Created attachment 581206 [details] build.log sci-libs/lapack was upgraded from v7 to v8 along with associated virtuals. This necessitated the uninstall of related reference packages. Today the virtuals was downgraded back to v7 and the reference files reinstalled. This causes the purge of sci-libs/lapack-8 as it was no longer a dependency of anything and conficted with the reference packages. Now sci-libs/scipy will not build. I rebuilt numpy and scikits_learn and they built fine without sci-libs/lapack. sci-libs/scipy is failing with: numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
Build log for scipy attached
Have you rebuilt numpy first?
Marris, I am sorry. The revised upgrade to lapack-3.8 is under review, and will be pushed to the tree next week. https://archives.gentoo.org/gentoo-dev/message/95beba3dc1c0f684ce1ec82d51988fc8 At the moment, do you have /usr/lib64/pkgconfig/blas.pc /usr/lib64/pkgconfig/cblas.pc /usr/lib64/pkgconfig/lapack.pc files from lapack-3.8?
at the moment sci-libs/lapack-3.8 is not installed because it blocks: blas-reference-20161223 and lapack-reference-3.7 which are required by: virtual/blas-3.7, virtual/lapack-3.7 and virtual/cbas-3.7 numpy and scikits_learn both build without sci-libs/lapack. scipy will not. When you redo sci-libs/lapack-3.8 you have to deal with this blockage. Originally virtuals were updated to 3.8 too which didn't have the circular blockage issue.
Hi, Please upgrade to virtual/blas-3.8 and virtual/lapack-3.8 to see if sci-libs/numpy could be built. Thanks! Benda
numpy builds but scipy still does not: lapack_opt_info: system_info: NOT AVAILABLE lapack_info: customize UnixCCompiler FOUND: language = f77 libraries = ['lapack'] library_dirs = ['/usr/lib64'] blas_info: customize UnixCCompiler libraries not found in ['', '/usr/lib64'] NOT AVAILABLE blas_src_info: NOT AVAILABLE NOT AVAILABLE /usr/lib64/python3.5/site-packages/numpy/distutils/system_info.py:614: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. self.calc_info() /usr/lib64/python3.5/site-packages/numpy/distutils/system_info.py:614: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. self.calc_info() /usr/lib64/python3.5/site-packages/numpy/distutils/system_info.py:614: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. self.calc_info()
Hi Harris, (In reply to Harris Landgarten from comment #6) > numpy builds but scipy still does not: > > lapack_opt_info: > system_info: > NOT AVAILABLE > > lapack_info: > customize UnixCCompiler > FOUND: > language = f77 > libraries = ['lapack'] > library_dirs = ['/usr/lib64'] I cannot reproduce this bug, could you please show your `emerge -pv virtual/blas virtual/lapack sci-libs/scipy dev-python/numpy` ?
I had: sci-libs/lapack eselect-ldso virtual/blas eselect-ldso virtual/cblas eselect-ldso virtual/lapack eselect-ldso When I turned eselect-ldso off scipy builds.
(In reply to Harris Landgarten from comment #8) > I had: > > sci-libs/lapack eselect-ldso > virtual/blas eselect-ldso > virtual/cblas eselect-ldso > virtual/lapack eselect-ldso > > When I turned eselect-ldso off scipy builds. I see, I still not reproduce this bug with USE=eselect-ldso on. Could you please show your output of `emerge -pv virtual/blas virtual/lapack sci-libs/scipy dev-python/numpy` ? The most important is the version of `dev-python/numpy`.
I am running all the latest versions inthe tree with default use flags When I had eselect-lsdo on scipy failed early in configure with cannot find cblas Unfortunately we are not starting from a clean slate. I think the issue might be that there is no eselect-cblas 0.2 I had mkl installed but had to uninstall it because it pulled in eselect-cblas which is not allowed by sci-libs/lapack
Hi Harris, Would you please just provide your output of emerge -pv virtual/blas virtual/lapack sci-libs/scipy dev-python/numpy ? It is hard to describe what's going on precisely with the actually command output.
(In reply to Benda Xu from comment #11) > It is hard to describe what's going on precisely with the actually command > output. s/with/without/
(In reply to Benda Xu from comment #3) > At the moment, do you have > > /usr/lib64/pkgconfig/blas.pc > /usr/lib64/pkgconfig/cblas.pc > /usr/lib64/pkgconfig/lapack.pc > > files from lapack-3.8? Please check this again, and provide the output of eselect blas list and eselect lapack list ?
I have: /usr/lib64/pkgconfig/blas.pc /usr/lib64/pkgconfig/cblas.pc /usr/lib64/pkgconfig/lapack.pc eselect blas list none found eselect lapack list none found cave contents sci-libs/lapack usr /usr/lib64 /usr/lib64/cmake /usr/lib64/cmake/lapack-3.8.0 /usr/lib64/cmake/lapack-3.8.0/lapack-targets.cmake /usr/lib64/cmake/lapack-3.8.0/lapack-targets-gentoo.cmake /usr/lib64/cmake/lapack-3.8.0/lapack-config.cmake /usr/lib64/cmake/lapack-3.8.0/lapack-config-version.cmake /usr/lib64/cmake/cblas-3.8.0 /usr/lib64/cmake/cblas-3.8.0/cblas-targets.cmake /usr/lib64/cmake/cblas-3.8.0/cblas-targets-gentoo.cmake /usr/lib64/cmake/cblas-3.8.0/cblas-config.cmake /usr/lib64/cmake/cblas-3.8.0/cblas-config-version.cmake /usr/lib64/pkgconfig /usr/lib64/pkgconfig/lapack.pc /usr/lib64/pkgconfig/blas.pc /usr/lib64/pkgconfig/cblas.pc /usr/lib64/libblas.so.3 -> libblas.so.3.8.0 /usr/lib64/libblas.so -> libblas.so.3 /usr/lib64/libcblas.so.3 -> libcblas.so.3.8.0 /usr/lib64/libcblas.so -> libcblas.so.3 /usr/lib64/liblapack.so.3 -> liblapack.so.3.8.0 /usr/lib64/liblapack.so -> liblapack.so.3 /usr/lib64/debug /usr/lib64/debug/usr /usr/lib64/debug/usr/lib64 /usr/lib64/debug/usr/lib64/libblas.so.3.8.0.debug /usr/lib64/debug/usr/lib64/libcblas.so.3.8.0.debug /usr/lib64/debug/usr/lib64/liblapack.so.3.8.0.debug /usr/lib64/libblas.so.3.8.0 /usr/lib64/libcblas.so.3.8.0 /usr/lib64/liblapack.so.3.8.0 /usr/include /usr/include/cblas.h /usr/include/cblas_f77.h /usr/include/cblas_test.h /usr/include/cblas_mangling.h /usr/share /usr/share/doc /usr/share/doc/lapack-3.8.0 /usr/share/doc/lapack-3.8.0/README.md note when eselect-ldso was enabled the eselect blas/lapack list gave reference instead on none now.
Hello, Could you please check and provide the 'site.cfg' generated by sci-libs/scipy? It should locate in /var/tmp/portage/sci-libs/scipy-${PV}/work/scipy-${PV}/site.cfg. I think it may be the direct reason causing this problem. By the way, could you provide your '/usr/lib64/pkgconfig/blas.pc', '/usr/lib64/pkgconfig/cblas.pc' and '/usr/lib64/pkgconfig/lapack.pc'?
Hi Harris, Got you information but they are not very helpful when USE=eselect-ldso is turned off. Would you please set USE=eselect-ldso show me your output of emerge -pv virtual/blas virtual/lapack sci-libs/scipy dev-python/numpy ? I am asking for the 3rd time because dev-python/numpy version is important to scipy build time configuration, especially location of cblas. You are using Paludis. Is it possible for you to give portage a shot? Paludis does not support EAPI-6. I am curious if your set up could work you have used portage to install scipy and cblas dependencies. Reference: https://archives.gentoo.org/gentoo-dev/message/e14746e37198ed8310f30fe2be168fb0 https://archives.gentoo.org/gentoo-dev-announce/message/9a2e0bd919ab926500394f06d4f1df18 Yours, Benda (In reply to Harris Landgarten from comment #14) > I have: > > /usr/lib64/pkgconfig/blas.pc > /usr/lib64/pkgconfig/cblas.pc > /usr/lib64/pkgconfig/lapack.pc > > eselect blas list > > none found > > eselect lapack list > > none found > cave contents sci-libs/lapack > > usr > /usr/lib64 > /usr/lib64/cmake > /usr/lib64/cmake/lapack-3.8.0 > /usr/lib64/cmake/lapack-3.8.0/lapack-targets.cmake > /usr/lib64/cmake/lapack-3.8.0/lapack-targets-gentoo.cmake > /usr/lib64/cmake/lapack-3.8.0/lapack-config.cmake > /usr/lib64/cmake/lapack-3.8.0/lapack-config-version.cmake > /usr/lib64/cmake/cblas-3.8.0 > /usr/lib64/cmake/cblas-3.8.0/cblas-targets.cmake > /usr/lib64/cmake/cblas-3.8.0/cblas-targets-gentoo.cmake > /usr/lib64/cmake/cblas-3.8.0/cblas-config.cmake > /usr/lib64/cmake/cblas-3.8.0/cblas-config-version.cmake > /usr/lib64/pkgconfig > /usr/lib64/pkgconfig/lapack.pc > /usr/lib64/pkgconfig/blas.pc > /usr/lib64/pkgconfig/cblas.pc > /usr/lib64/libblas.so.3 -> libblas.so.3.8.0 > /usr/lib64/libblas.so -> libblas.so.3 > /usr/lib64/libcblas.so.3 -> libcblas.so.3.8.0 > /usr/lib64/libcblas.so -> libcblas.so.3 > /usr/lib64/liblapack.so.3 -> liblapack.so.3.8.0 > /usr/lib64/liblapack.so -> liblapack.so.3 > /usr/lib64/debug > /usr/lib64/debug/usr > /usr/lib64/debug/usr/lib64 > /usr/lib64/debug/usr/lib64/libblas.so.3.8.0.debug > /usr/lib64/debug/usr/lib64/libcblas.so.3.8.0.debug > /usr/lib64/debug/usr/lib64/liblapack.so.3.8.0.debug > /usr/lib64/libblas.so.3.8.0 > /usr/lib64/libcblas.so.3.8.0 > /usr/lib64/liblapack.so.3.8.0 > /usr/include > /usr/include/cblas.h > /usr/include/cblas_f77.h > /usr/include/cblas_test.h > /usr/include/cblas_mangling.h > /usr/share > /usr/share/doc > /usr/share/doc/lapack-3.8.0 > /usr/share/doc/lapack-3.8.0/README.md > > note when eselect-ldso was enabled the eselect blas/lapack list gave > reference instead on none now.
eselect-ldso back on. dev-python/numpy-1.16.1:0::installed cat /usr/lib64/pkgconfig/lapack.pc libdir=/usr/lib64 includedir=/usr/include Name: LAPACK Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage Version: 3.8.0 URL: http://www.netlib.org/lapack/ Libs: -L${libdir} -llapack cat /usr/lib64/pkgconfig/blas.pc libdir=/usr/lib64 includedir=/usr/include Name: BLAS Description: FORTRAN reference implementation of BLAS Basic Linear Algebra Subprograms Version: 3.8.0 URL: http://www.netlib.org/blas/ Libs: -L${libdir} -lblas cat /usr/lib64/pkgconfig/cblas.pc libdir=/usr/lib64 includedir=/usr/include Name: CBLAS Description: C Standard Interface to BLAS Basic Linear Algebra Subprograms Version: 3.8.0 URL: http://www.netlib.org/blas/#_cblas Libs: -L${libdir} -lcblas Cflags: -I${includedir} Requires.private: blas eselect blas list Available BLAS/CBLAS (lib32) candidates: (none found) Available BLAS/CBLAS (lib64) candidates: [1] reference * sudo eselect lapack list Available LAPACK (lib32) candidates: (none found) Available LAPACK (lib64) candidates: [1] reference * note: scipy is now building with eselect-ldso on so I can no longer reproduce the bug.
this has to be tested on a clean install with first-time installation setting eselect-ldso on. I can no longer do that.
Hi Harris, thanks for the report. I think we can close this bug. Sorry for the confusion regarding lapack-3.8 reversion and re-inclusion. Feel free to open new bugs when you find other reverse dependency breakages. Benda
