Linking of the octave binary fails with the forced -Wl,--as-needed (which is done in gentoo in current gcc versions). The reason is that liboctave uses libpthread functions but is not linked with -lpthread. The solution is of course to add -lpthread to the link flags of liboctave. I append a patch. Here is the relevant error during emerge: x86_64-pc-linux-gnu-g++ -I/usr/include/freetype2 -I. -I.. -I../liboctave -I../src -I../libcruft/misc -DHAVE_CONFIG_H -Wall -W -Wshadow -Wold-style-cas t -Wformat -march=native -O2 -fno-ident -pipe -I/usr/include/freetype2 -rdynamic \ -L.. -fPIC -o octave \ main.o \ -L../liboctave -L../libcruft -L../src -Wl,-rpath -Wl,/usr/lib64/octave-3.2.0 \ -loctinterp -loctave -lcruft \ -lamd \ -llapack -lblas -lblas \ -larpack -L/usr/X11R6/lib -lGL -lGLU \ -L/usr/lib64 -lX11 -lreadline -lncurses -ldl -lblas -lz -lm -lfreetype -lz -L/usr/X11R6/lib -lGL -lGLU -L/usr/X11R6/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.0/../../.. -lz -lgfortranbegin -lgfortran -lm -lfreetype -lGL -lGLU ../liboctave/liboctave.so: undefined reference to `pthread_mutexattr_destroy' ../liboctave/liboctave.so: undefined reference to `pthread_mutexattr_init' ../liboctave/liboctave.so: undefined reference to `pthread_mutexattr_settype' collect2: ld returned 1 exit status
Created attachment 197222 [details, diff] Patch for liboctave/Makefile.in to include -lpthread dependency
I have the same bug. I am using the science overlay to get octave-3.2.0 I'm currently struggling to do my first patch ever to confirm the fix... I copied your patch to: # cp Desktop/octave-pthread.patch /var/tmp/portage/sci-mathematics/octave-3.2.0/work/octave-3.2.0/ run patch -p0? since your filenames are relitave to this location: --- liboctave/Makefile.in +++ liboctave/Makefile.in run the following: octave-3.2.0 # patch -p0 <octave-pthread.patch # emerge --digest octave same error! ln -s liboctinterp.so liboctinterp.so.3.2.0 i686-pc-linux-gnu-g++ -I. -I.. -I../liboctave -I../src -I../libcruft/misc -DHAVE_CONFIG_H -mieee-fp -I/usr/include/freetype2 -Wall -W -Wshadow -Wold-style-cast -Wformat -march=athlon64 -O2 -pipe -rdynamic \ -L.. -fPIC -Wl,-O1 -o octave \ main.o \ -L../liboctave -L../libcruft -L../src -Wl,-rpath -Wl,/usr/lib/octave-3.2.0 \ -loctinterp -loctave -lcruft \ \ -llapack -lblas -lblas \ -lftgl -lfreetype -lz -L/usr/X11R6/lib -lGL -lGLU \ -lX11 -lreadline -lncurses -ldl -lblas -lz -lm -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2 -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../.. -lz -lgfortranbegin -lgfortran -lm ../liboctave/liboctave.so: undefined reference to `pthread_mutexattr_destroy' ../liboctave/liboctave.so: undefined reference to `pthread_mutexattr_init' ../liboctave/liboctave.so: undefined reference to `pthread_mutexattr_settype' collect2: ld returned 1 exit status make[2]: *** [octave] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory `/var/tmp/portage/sci-mathematics/octave-3.2.0/work/octave-3.2.0/src' make[1]: *** [src] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-mathematics/octave-3.2.0/work/octave-3.2.0' make: *** [all] Error 2 * * ERROR: sci-mathematics/octave-3.2.0 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3157: Called die * The specific snippet of code: * emake || die "emake failed"; * The die message: * emake failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-mathematics/octave-3.2.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/octave-3.2.0/temp/environment'. * I'm not saying the patch dident work (it is probably me) .
(In reply to comment #2) > I'm currently struggling to do my first patch ever to confirm the fix... The bugtracker is not a support forum. There are certainly some howto's in the net. Please ask in a forum or on a user mailing list for help if you cannot find out. Roughly speaking, you have to copy the ebuild directory to a local overlay, put the patch in the corresponding files/ directory and add a corresponding epatch command to the src_unpack or src_prepare function (depending on the EAPI).
Hi Martin, Thanks much for the report and patch. Strangely, everything compiles fine for me on x86 and amd64 despite the --as-needed. I am not quite sure why. In any case, since the patch is fairly unobtrusive I've just added it to the ebuild which should hopefully fix your problems. Thanks again, Markus
Thanks for the fix. (In reply to comment #4) > Strangely, everything > compiles fine for me on x86 and amd64 despite the --as-needed. For me it failed on both. There are quite a few possible explanations, but I have not tried which one applies: 1. The _forced_ --Wl,--as-needed is perhaps only in new gcc versions (I use gcc-4.4). If it is not forced, it depends on _where_ it occurs on the linking line: The problem arises only if it occurs before the -loctave option. 2. It might also play a role that I have "export LD_BIND_NOW=1" in my profile (although it would surprise me, if this would really be relevant here). 3. Perhaps the function calls are only compiled if certain USE flags (i.e. ./configure options) are set; or perhaps vice versa, if certain USE flags are set then a certain library might be linked against liboctave which in turn links to libthreads. The USE flags for octave were in my case: USE="doc emacs readline zlib -curl -debug -fftw -hdf5 -sparse -xemacs"
*** Bug 277466 has been marked as a duplicate of this bug. ***
