'emerge -uvDN sci-libs/atlas' complains at the end: ... >>> Regenerating /etc/ld.so.cache... >>> Original instance of package unmerged safely. * Creating atlas alternative module for cblas !!! Error: Can't load module cblas exiting * Creating atlas-threads alternative module for cblas !!! Error: Can't load module cblas exiting * Creating atlas alternative module for blas !!! Error: Can't load module blas exiting * Creating atlas-threads alternative module for blas !!! Error: Can't load module blas exiting * Creating atlas alternative module for lapack !!! Error: Can't load module lapack exiting * Creating atlas-threads alternative module for lapack !!! Error: Can't load module lapack exiting >>> sci-libs/atlas-3.10.0 merged. >>> Regenerating /etc/ld.so.cache... >>> Auto-cleaning packages... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date. If I then try to emerge digikam, which depends on sci-libs/clapack, 'emerge clapack' fails with: >>> Emerging (1 of 21) sci-libs/clapack-3.2.1-r6 * clapack-3.2.1-CMAKE.tgz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... ... loading initial cache file /var/tmp/portage/sci-libs/clapack-3.2.1-r6/work/clapack-3.2.1_build/gentoo_common_config.cmake Re-run cmake no build system arguments -- The C compiler identification is GNU 4.6.3 -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") -- checking for module 'blas' -- package 'blas' not found CMake Error at CMakeLists.txt:53 (message): --> BLAS libraries needed but not found.
Similarly sci-libs/arpack fails to emerge: >>> Emerging (1 of 26) sci-libs/arpack-3.1.2 * arpack-ng_3.1.2.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] ... >>> Configuring source in /var/tmp/portage/sci-libs/arpack-3.1.2/work/arpack-ng_3.1.2 ... Package blas was not found in the pkg-config search path. Perhaps you should add the directory containing `blas.pc' to the PKG_CONFIG_PATH environment variable No package 'blas' found Package lapack was not found in the pkg-config search path. Perhaps you should add the directory containing `lapack.pc' to the PKG_CONFIG_PATH environment variable No package 'lapack' found >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/arpack-3.1.2/work/arpack-3.1.2_build" * econf: updating arpack-ng_3.1.2/config.guess with /usr/share/gnuconfig/config.guess ... checking for ATL_xerbla in -latlas... yes checking for sgemm_ in -lf77blas... yes checking for cblas_dgemm in -lcblas... no checking for sgemm_ in -lblas... 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 configure: error: Cannot find BLAS libraries !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-libs/arpack-3.1.2/work/arpack-3.1.2_build/config.log * ERROR: sci-libs/arpack-3.1.2 failed (configure phase):
The issue persist even after 'emerge -uvDNe world'.
re-sync science overlay, and re-install eselect. thanks.
Thanks Sebastien, but it still not works: root@cheetahnew:/root(19)# emerge -pvD eselect These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] app-admin/eselect-1.3.2-r100::science USE="doc" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB root@cheetahnew:/root(20)# eselect blas list Available providers for blas: [1] atlas [2] atlas-threads [3] eigen [4] mkl32-dynamic [5] mkl32-dynamic-openmp [6] mkl32-gfortran [7] mkl32-gfortran-openmp [8] mkl32-intel [9] mkl32-intel-openmp [10] mkl64-dynamic [11] mkl64-dynamic-openmp [12] mkl64-gfortran [13] mkl64-gfortran-openmp [14] mkl64-int64-dynamic [15] mkl64-int64-dynamic-openmp [16] mkl64-int64-gfortran [17] mkl64-int64-gfortran-openmp [18] mkl64-int64-intel [19] mkl64-int64-intel-openmp [20] mkl64-intel [21] mkl64-intel-openmp root@cheetahnew:/root(21)# eselect blas set atlas-threads !!! Error: Refusing to overwrite /usr/lib64/pkgconfig/blas.pc: is not a symlink (use --force to override) !!! Error: Could not set provider atlas-threads for alternative blas: see previous errors Call stack: * do_set (alternatives.bash:301) * check_do (core.bash:24) * do_action (core.bash:89) * main (eselect:202) exiting root@cheetahnew:/root(23)# eselect blas set -2 !!! Error: Refusing to overwrite /usr/lib64/pkgconfig/blas.pc: is not a symlink (use --force to override) !!! Error: Could not set provider atlas-threads for alternative blas: see previous errors Call stack: * do_set (alternatives.bash:301) * check_do (core.bash:24) * do_action (core.bash:89) * main (eselect:202) exiting -rw-r--r-- 1 root root 205 Sep 21 20:21 /usr/lib64/pkgconfig/blas.pc root@cheetahnew:/root(25)# cat /usr/lib64/pkgconfig/blas.pc prefix=/usr libdir=/usr/lib64 Name: blas Description: Basic Linear Algebra Subprograms F77 reference implementations Version: URL: http://www.netlib.org/blas/ Libs: -L/usr/lib64 -lblas Libs.private: -lm root@cheetahnew:/root(26)# qfile -v /usr/lib64/pkgconfig/blas.pc sci-libs/lapack-reference-3.4.1 (/usr/lib64/pkgconfig/blas.pc) The same error (Refusing to overwrite /usr/lib64/pkgconfig/blas.pc: is not a symlink (use --force to override)) is shown emerging atlas: >>> Original instance of package unmerged safely. * Creating atlas alternative module for cblas * Creating atlas-threads alternative module for cblas * Creating atlas alternative module for blas !!! Error: Refusing to overwrite //usr/lib64/pkgconfig/blas.pc: is not a symlink (use --force to override) !!! Error: Could not set provider atlas for alternative blas: see previous errors Call stack: * do_set (alternatives.bash:301)
If I remove lapack-reference the error disappears.
