Bug 420315 – sci-mathematics/octave-3.6.2 fails to emerge due to undefined reference to `_gfortran_transfer_real_write@GFORTRAN_1.4' in sci-mathematics/octave-3.6.2/work/octave-3.6.2_build/libcruft/.libs/libcruft.so

• Status: RESOLVED DUPLICATE of bug 420409
• Product: Gentoo Linux

[Description Juergen Rose 2012-06-08 20:14:39 UTC]

'emerge octave' fails with:
...
creating .DOCSTRINGS from .cc source files
/var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2/build-aux/move-if-change .DOCSTRINGS DOCSTRINGS
DOCSTRINGS is unchanged
touch .DOCSTRINGS
/var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2_build/libcruft/.libs/libcruft.so: undefined reference to `_gfortran_transfer_real_write@GFORTRAN_1.4'
/var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2_build/libcruft/.libs/libcruft.so: undefined reference to `_gfortran_transfer_character_write@GFORTRAN_1.4'
/var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2_build/libcruft/.libs/libcruft.so: undefined reference to `_gfortran_transfer_integer_write@GFORTRAN_1.4'
collect2: ld returned 1 exit status
make[3]: *** [octave] Error 1




root@lynx:/root(23)# emerge --info '=sci-mathematics/octave-3.6.2'
Portage 2.1.10.65 (default/linux/amd64/10.0/desktop, gcc-4.6.3, glibc-2.15-r2, 3.4.0-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.4.0-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.1
Timestamp of tree: Fri, 08 Jun 2012 17:35:01 +0000
app-shells/bash:          4.2_p29
dev-java/java-config:     2.1.12
dev-lang/python:          2.7.3-r2, 3.2.3-r1
dev-util/cmake:           2.8.8-r2
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.10.2
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.5, 1.12.1
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2, 4.6.3
sys-devel/gcc-config:     1.7.2
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.4 (virtual/os-headers)
sys-libs/glibc:           2.15-r2
Repositories: gentoo lordvan x11 bicatali sage-on-gentoo science dilfridge arcon ibormuth java-overlay proaudio sunrise lisp local x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.3 cadsoft Oracle-BCLA-JavaSE"
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/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /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="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch 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"
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 --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/lordvan /var/lib/layman/x11 /var/lib/layman/bicatali /var/lib/layman/sage-on-gentoo /var/lib/layman/science /var/lib/layman/dilfridge /var/lib/layman/arcon /var/lib/layman/ibormuth /var/lib/layman/java-overlay /var/lib/layman/pro-audio /var/lib/layman/sunrise /var/lib/layman/lisp /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 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 dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc 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 fpx fts3 fuse g3dvl galago garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gtk3 gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos kpathsea kqemu kvm ladspa lame lapack laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc live lua lzo mad mail maildir mapnik math matroska media-library mkl mmx mmxext mng 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 obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pam pango pcre pda pdf perl 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 readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter vaapi video virtualbox visio vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml 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 cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="canon fuji" 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr" 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_TARGETS="python3_2 python2_7" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nv 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


root@lynx:/root(26)# emerge -pqv '=sci-mathematics/octave-3.6.2'
[ebuild     U ] sci-mathematics/octave-3.6.2 [3.6.1] USE="X curl doc fftw glpk gnuplot imagemagick opengl qhull qrupdate readline sparse zlib -static-libs"

[Comment 1 Adrian Bassett 2012-06-09 06:47:55 UTC]

(In reply to comment #0)
> 'emerge octave' fails with:
> ...
> creating .DOCSTRINGS from .cc source files
> /var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2/build-aux/
> move-if-change .DOCSTRINGS DOCSTRINGS
> DOCSTRINGS is unchanged
> touch .DOCSTRINGS
> /var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2_build/
> libcruft/.libs/libcruft.so: undefined reference to
> `_gfortran_transfer_real_write@GFORTRAN_1.4'
> /var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2_build/
> libcruft/.libs/libcruft.so: undefined reference to
> `_gfortran_transfer_character_write@GFORTRAN_1.4'
> /var/tmp/portage/sci-mathematics/octave-3.6.2/work/octave-3.6.2_build/
> libcruft/.libs/libcruft.so: undefined reference to
> `_gfortran_transfer_integer_write@GFORTRAN_1.4'
> collect2: ld returned 1 exit status
> make[3]: *** [octave] Error 1
> 

I found that both 3.6.1 and 3.6.2 failed with gcc-4.6.3 but emerged OK with 4.5.3.

[Comment 2 Juergen Rose 2012-06-10 10:41:22 UTC]

I have here at least five systems, where I was able to emerge octave-3.6.2 with x86_64-pc-linux-gnu-4.6.3 and three systems with the undefined reference to _gfortran_transfer_integer_write@GFORTRAN_1.4. It looks like the undefined reference to _gfortran_transfer_integer_write@GFORTRAN_1.4 occurs on all systems, where I did not 'emerge -uvDNe system' after gcc-upgrade.

[Comment 3 Sven E. 2012-06-10 22:57:44 UTC]

This is not really an octave bug. IT is a sort of gcc bug in combination with gentoo's slotting etc. . I assume toolchain needs to look into this, because knowledge of the whole toolchain etc. will be needed.

Here is what I found, did and what I think causes the whole problem:

The error message about the undefined reference usually implies there's a lib linking problem, well at least some linkign issue.

The named symbol is in libgfortran and as can be observed the symbol is versioned.

Now while there are several slots of gcc installed, there are multiple libgfortran instances. On the system I inspeced the named versioned symbol only existed in the 4.6.x branch of gcc.

Now here's the fun part: Even though the ABI changed, the actual version of the .so did not change.

Because of this, I assume this is what happens: During the build of octave, when linking is done, the libgfortran of the active gcc is used. This version includes the symbol though. But other libs, that were linked to an older version ob libgfortran don't 'know' anything about this 'new' versioned symbol.

What is a little weird though is this: When LD resolves the libs and links gfortran, it would resolve to the newest libgfortran (or the one active due to compiler selection). This libgfortran would then be used. That would work perfectly well, as long as the API and ABI are the same. The fact it does not work made me think it has to be an ABI problem.

So I started rebuilding every package linked against gfortran and then reemerge octave after each of the packages. In my case arpack was the package that made the difference, if I am right, it could be any package linked against gfortran for others.

It might even be, that the problem only occurs with libs linked against gfortran using some specific linker flags, that I cannot tell.

So, revdep cannot solve the problem right now, since gfortran has the same versioning info and revdep itselfg cannot 'see' the ABI change. gcc-config needs to switch libgfortran otherwise different linker problems might occur in other cases. That's what makes me believe this needs to be investigated by toolchain, to find a work around that works for average users, except telling them to reemerge everything linked against libgfortran.

I hope this can help in fixing this error, after switching to gcc-4.6 do a revdep-rebuild on libgfortran and you should be good to go as a temporary workaround. 

For the time being it might be wise to add an informational message to the ebuild.

[Comment 4 Sven E. 2012-06-10 23:11:10 UTC]

(In reply to comment #2)
> I have here at least five systems, where I was able to emerge octave-3.6.2
> with x86_64-pc-linux-gnu-4.6.3 and three systems with the undefined
> reference to _gfortran_transfer_integer_write@GFORTRAN_1.4. It looks like
> the undefined reference to _gfortran_transfer_integer_write@GFORTRAN_1.4
> occurs on all systems, where I did not 'emerge -uvDNe system' after
> gcc-upgrade.

I would be interested in this: On the systems where octave does not build, what packages are listed for 'emerge -uvDNep system' and also for a revdep-rebuild libgfortran.

Does only reemerging these packages that match both conditions fix the octave build issue?

[Comment 5 Juergen Rose 2012-06-11 11:31:10 UTC]

At "lynx", where I found the bug, 'emerge -uvDNe systems' just runs for several hours. At a second affected system ("grizzly") 'revdep-rebuild --library libgfortran' does not reemerge any package:

root@grizzly:/root(28)# revdep-rebuild --library libgfortran
 * Configuring search environment for revdep-rebuild
 * Environment mismatch from previous run, deleting temporary files...
 * Checking reverse dependencies
 * Packages containing binaries and libraries using libgfortran
 * will be emerged.
 * Collecting system binaries and libraries
 * Generated new 1_files.rr
 * Checking dynamic linking 
[ 100% ]                 
 * There are no dynamic links to libgfortran... All done. 


I will attach the result of 'emerge -uvDNep system'

[Comment 6 Juergen Rose 2012-06-11 11:32:40 UTC]

Created attachment 314969 [details]
The result of 'emerge -uvDNep system'

[Comment 7 Sven E. 2012-06-11 12:02:28 UTC]

MY fault, I guess. Here's the exct command I used:

revdep-rebuild -L libgfortran.so.3 -- -ptv

For me this yields:



[ebuild   R    ] sci-mathematics/octave-3.6.2  USE="X curl glpk gnuplot imagemagick opengl qhull qrupdate readline sparse zlib -doc -fftw -static-libs" 0 kB
[ebuild   R    ] dev-lang/R-2.15.0  USE="X cairo java jpeg lapack nls openmp png readline tiff -bash-completion -doc -icu -minimal -perl -profile -static-libs -tk" 23,629 kB
[ebuild   R    ] sci-libs/qrupdate-1.1.2  USE="-static-libs" 0 kB
[ebuild   R    ] sci-libs/arpack-96-r3  USE="-doc -examples -mpi -static-libs" 0 kB
[ebuild   R    ] sci-libs/lapack-reference-3.2.1-r1  USE="-doc" 0 kB
[ebuild   R    ] sci-libs/blas-reference-20070226-r2  USE="-doc" 0 kB
[ebuild   R    ] sci-libs/amd-2.2.3  USE="-doc -static-libs" 256 kB

Where (of course) the interesting packages for a rebuild are: qrupdate, arpack, lapack, blas and amd.

Looking at your system output, it might be, that rebuilding blas+lapack already worked in your case (on your systems where you rebuilt system with emptytree)h.



(In reply to comment #5)
> At "lynx", where I found the bug, 'emerge -uvDNe systems' just runs for
> several hours. At a second affected system ("grizzly") 'revdep-rebuild
> --library libgfortran' does not reemerge any package:
> 
> root@grizzly:/root(28)# revdep-rebuild --library libgfortran
>  * Configuring search environment for revdep-rebuild
>  * Environment mismatch from previous run, deleting temporary files...
>  * Checking reverse dependencies
>  * Packages containing binaries and libraries using libgfortran
>  * will be emerged.
>  * Collecting system binaries and libraries
>  * Generated new 1_files.rr
>  * Checking dynamic linking 
> [ 100% ]                 
>  * There are no dynamic links to libgfortran... All done. 
> 
> 
> I will attach the result of 'emerge -uvDNep system'

[Comment 8 Juergen Rose 2012-06-12 07:19:53 UTC]

'revdep-rebuild -L libgfortran.so.3 -- -ptv' yields:

emerge --complete-graph=y --oneshot  -ptv dev-lang/R:0 dev-perl/PDL:0 sci-chemistry/apbs:0 sci-chemistry/molrep:0 sci-chemistry/pdb2pqr:0 sci-libs/amd:0 sci-libs/arpack:0 sci-libs/atlas:0 sci-libs/cbflib:0 sci-libs/ccp4-libs:0 sci-libs/hdf5:0 sci-libs/pgplot:0 sci-libs/plplot:0 sci-libs/qrupdate:0 sci-libs/scipy:0 sci-mathematics/dataplot:0 sci-mathematics/octave:0 sci-physics/root:0 sys-cluster/openmpi:0
..........

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

Calculating dependencies... done!
[ebuild   R    ] sci-physics/root-5.32.03-r2::science  USE="X doc emacs examples fftw fits graphviz kerberos ldap math mpi mysql odbc opengl openmp postgres python qt4 reflex ssl xft xml -afs -avahi -clarens -htmldoc -oracle (-prefix) -pythia6 -pythia8 -ruby -test -xinetd -xrootd" 0 kB
[ebuild   R    ] sci-mathematics/dataplot-20090821  USE="X examples gd opengl" 0 kB
[ebuild   R    ] sci-libs/scipy-0.10.1  USE="doc -test -umfpack" 0 kB
[ebuild   R    ] sci-libs/pgplot-5.2.2-r4  USE="doc motif tk" 0 kB
[ebuild   R    ] sci-chemistry/pdb2pqr-1.7.0-r2  USE="doc examples pdb2pka -opal" 0 kB
[ebuild   R    ] sci-chemistry/molrep-11.0.03-r1  0 kB
[ebuild   R    ] dev-lang/R-2.15.0  USE="X bash-completion cairo doc icu java jpeg lapack nls openmp perl png readline tiff tk -minimal -profile -static-libs" 0 kB
[ebuild   R    ] sci-libs/plplot-5.9.9  USE="X cairo cxx doc examples fortran gd java jpeg latex lua ocaml octave pdf perl png python qhull qt4 svg tcl threads tk truetype wxwidgets -ada -d -dynamic -test" 0 kB
[ebuild     U  ]  sci-mathematics/octave-3.6.2 [3.6.1] USE="X curl doc fftw glpk gnuplot imagemagick opengl qhull qrupdate readline sparse zlib -static-libs" 0 kB
[ebuild   R    ]   sci-libs/qrupdate-1.1.2  USE="-static-libs" 0 kB
[ebuild   R    ] sci-libs/ccp4-libs-6.1.3-r11  0 kB
[ebuild   R    ] sci-chemistry/apbs-1.3-r2  USE="arpack doc examples openmp python tools -fetk -mpi -static-libs" 0 kB
[ebuild   R    ] dev-perl/PDL-2.4.7  USE="fftw gsl -badval" 0 kB
[ebuild   R    ] sci-libs/arpack-96-r3  USE="doc examples mpi -static-libs" 0 kB
[ebuild   R    ] sci-libs/atlas-3.8.4::science  USE="doc fortran lapack threads -static-libs" 0 kB
[ebuild   R    ] sci-libs/hdf5-1.8.9-r1  USE="examples fortran mpi szip zlib -cxx -debug -fortran2003 -static-libs -threads" 0 kB
[ebuild   R    ] sci-libs/cbflib-0.9.2.4  USE="doc -test" 0 kB
[ebuild   R    ] sci-libs/amd-2.2.3  USE="doc -static-libs" 0 kB
[ebuild   R    ] sys-cluster/openmpi-1.6-r1  USE="cxx fortran ipv6 romio threads -heterogeneous -mpi-threads -vt" OPENMPI_FABRICS="-dapl -knem -ofed -open-mx -psm -sctp" OPENMPI_OFED_FEATURES="-connectx-xrc -control-hdr-padding -dynamic-sl -failover -rdmacm" OPENMPI_RM="-pbs -slurm" 0 kB


If I than run 'revdep-rebuild -L libgfortran.so.3 -- -tv', octave-3.6.2 is successfully emerged. But one day later octave-3.6.2-r1 fails to compile. I will file a separate bug for this.

[Comment 9 Kacper Kowalik (Xarthisius) (RETIRED) 2012-06-12 09:39:13 UTC]

*** This bug has been marked as a duplicate of bug 420409 ***