Hi Everyone, Though it is actually not a Debian specific question (since on pure Debian builts/links fine), I hope to find help and wisdom here.
We (neurodebian) have a package for AFNI which we have been cooking for a while... with a recent change to force -Wl,--no-undefined I got into a weird linking issue which happens only on Ubuntu boxes (11.10 and up) while building fine on Debian. In the gcc call where linking '-lgsl -lgslcblas' fails for no obvious for me reason -- order of libraries inclusion is fine, symbols are there (even found/reported by ld) but still then reported not found. What could be the reason? The only obvious difference from Debian builds is addition of -Wl,-Bsymbolic-functions for linking calls but even if I remove it for this specific call -- nothing changes (although may be it is an effect of gsl being built with it?) See below what I am talking about and please find complete logs at http://neuro.debian.net/_files/_buildlogs/afni/0.20130830~dfsg.1 so here it is -- gslcblas has the definitions, I do have -lgsl -lgslcblas, according to strace gslcblas is read at least -- but references are still undefined: ~/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu/avovk# nm -D /usr/lib/libgslcblas.so | grep cblas_dgemv 000000000000ea00 T cblas_dgemv ~/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu/avovk# gcc --param ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wno-unused -fopenmp -DUSE_OMP -Wl,-z,now -Wl,-z,relro -Wl,--no-undefined CMakeFiles/3dkmeans.dir/3dkmeans.c.o CMakeFiles/3dkmeans.dir/cluster_floatNOMASK.c.o CMakeFiles/3dkmeans.dir/thd_segtools_fNM.c.o -o 3dkmeans ../libmri.so ../libmrix.so ../coxplot/libcoxplot.so libsegtools.so -lSM -lICE -lX11 -lXext -lXm -lXmHTML ../libmri.so -lvolpack -lnetcdf -lXt -lf2c -lgiftiio -lnifticdf -lniftiio -lz -lnifticdf -lniftiio -lz -lgsl -lgslcblas -lm -Wl,-rpath,"/tmp/buildd/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu:/tmp/buildd/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu/coxplot:/tmp/buildd/a fni-0.20130830~dfsg.1/build-x86_64-linux-gnu/avovk:" -DNDEBUG /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgsl.so: undefined reference to `cblas_ztrsv' /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgsl.so: undefined reference to `cblas_scasum' ... and here you can see that ld finds the definition but then reports that it is undefined in libgsl.so (which is factually true but I thought it would use the one from libgslcblas by then). ~/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu/avovk# /usr/bin/ld --verbose -t -y cblas_ztrsv --sysroot=/ --build-id --no-add-needed --as-needed --eh-frame-hdr -m elf_x86_64 --hash-style=gnu -dynamic-linker /lib64/ld-linux-x86-64.so.2 -z relro -o 3dkmeans /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.7/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/4.7 -L/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.7/../../.. -z now -z relro --no-undefined CMakeFiles/3dkmeans.dir/3dkmeans.c.o CMakeFiles/3dkmeans.dir/cluster_floatNOMASK.c.o CMakeFiles/3dkmeans.dir/thd_segtools_fNM.c.o ../libmri.so ../libmrix.so ../coxplot/libcoxplot.so libsegtools.so -lSM -lICE -lX11 -lXext -lXm -lXmHTML ../libmri.so -lvolpack -lnetcdf -lXt -lf2c -lgiftiio -lnifticdf -lniftiio -lz -lnifticdf -lniftiio -lz -lgsl -lgslcblas -lm -rpath /tmp/buildd/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu:/tmp/buildd/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu/coxplot:/tmp/buildd/afni-0.20130830~dfsg.1/build-x86_64-linux-gnu/avovk: -lgomp -lgcc --as-needed -lgcc_s -lpthread -lc -lgcc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/4.7/crtend.o /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/crtn.o 2>&1 | grep -e 'gsl' -e 'cblas_ztrsv' | head -20 ... attempt to open /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgsl.so succeeded -lgsl (/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgsl.so) /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgsl.so: reference to cblas_ztrsv ... attempt to open /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgslcblas.so succeeded -lgslcblas (/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgslcblas.so) /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgslcblas.so: definition of cblas_ztrsv /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgsl.so: undefined reference to `cblas_ztrsv' /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/libgsl.so: undefined reference to `cblas_scasum' ......... probably needless to say that adding -lcblas works around this issue. Thanks in advance for the hints! -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130903154232.gp27...@onerussian.com
