Bug 694360 – sci-mathematics/octave-5.1.0 - src_configure(): ld: warning: libgfortran.so.3, needed by /usr/lib64/blas/reference/libblas.so, not found (try using -rpath or -rpath-link) // ld: /usr/lib64/blas/reference/libblas.so: undefined reference to `_gfortran_stop_

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Samuel Bernardo 2019-09-14 13:22:01 UTC]

The error below could be related to the following:
https://savannah.gnu.org/bugs/?49547


checking how to hardcode library paths into programs... immediate
checking for sgemm_ in -L/usr/lib64/blas/reference -lblas... no
checking if sgemm_ is being linked in already... no
checking for sgemm_ in -lopenblas... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lmkl_intel_lp64... no
checking for sgemm_ in -lmkl... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -L/usr/lib64/blas/reference -lblas... no
checking if sgemm_ is being linked in already... no
checking for sgemm_ in -lopenblas... (cached) no
checking for ATL_xerbla in -latlas... (cached) no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lmkl_intel_lp64... (cached) no
checking for sgemm_ in -lmkl... (cached) no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lcxml... (cached) no
checking for sgemm_ in -ldxml... (cached) no
checking for sgemm_ in -lscs... (cached) no
checking for sgemm_ in -lcomplib.sgimath... (cached) no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
configure: error: BLAS and LAPACK libraries are required

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-mathematics/octave-5.1.0/work/octave-5.1.0/config.log
 * ERROR: sci-mathematics/octave-5.1.0::gentoo failed (configure phase):
 *   econf failed
 * 
 * Call stack:
 *               ebuild.sh, line  125:  Called src_configure
 *             environment, line 5094:  Called econf '--localstatedir=/var/state/octave' '--with-blas=-L/usr/lib64/blas/reference -lblas' '--with-lapack=-L/usr/lib64/lapack/reference -L/usr/lib64/blas/reference -llapack -lblas' '--disable-64' '--disable-jit' '--enable-shared' '--with-z' '--with-bz2' '--disable-static' '--enable-docs' '--enable-java' '--enable-readline' '--with-curl' '--with-fftw3' '--with-fftw3f' '--enable-fftw-threads' '--with-glpk' '--with-hdf5' '--with-magick=ImageMagick' '--with-opengl' '--with-fltk' '--with-openssl' '--with-portaudio' '--with-qhull' '--with-qrupdate' '--with-qt=5' '--with-sndfile' '--with-arpack' '--with-umfpack' '--with-colamd' '--with-ccolamd' '--with-cholmod' '--with-cxsparse' '--with-x'
 *        phase-helpers.sh, line  718:  Called __helpers_die 'econf failed'
 *   isolated-functions.sh, line  119:  Called die
 * The specific snippet of code:
 *              die "$@"
 * 
 * If you need support, post the output of `emerge --info '=sci-mathematics/octave-5.1.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-mathematics/octave-5.1.0::gentoo'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM=oracle-jdk-bin-1.8  CLASSPATH="" JAVA_HOME="/opt/oracle-jdk-bin-1.8.0.202"
JAVACFLAGS="-source 1.6 -target 1.6" COMPILER=""

[Comment 1 Samuel Bernardo 2019-09-14 13:27:34 UTC]

Created attachment 589812 [details]
config.log

Additional logs related to the configuration error and missing dependencies

[Comment 2 Jeroen Roovers (RETIRED) 2019-09-15 08:32:35 UTC]

Apparently libblas needs to be rebuilt.

[Comment 3 Samuel Bernardo 2019-10-01 18:53:27 UTC]

Configure failed even when installing sci-libs/blas-reference-20161223
/usr/lib64/libblas.so

[Comment 4 Samuel Bernardo 2019-10-26 17:31:42 UTC]

re-emerge lapack-reference besides blas-reference and octave compiles now.
Maybe missing here some glibc or gcc update dependencies...

[Comment 5 Samuel Bernardo 2019-10-26 18:01:19 UTC]

Add an old reference about this issue in Gentoo forum:
https://forums.gentoo.org/viewtopic-t-1073912-start-0.html