" 0 kB [1] Total: 1 package (1 new), Size of downloads: 0 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/science
(In reply to comment #9) > it is in the science overlay: but also depends on various experimental packages from java-overlay :( This scilab ebuild seems very preliminary. I cannot even get to the compile stage. The issue in comment #8 seems to be fixed by the patches # fix for jgraphx epatch "${FILESDIR}"/${P}-scilib-fix.patch epatch "${FILESDIR}"/${P}-nojavacheckversion.patch In my oppinion these to very much look like the solution to the jgraphx problem :) For applying patches I recommend the 10 minute guide http://stephenjungels.com/jungels.net/articles/diff-patch-ten-minutes.html and the man page of diff and patch of course. There is a new upstream release 5.2.2, but I doubt that this fixes many things. This package definitely needs some tender loving care.
Oh, I did not read carefully, > /usr/lib64/scilab and /usr/lib/scilab does not yet exist. I applied the > scilab-nojavacheckversion.patch manually: > > orca scilab-5.2.1 # cat > /var/lib/layman/science/sci-mathematics/scilab/files/scilab-5.2.1-nojavacheckversion.patch > ... > - AC_JAVA_CHECK_VERSION_PACKAGE([jgraphx],[import > com.mxgraph.view.mxGraph;],$JGRAPHX,[1.2.0.7],[mxGraph.VERSION]) > + > #AC_JAVA_CHECK_VERSION_PACKAGE([jgraphx],[import > com.mxgraph.view.mxGraph;],$JGRAPHX,[1.2.0.7],[mxGraph.VERSION]) This patches configure.ac, but not the configure script. A program called autoconf is used to create the configure script. That is why the ebuild calls 'eautoreconf' and you have to do this manually in case you change configure.ac
Seven weeks later, is still anybody iterested in scilab-5.2.1?
(In reply to comment #12) > Seven weeks later, is still anybody iterested in scilab-5.2.1? These days all the action is in bug 237572. *** This bug has been marked as a duplicate of bug 237572 ***
