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Bug 649894 - sci-mathematics/octave-4.2.1 configure: error: A BLAS library was detected but found incompatible with your Fortran 77 compiler settings.
Summary: sci-mathematics/octave-4.2.1 configure: error: A BLAS library was detected bu...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal with 1 vote (vote)
Assignee: Gentoo Science Mathematics related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2018-03-08 05:03 UTC by Anton Kochkov
Modified: 2020-06-04 13:27 UTC (History)
3 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (octave_build.log,23.96 KB, text/plain)
2018-03-08 05:03 UTC, Anton Kochkov
Details
emerge --info output (emerge_info.log,5.20 KB, text/plain)
2018-03-08 05:03 UTC, Anton Kochkov
Details
config.log (config.log,266.67 KB, text/x-log)
2018-03-14 04:14 UTC, Anton Kochkov
Details

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Description Anton Kochkov 2018-03-08 05:03:27 UTC
Created attachment 522922 [details]
build.log

configure: error: A BLAS library was detected but found incompatible with your Fortran 77 compiler settings.

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-mathematics/octave-4.2.1/work/octave-4.2.1/config.log
 [31;01m*[0m ERROR: sci-mathematics/octave-4.2.1::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 4671:  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' '--without-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  666:  Called __helpers_die 'econf failed'
 [31;01m*[0m   isolated-functions.sh, line  117:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		die "$@"
 [31;01m*[0m
Comment 1 Anton Kochkov 2018-03-08 05:03:42 UTC
Created attachment 522924 [details]
emerge --info output
Comment 2 Jeroen Roovers (RETIRED) gentoo-dev 2018-03-09 06:06:02 UTC
Comment on attachment 522922 [details]
build.log

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-mathematics/octave-4.2.1/work/octave-4.2.1/config.log

Yes?
Comment 3 François Bissey 2018-03-09 06:34:54 UTC
gcc-7 strikes again. I think we will find that blas is linked to libgfortran.so.3 when gfortran-7 wants to link to libgfortran.so.4.
Comment 4 Anton Kochkov 2018-03-14 04:14:59 UTC
Created attachment 523846 [details]
config.log

Attaching the config log, sorry for the delay.
Comment 5 François Bissey 2018-03-14 04:18:46 UTC
Exactly what I thought:
configure:38799: 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/7.3.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../.. -lgfortran -lm -lquadmath >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: libgfortran.so.3, needed by /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libblas.so, not found (try using -rpath or -rpath-link)
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_stop_string@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_string_len_trim@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write_done@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_character_write@GFORTRAN_1.4'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_integer_write@GFORTRAN_1.4'
collect2: error: ld returned 1 exit status

blas and lapack and then all their dependencies needs rebuilding with the new compiler.
Comment 6 Erik Quaeghebeur 2018-07-11 10:39:35 UTC
I was hit by this as well, so I can confirm (mostly stable amd64).

(In reply to François Bissey from comment #5)
> blas and lapack and then all their dependencies needs rebuilding with the
> new compiler.
I did

1. emerge -1qva blas-reference lapack-reference
2. revdep-rebuild -- -1qva

which emerged arpack, qrupdate, scipy, hdf5, and finally octave without issues for me.
Comment 7 Masn6n0 2018-08-26 10:37:29 UTC
Same error with octave-4.2.2

emerge -1qva blas-reference lapack-reference

did help.
Comment 8 Reva Denis 2019-04-17 11:01:34 UTC
(In reply to Masn6n0 from comment #7)
> Same error with octave-4.2.2
> 
> emerge -1qva blas-reference lapack-reference
> 
> did help.

So do I
Comment 9 Anton Kochkov 2019-11-29 16:58:20 UTC
Not reproducible anymore with newer GCC (8 and higher) and Octave 5.x versions
Comment 10 Andreas Sturmlechner gentoo-dev 2020-06-04 13:27:28 UTC
Thanks for checking back, will cleanup old.