Bug 674434 – sci-mathematics/octave-4.4.1 configure: error: ld: warning: libgfortran.so.4, needed by /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so, not found (try using -rpath or -rpath-link)

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Anton Kochkov 2019-01-03 17:07:04 UTC]

Created attachment 559700 [details]
config.log

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-4.4.1/work/octave-4.4.1/config.log
 [31;01m*[0m ERROR: sci-mathematics/octave-4.4.1::gentoo failed (configure phase):
 [31;01m*[0m   econf failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line  124:  Called src_configure
 [31;01m*[0m             environment, line 5001:  Called econf '--localstatedir=/var/state/octave' '--with-blas=-lblas' '--with-lapack=-llapack -lblas' '--disable-64' '--disable-jit' '--enable-shared' '--with-z' '--with-bz2' '--without-OSMesa' '--disable-static' '--disable-docs' '--disable-java' '--enable-readline' '--without-curl' '--without-fftw3' '--without-fftw3f' '--disable-fftw-threads' '--with-glpk' '--without-hdf5' '--with-magick=ImageMagick' '--with-opengl' '--with-fltk' '--with-openssl' '--without-portaudio' '--with-qhull' '--with-qrupdate' '--without-qt' '--without-sndfile' '--with-arpack' '--with-umfpack' '--with-colamd' '--with-ccolamd' '--with-cholmod' '--with-cxsparse' '--with-x'
 [31;01m*[0m        phase-helpers.sh, line  718:  Called __helpers_die 'econf failed'
 [31;01m*[0m   isolated-functions.sh, line  119:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		die "$@"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-mathematics/octave-4.4.1::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-mathematics/octave-4.4.1::gentoo'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM=  CLASSPATH="" JAVA_HOME=""
JAVACFLAGS="" COMPILER=""
and of course, the output of emerge --info =octave-4.4.1
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-mathematics/octave-4.4.1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/octave-4.4.1/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-mathematics/octave-4.4.1/work/octave-4.4.1'
 [31;01m*[0m S: '/var/tmp/portage/sci-mathematics/octave-4.4.1/work/octave-4.4.1'

[Comment 1 Anton Kochkov 2019-01-03 17:07:29 UTC]

Created attachment 559702 [details]
emerge --info output

[Comment 2 Jeroen Roovers (RETIRED) 2019-01-04 06:33:36 UTC]

Comment on attachment 559700 [details]
config.log

configure:29161: checking for sgemm_ in -lblas
configure:29189: x86_64-pc-linux-gnu-gcc -o conftest -march=native -O2 -pipe -pthread -fopenmp  -Wl,-O1 -Wl,--as-needed -Wl,-z,defs conftest.c -lblas  -lm   -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../.. -lgfortran -lm -lquadmath >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: libgfortran.so.4, needed by /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so, not found (try using -rpath or -rpath-link)
/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write_done@GFORTRAN_7'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_stop_string@GFORTRAN_7'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write@GFORTRAN_7'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_integer_write@GFORTRAN_7'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_string_len_trim@GFORTRAN_7'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_character_write@GFORTRAN_7'
collect2: error: ld returned 1 exit status

[Comment 3 Fabio Rossi 2019-03-16 16:45:12 UTC]

The error happens because you are trying to build octave with a different gcc version than that used to build its dependencies lapack and blas (and the old version of gcc has been uninstalled). revdep-rebuild should solve the problem

Shouldn't FEATURE=preserved-libs mechanism in charge of detecting this sort of problems, in the specific case after unmerge of gcc with needed lib?

[Comment 4 Anton Kochkov 2019-03-20 17:39:55 UTC]

(In reply to Fabio Rossi from comment #3)
> The error happens because you are trying to build octave with a different
> gcc version than that used to build its dependencies lapack and blas (and
> the old version of gcc has been uninstalled). revdep-rebuild should solve
> the problem
> 
> Shouldn't FEATURE=preserved-libs mechanism in charge of detecting this sort
> of problems, in the specific case after unmerge of gcc with needed lib?

You are right, problem was solved with revdep-rebuild.

[Comment 5 Fabio Rossi 2019-03-21 14:27:04 UTC]

For future reference, the revdep-rebuild is only a workaround but it's a general known problem with portage, see also #459038