octave 3.2.4_0 does not build; problem with g95?

[MartinBuchmann (Martin Buchmann)]

Hi,

I am hoping this was not reported yet, couldn't find something similar. I was trying to upgrade from 3.2.3_2 to 3.2.4_0 but the built failed due to some compilation problem, see below and the attached log. System is 10.6.3, XCode 3.2.2 on a MacBook (Intel).

/usr/bin/gcc-4.2 -c -I/opt/local/include -I/opt/local/include -fPIC -I. -I.. -I../liboctave -I../src -I../libcruft/misc  -DHAVE_CONFIG_H -mieee-fp -Wall -W -Wshadow -Wformat -O2 -arch x86_64 -D_THREAD_SAFE  kpse-xfns.c -o pic/kpse-xfns.o
kpse-xfns.c: In function 'octave_basename':
kpse-xfns.c:62: warning: implicit declaration of function 'basename'
kpse-xfns.c:62: warning: cast to pointer from integer of different size
rm -f liboctave.dylib
/usr/bin/g++-4.2 -dynamiclib -single_module -L/opt/local/lib -install_name /opt/local/lib/octave-3.2.4/liboctave.dylib -o liboctave.dylib \
	pic/oct-locbuf.o pic/CollocWt.o pic/DASPK.o pic/DASRT.o pic/DASSL.o pic/LSODE.o pic/ODES.o pic/Quad.o pic/Range.o pic/data-conv.o pic/dir-ops.o pic/file-ops.o pic/file-stat.o pic/glob-match.o pic/idx-vector.o pic/lo-ieee.o pic/lo-mappers.o pic/lo-specfun.o pic/lo-sysdep.o pic/lo-utils.o pic/mach-info.o pic/oct-alloc.o pic/oct-env.o pic/oct-fftw.o pic/oct-group.o pic/oct-mutex.o pic/oct-md5.o pic/oct-norm.o pic/oct-passwd.o pic/oct-rand.o pic/oct-shlib.o pic/oct-spparms.o pic/oct-syscalls.o pic/oct-time.o pic/oct-uname.o pic/prog-args.o pic/regex-match.o pic/sparse-sort.o pic/sparse-util.o pic/str-vec.o pic/Array-C.o pic/Array-b.o pic/Array-ch.o pic/Array-i.o pic/Array-d.o pic/Array-f.o pic/Array-fC.o pic/Array-s.o pic/Array-str.o pic/Array-voidp.o pic/Array-idx-vec.o pic/MArray-C.o pic/MArray-ch.o pic/MArray-i.o pic/MArray-d.o pic/MArray-f.o pic/MArray-fC.o pic/MArray-s.o pic/MSparse-C.o pic/MSparse-d.o pic/Sparse-C.o pic/Sparse-b.o pic/Sparse-d.o pic/oct-inttypes.o pic/Array-util.o pic/CColVector.o pic/CDiagMatrix.o pic/CMatrix.o pic/CNDArray.o pic/CRowVector.o pic/CmplxAEPBAL.o pic/CmplxCHOL.o pic/CmplxGEPBAL.o pic/CmplxHESS.o pic/CmplxLU.o pic/CmplxQR.o pic/CmplxQRP.o pic/CmplxSCHUR.o pic/CmplxSVD.o pic/EIG.o pic/fEIG.o pic/boolMatrix.o pic/boolNDArray.o pic/chMatrix.o pic/chNDArray.o pic/dColVector.o pic/dDiagMatrix.o pic/dMatrix.o pic/dNDArray.o pic/dRowVector.o pic/dbleAEPBAL.o pic/dbleCHOL.o pic/dbleGEPBAL.o pic/dbleHESS.o pic/dbleLU.o pic/dbleQR.o pic/dbleQRP.o pic/dbleSCHUR.o pic/dbleSVD.o pic/boolSparse.o pic/CSparse.o pic/dSparse.o pic/MSparse.o pic/Sparse.o pic/SparseCmplxLU.o pic/SparsedbleLU.o pic/SparseCmplxCHOL.o pic/SparsedbleCHOL.o pic/SparseCmplxQR.o pic/SparseQR.o pic/MatrixType.o pic/PermMatrix.o pic/int8NDArray.o pic/uint8NDArray.o pic/int16NDArray.o pic/uint16NDArray.o pic/int32NDArray.o pic/uint32NDArray.o pic/int64NDArray.o pic/uint64NDArray.o pic/fCColVector.o pic/fCRowVector.o pic/fCDiagMatrix.o pic/fCMatrix.o pic/fCNDArray.o pic/fColVector.o pic/fRowVector.o pic/fDiagMatrix.o pic/fMatrix.o pic/fNDArray.o pic/fCmplxAEPBAL.o pic/fCmplxCHOL.o pic/fCmplxGEPBAL.o pic/fCmplxHESS.o pic/fCmplxLU.o pic/fCmplxSCHUR.o pic/fCmplxSVD.o pic/fCmplxQR.o pic/fCmplxQRP.o pic/floatAEPBAL.o pic/floatCHOL.o pic/floatGEPBAL.o pic/floatHESS.o pic/floatLU.o pic/floatSCHUR.o pic/floatSVD.o pic/floatQR.o pic/floatQRP.o pic/mx-cdm-dm.o pic/mx-dm-cdm.o pic/mx-cs-cdm.o pic/mx-cs-dm.o pic/mx-cs-m.o pic/mx-cs-nda.o pic/mx-cdm-cs.o pic/mx-cdm-cm.o pic/mx-cdm-m.o pic/mx-cdm-s.o pic/mx-cm-cdm.o pic/mx-cm-dm.o pic/mx-cm-m.o pic/mx-cnda-nda.o pic/mx-cm-s.o pic/mx-cnda-s.o pic/mx-dm-cs.o pic/mx-dm-cm.o pic/mx-m-cs.o pic/mx-nda-cs.o pic/mx-m-cdm.o pic/mx-m-cm.o pic/mx-nda-cnda.o pic/mx-s-cdm.o pic/mx-s-cm.o pic/mx-s-cnda.o pic/mx-dm-m.o pic/mx-dm-s.o pic/mx-m-dm.o pic/mx-s-dm.o pic/mx-fcdm-fdm.o pic/mx-fdm-fcdm.o pic/mx-fcs-fcdm.o pic/mx-fcs-fdm.o pic/mx-fcs-fm.o pic/mx-fcs-fnda.o pic/mx-fcdm-fcs.o pic/mx-fcdm-fcm.o pic/mx-fcdm-fm.o pic/mx-fcdm-fs.o pic/mx-fcm-fcdm.o pic/mx-fcm-fdm.o pic/mx-fcm-fm.o pic/mx-fcnda-fnda.o pic/mx-fcm-fs.o pic/mx-fcnda-fs.o pic/mx-fdm-fcs.o pic/mx-fdm-fcm.o pic/mx-fm-fcs.o pic/mx-fnda-fcs.o pic/mx-fm-fcdm.o pic/mx-fm-fcm.o pic/mx-fnda-fcnda.o pic/mx-fs-fcdm.o pic/mx-fs-fcm.o pic/mx-fs-fcnda.o pic/mx-fdm-fm.o pic/mx-fdm-fs.o pic/mx-fm-fdm.o pic/mx-fs-fdm.o pic/mx-pm-m.o pic/mx-m-pm.o pic/mx-pm-cm.o pic/mx-cm-pm.o pic/mx-pm-fm.o pic/mx-fm-pm.o pic/mx-pm-fcm.o pic/mx-fcm-pm.o pic/mx-s-i8nda.o pic/mx-i8nda-s.o pic/mx-s-ui8nda.o pic/mx-ui8nda-s.o pic/mx-s-i16nda.o pic/mx-i16nda-s.o pic/mx-s-ui16nda.o pic/mx-ui16nda-s.o pic/mx-s-i32nda.o pic/mx-i32nda-s.o pic/mx-s-ui32nda.o pic/mx-ui32nda-s.o pic/mx-s-i64nda.o pic/mx-i64nda-s.o pic/mx-s-ui64nda.o pic/mx-ui64nda-s.o pic/mx-fs-i8nda.o pic/mx-i8nda-fs.o pic/mx-fs-ui8nda.o pic/mx-ui8nda-fs.o pic/mx-fs-i16nda.o pic/mx-i16nda-fs.o pic/mx-fs-ui16nda.o pic/mx-ui16nda-fs.o pic/mx-fs-i32nda.o pic/mx-i32nda-fs.o pic/mx-fs-ui32nda.o pic/mx-ui32nda-fs.o 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pic/mx-i32nda-ui8nda.o pic/mx-i32nda-i16nda.o pic/mx-i32nda-ui16nda.o pic/mx-i32nda-ui32nda.o pic/mx-i32nda-i64nda.o pic/mx-i32nda-ui64nda.o pic/mx-i64nda-i8nda.o pic/mx-i64nda-ui8nda.o pic/mx-i64nda-i16nda.o pic/mx-i64nda-ui16nda.o pic/mx-i64nda-i32nda.o pic/mx-i64nda-ui32nda.o pic/mx-i64nda-ui64nda.o pic/mx-ui8nda-i8nda.o pic/mx-ui8nda-i16nda.o pic/mx-ui8nda-ui16nda.o pic/mx-ui8nda-i32nda.o pic/mx-ui8nda-ui32nda.o pic/mx-ui8nda-i64nda.o pic/mx-ui8nda-ui64nda.o pic/mx-ui16nda-i8nda.o pic/mx-ui16nda-ui8nda.o pic/mx-ui16nda-i16nda.o pic/mx-ui16nda-i32nda.o pic/mx-ui16nda-ui32nda.o pic/mx-ui16nda-i64nda.o pic/mx-ui16nda-ui64nda.o pic/mx-ui32nda-i8nda.o pic/mx-ui32nda-ui8nda.o pic/mx-ui32nda-i16nda.o pic/mx-ui32nda-ui16nda.o pic/mx-ui32nda-i32nda.o pic/mx-ui32nda-i64nda.o pic/mx-ui32nda-ui64nda.o pic/mx-ui64nda-i8nda.o pic/mx-ui64nda-ui8nda.o pic/mx-ui64nda-i16nda.o pic/mx-ui64nda-ui16nda.o pic/mx-ui64nda-i32nda.o pic/mx-ui64nda-ui32nda.o pic/mx-ui64nda-i64nda.o pic/vx-ccv-cv.o pic/vx-ccv-s.o pic/vx-crv-rv.o pic/vx-crv-s.o pic/vx-cs-cv.o pic/vx-cs-rv.o pic/vx-cv-ccv.o pic/vx-cv-cs.o pic/vx-rv-crv.o pic/vx-rv-cs.o pic/vx-s-ccv.o pic/vx-s-crv.o pic/vx-fccv-fcv.o pic/vx-fccv-fs.o pic/vx-fcrv-frv.o pic/vx-fcrv-fs.o pic/vx-fcs-fcv.o pic/vx-fcs-frv.o pic/vx-fcv-fccv.o pic/vx-fcv-fcs.o pic/vx-frv-fcrv.o pic/vx-frv-fcs.o pic/vx-fs-fccv.o pic/vx-fs-fcrv.o pic/smx-sm-cs.o pic/smx-cs-sm.o pic/smx-scm-s.o pic/smx-s-scm.o pic/smx-scm-sm.o pic/smx-sm-scm.o pic/smx-m-sm.o pic/smx-m-scm.o pic/smx-cm-sm.o pic/smx-cm-scm.o pic/smx-sm-m.o pic/smx-scm-m.o pic/smx-sm-cm.o pic/smx-scm-cm.o pic/smx-bm-sbm.o pic/smx-sbm-bm.o pic/f2c-main.o pic/filemode.o pic/getopt.o pic/getopt1.o pic/lo-cieee.o pic/lo-cutils.o pic/md5.o pic/mkdir.o pic/oct-getopt.o pic/randgamma.o pic/randmtzig.o pic/randpoisson.o pic/rename.o pic/rmdir.o pic/strftime.o pic/strptime.o pic/strcasecmp.o pic/strncase.o pic/tempname.o pic/tempnam.o pic/cmd-edit.o pic/cmd-hist.o pic/oct-rl-edit.o pic/oct-rl-hist.o pic/pathsearch.o pic/kpse-xfns.o -L../libcruft -L.  -lcruft -lcholmod -lmetis -lumfpack -lamd -lcamd -lcolamd -lccolamd -lcxsparse  -lqrupdate -llapack -lcblas -lf77blas -latlas -lfftw3 -lfftw3f -lreadline  -L/opt/local/lib -lpcre -lreadline  -lncurses -lhdf5 -lz -lm  -L/opt/local/lib -L/opt/local/bin/../lib/g95/x86_64-apple-darwin10/4.2.4/ -L/opt/local/bin/../lib/g95/x86_64-apple-darwin10/4.2.4 -L/opt/local/lib/g95/x86_64-apple-darwin10/4.2.4/ -L/usr/lib/gcc// -L/opt/local/bin/../lib/g95/x86_64-apple-darwin10/4.2.4/// -L/opt/local/lib/g95/x86_64-apple-darwin10/4.2.4/// -L/usr/lib// -lhdf5 -lz -lf95 -lm -D_THREAD_SAFE  
Undefined symbols:
  "__g95_stop_string", referenced from:
      _dgqvec_ in libqrupdate.a(dgqvec.o)
      _cgqvec_ in libqrupdate.a(cgqvec.o)
      _sgqvec_ in libqrupdate.a(sgqvec.o)
      _zgqvec_ in libqrupdate.a(zgqvec.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [liboctave.dylib] Error 1
make[1]: *** [liboctave] Error 2
make: *** [all] Error 2

[ryandesign (Ryan Carsten Schmidt)]

Since "-L/opt/local/lib" is listed first in that line, before "-L../libcruft -L.", I guess it's incorrectly trying to link with your existing older version of octave and not finding some symbols that were newly added in the new version of octave. Try deactivating your older version first, then building the new one.

sudo port deactivate octave
sudo port clean octave
sudo port upgrade octave

[MartinBuchmann (Martin Buchmann)]

Hmm, good idea, but it did not change anything. I am still ending up with the same error.

[ryandesign (Ryan Carsten Schmidt)]

Ok, next idea. Are you using the +g95 variant of octave? I know octave builds for me on 10.6.3 with either the +gcc43 or +gcc44 variants so try one of those.

[MartinBuchmann (Martin Buchmann)]

Indeed, I was using the +g95 variant due to reasons I cannot remember. I uninstalled octave, did a clean --all and tried to install it with the gcc43 and gcc44 option. Without success, see below what I assume is the interesting part of the output:

/usr/bin/make -C liboctave all
rm -f liboctave.dylib
/opt/local/bin/g++-mp-4.4 -dynamiclib -single_module -L/opt/local/lib -install_name /opt/local/lib/octave-3.2.4/liboctave.dylib -o liboctave.dylib \
	pic/oct-locbuf.o pic/CollocWt.o pic/DASPK.o pic/DASRT.o pic/DASSL.o pic/LSODE.o pic/ODES.o pic/Quad.o pic/Range.o pic/data-conv.o pic/dir-ops.o pic/file-ops.o pic/file-stat.o pic/glob-match.o pic/idx-vector.o pic/lo-ieee.o pic/lo-mappers.o pic/lo-specfun.o pic/lo-sysdep.o pic/lo-utils.o pic/mach-info.o pic/oct-alloc.o pic/oct-env.o pic/oct-fftw.o pic/oct-group.o pic/oct-mutex.o pic/oct-md5.o pic/oct-norm.o pic/oct-passwd.o pic/oct-rand.o pic/oct-shlib.o pic/oct-spparms.o pic/oct-syscalls.o pic/oct-time.o pic/oct-uname.o pic/prog-args.o pic/regex-match.o pic/sparse-sort.o pic/sparse-util.o pic/str-vec.o pic/Array-C.o pic/Array-b.o pic/Array-ch.o pic/Array-i.o pic/Array-d.o pic/Array-f.o pic/Array-fC.o pic/Array-s.o pic/Array-str.o pic/Array-voidp.o pic/Array-idx-vec.o pic/MArray-C.o pic/MArray-ch.o pic/MArray-i.o pic/MArray-d.o pic/MArray-f.o pic/MArray-fC.o pic/MArray-s.o pic/MSparse-C.o pic/MSparse-d.o pic/Sparse-C.o pic/Sparse-b.o pic/Sparse-d.o pic/oct-inttypes.o pic/Array-util.o pic/CColVector.o pic/CDiagMatrix.o pic/CMatrix.o pic/CNDArray.o pic/CRowVector.o pic/CmplxAEPBAL.o pic/CmplxCHOL.o pic/CmplxGEPBAL.o pic/CmplxHESS.o pic/CmplxLU.o pic/CmplxQR.o pic/CmplxQRP.o pic/CmplxSCHUR.o pic/CmplxSVD.o pic/EIG.o pic/fEIG.o pic/boolMatrix.o pic/boolNDArray.o pic/chMatrix.o pic/chNDArray.o pic/dColVector.o pic/dDiagMatrix.o pic/dMatrix.o pic/dNDArray.o pic/dRowVector.o pic/dbleAEPBAL.o pic/dbleCHOL.o pic/dbleGEPBAL.o pic/dbleHESS.o pic/dbleLU.o pic/dbleQR.o pic/dbleQRP.o pic/dbleSCHUR.o pic/dbleSVD.o pic/boolSparse.o pic/CSparse.o pic/dSparse.o pic/MSparse.o pic/Sparse.o pic/SparseCmplxLU.o pic/SparsedbleLU.o pic/SparseCmplxCHOL.o pic/SparsedbleCHOL.o pic/SparseCmplxQR.o pic/SparseQR.o pic/MatrixType.o pic/PermMatrix.o pic/int8NDArray.o pic/uint8NDArray.o pic/int16NDArray.o pic/uint16NDArray.o pic/int32NDArray.o pic/uint32NDArray.o pic/int64NDArray.o pic/uint64NDArray.o pic/fCColVector.o pic/fCRowVector.o pic/fCDiagMatrix.o pic/fCMatrix.o pic/fCNDArray.o 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pic/vx-ccv-s.o pic/vx-crv-rv.o pic/vx-crv-s.o pic/vx-cs-cv.o pic/vx-cs-rv.o pic/vx-cv-ccv.o pic/vx-cv-cs.o pic/vx-rv-crv.o pic/vx-rv-cs.o pic/vx-s-ccv.o pic/vx-s-crv.o pic/vx-fccv-fcv.o pic/vx-fccv-fs.o pic/vx-fcrv-frv.o pic/vx-fcrv-fs.o pic/vx-fcs-fcv.o pic/vx-fcs-frv.o pic/vx-fcv-fccv.o pic/vx-fcv-fcs.o pic/vx-frv-fcrv.o pic/vx-frv-fcs.o pic/vx-fs-fccv.o pic/vx-fs-fcrv.o pic/smx-sm-cs.o pic/smx-cs-sm.o pic/smx-scm-s.o pic/smx-s-scm.o pic/smx-scm-sm.o pic/smx-sm-scm.o pic/smx-m-sm.o pic/smx-m-scm.o pic/smx-cm-sm.o pic/smx-cm-scm.o pic/smx-sm-m.o pic/smx-scm-m.o pic/smx-sm-cm.o pic/smx-scm-cm.o pic/smx-bm-sbm.o pic/smx-sbm-bm.o pic/f2c-main.o pic/filemode.o pic/getopt.o pic/getopt1.o pic/lo-cieee.o pic/lo-cutils.o pic/md5.o pic/mkdir.o pic/oct-getopt.o pic/randgamma.o pic/randmtzig.o pic/randpoisson.o pic/rename.o pic/rmdir.o pic/strftime.o pic/strptime.o pic/strcasecmp.o pic/strncase.o pic/tempname.o pic/tempnam.o pic/cmd-edit.o pic/cmd-hist.o pic/oct-rl-edit.o pic/oct-rl-hist.o pic/pathsearch.o pic/kpse-xfns.o -L../libcruft -L.  -lcruft -lcholmod -lmetis -lumfpack -lamd -lcamd -lcolamd -lccolamd -lcxsparse  -lqrupdate -llapack -lcblas -lf77blas -latlas -lfftw3 -lfftw3f -lreadline  -L/opt/local/lib -lpcre -lreadline  -lncurses -lhdf5 -lz -lm  -L/opt/local/lib -L/opt/local/lib/gcc44/gcc/x86_64-apple-darwin10/4.4.4 -L/opt/local/lib/gcc44/gcc/x86_64-apple-darwin10/4.4.4/../../.. -lhdf5 -lz -lm -lgfortranbegin -lgfortran -D_THREAD_SAFE  
Undefined symbols:
  "__g95_filename", referenced from:
      _dgqvec_ in libqrupdate.a(dgqvec.o)
      _cgqvec_ in libqrupdate.a(cgqvec.o)
      _sgqvec_ in libqrupdate.a(sgqvec.o)
      _zgqvec_ in libqrupdate.a(zgqvec.o)
  "__g95_stop_string", referenced from:
      _dgqvec_ in libqrupdate.a(dgqvec.o)
      _cgqvec_ in libqrupdate.a(cgqvec.o)
      _sgqvec_ in libqrupdate.a(sgqvec.o)
      _zgqvec_ in libqrupdate.a(zgqvec.o)
  "__g95_line", referenced from:
      _dgqvec_ in libqrupdate.a(dgqvec.o)
      _cgqvec_ in libqrupdate.a(cgqvec.o)
      _sgqvec_ in libqrupdate.a(sgqvec.o)
      _zgqvec_ in libqrupdate.a(zgqvec.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [liboctave.dylib] Error 1
make[1]: *** [liboctave] Error 2
make: *** [all] Error 2
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_octave/work/octave-3.2.4" && /usr/bin/make all " returned error 2
DEBUG: Backtrace: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_octave/work/octave-3.2.4" && /usr/bin/make all " returned error 2
    while executing
"command_exec build"
    (procedure "portbuild::build_main" line 9)
    invoked from within
"$procedure $targetname"

[MartinBuchmann (Martin Buchmann)]

Hi again,

after deinstalling most of octaves dependencies and reinstalling it "from scratch" with the gcc44 option it builts fine. I think there is a problem in the +g95 variant and for me special problems arose after i tried to install octave with gcc4(3|4) but dependencies like arpack and qrupdate where built with +g95. Just a guess, at least it is now working for me.

Thanks

Martin

[tenomoto (Takeshi Enomoto)]

I updated qrupdate (r70385, r70460) to make g95 variant back. For arpack see #25186. See also #21797.

[jmroot (Joshua Root)]

I guess we can call this a dupe of #21797.