Created attachment 414722 [details] config.log 'emerge grass' fails with: ... checking whether to use BLAS... yes checking for location of BLAS includes... checking for location of BLAS library... checking for cblas.h... yes checking for dnrm2_ in -lblas... no checking for dnrm2_ in -lblas... no configure: error: *** Unable to locate BLAS library. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-geosciences/grass-7.0.1/work/grass-7.0.1/config.log * ERROR: sci-geosciences/grass-7.0.1::gentoo failed (configure phase): * econf failed atlas is installed: root@lynx:/root(59)# qlist -Iv blas app-doc/blas-docs-3.3 virtual/blas-2.1-r3 virtual/cblas-2.0-r3 root@lynx:/root(60)# eselect blas list Available providers for blas: [1] atlas * [2] atlas-threads [3] mkl32-dynamic [4] mkl32-dynamic-openmp [5] mkl32-gfortran [6] mkl32-gfortran-openmp [7] mkl32-intel [8] mkl32-intel-openmp [9] mkl64-dynamic [10] mkl64-dynamic-openmp [11] mkl64-gfortran [12] mkl64-gfortran-openmp [13] mkl64-int64-dynamic [14] mkl64-int64-dynamic-openmp [15] mkl64-int64-gfortran [16] mkl64-int64-gfortran-openmp [17] mkl64-int64-intel [18] mkl64-int64-intel-openmp [19] mkl64-intel [20] mkl64-intel-openmp root@lynx:/root(61)# qlist -Iv atlas sci-libs/atlas-3.10.1-r2
This appears to be a missing dependency on sci-libs/cblas-reference, however there are other issues being fixed in the ebuild at the moment. When those fixes are pushed out I will include this fix as well and will update this bug.
This should now be resolved in sci-geosciences/grass-7.0.1-r1. If you still get this issue, please reopen this bug.
(In reply to Sam Jorna (wraeth) from comment #2) > This should now be resolved in sci-geosciences/grass-7.0.1-r1. If you still > get this issue, please reopen this bug. "cblas-reference" is mow installed, but configure still does not find BLAS library: root@impala:/root(9)# qlist -Iv reference sci-libs/cblas-reference-20110218-r1 root@impala:/root(12)# qlist -v sci-libs/cblas-reference | grep lib /usr/lib64/pkgconfig/refcblas.pc /usr/lib64/librefcblas.so.20110218 /usr/lib64/librefcblas.so -> librefcblas.so.20110218 /etc/env.d/alternatives/cblas/reference/usr/lib64/pkgconfig/cblas.pc -> ../../../../../../../../../../../../../../../usr/lib64/pkgconfig/refcblas.pc root@impala:/root(13)# emerge -uvDN grass These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild NS ] sci-geosciences/grass-7.0.1-r1:7::gentoo [7.0.0:6::x-portage] USE="X blas cxx fftw gdal geos lapack mysql netcdf nls odbc opengl openmp png postgres readline sqlite threads tiff truetype -debug -opencl" PYTHON_TARGETS="python2_7" 0 KiB Total: 1 package (1 in new slot), Size of downloads: 0 KiB ... >>> Emerging (1 of 1) sci-geosciences/grass-7.0.1-r1::gentoo * grass-7.0.1.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking grass-7.0.1.tar.gz to /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work >>> Source unpacked in /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work >>> Preparing source in /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work/grass-7.0.1 ... * Applying grass-7.0.1-include-errno.patch ... [ ok ] * Applying grass-7.0.1-declare-inespg.patch ... [ ok ] * Running autoconf ... [ ok ] * Fixing shebang in /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work/grass-7.0.1/man/build_class_rest.py. * Fixing shebang in /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work/grass-7.0.1/man/build_rest.py. ... * Fixing shebang in /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work/grass-7.0.1/imagery/i.atcorr/create_iwave.py. >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work/grass-7.0.1 ... * Requested wxWidgets: unicode 2.8 * Using wxWidgets: gtk2-unicode-release-2.8 * econf: updating grass-7.0.1/config.sub with /usr/share/gnuconfig/config.sub * econf: updating grass-7.0.1/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --enable-shared --disable-w11 --with-cxx --with-tiff --with-png --with-postgres --with-mysql --with-mysql-includes=/usr/include/mysql --with-mysql-libs=/usr/lib64/mysql --with-sqlite --with-opengl --with-odbc --with-fftw --with-blas --with-lapack --with-cairo --with-freetype --with-freetype-includes=/usr/include/freetype2 --with-nls --with-readline --without-opendwg --with-regex --with-pthread --with-openmp --without-opencl --with-gdal=/usr/bin/gdal-config --without-liblas --with-wxwidgets=/usr/lib64/wx/config/gtk2-unicode-release-2.8 --with-netcdf=/usr/bin/nc-config --with-geos=/usr/bin/geos-config --with-proj-includes=/usr/include/libprojectM --with-proj-libs=/usr/lib64 --with-proj-share=/usr/share/proj/ --with-x loading site script /usr/share/config.site ... checking for location of BLAS library... checking for cblas.h... yes checking for dnrm2_ in -lblas... no checking for dnrm2_ in -lblas... no configure: error: *** Unable to locate BLAS library. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-geosciences/grass-7.0.1-r1/work/grass-7.0.1/config.log * ERROR: sci-geosciences/grass-7.0.1-r1::gentoo failed (configure phase): * econf failed
Created attachment 414934 [details] config.log wiht cblas-reference-20110218-r1
portage has only [I] sci-libs/cblas-reference Available versions: 20030223-r4 (~)20030223-r5 You have cblas-reference-20110218-r1
(In reply to Ian Delaney from comment #5) > portage has only > > [I] sci-libs/cblas-reference > Available versions: 20030223-r4 (~)20030223-r5 > > > You have cblas-reference-20110218-r1 cblas-reference-20110218-r1 is from science overlay: root@lynx:/root(8)# emerge -pvD cblas-reference These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/cblas-reference-20110218-r1::science USE="-int64 -static-libs" ABI_X86="(64) -32 (-x32)" 0 KiB Does the grass-7.0.1 really require this 12 years old version of cblas-reference and does not work with the 4 years old version?
sci-geosciences/grass must be able to be built with the dependencies that are available in the Gentoo repository; meaning that building with dependencies supplied by overlays was not tested, and can also differ between which overlay supplies the dependency. I will have a look and see what changes may be required to build with the newer version, however note that support for the current version of cblas-reference that is in the Gentoo repository cannot be dropped.
Yes. grass was in fact pmasked for removal. It exists in the tree now only because we picked it up and restored if from oblivion. Yes it is better that cblas-reference be updated. Feel free to make a bug to the project or team to have it added from the science overlay.
sci-libs/cblas-reference-20110218-r1::science currently fails to build on my system (bug 563674). As stated, grass needs to be able to build against the version that's in the Gentoo repository, which it does. This can be reinvestigated once that is resolved and in the main tree.
(In reply to Sam Jorna (wraeth) from comment #9) > sci-libs/cblas-reference-20110218-r1::science currently fails to build on my > system (bug 563674). As stated, grass needs to be able to build against the > version that's in the Gentoo repository, which it does. > > This can be reinvestigated once that is resolved and in the main tree. I masked >=sci-libs/cblas-reference-20110218 and emerged cblas-reference-20030223-r5. But 'MAKEOPTS=-j1 emerge -v1 grass' fails as before: root@lynx:/root(16)# qlist -Iv cblas-reference sci-libs/cblas-reference-20030223-r5 root@lynx:/root(17)# MAKEOPTS=-j1 emerge -v1 grass These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild NS ] sci-geosciences/grass-7.0.1-r3:7::gentoo [7.0.0:6::local] USE="X blas cxx fftw geos lapack mysql netcdf nls odbc opengl openmp png postgres readline sqlite threads tiff truetype -debug -liblas -opencl" PYTHON_TARGETS="python2_7" 0 KiB Total: 1 package (1 in new slot), Size of downloads: 0 KiB >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-geosciences/grass-7.0.1-r3::gentoo * grass-7.0.1.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking grass-7.0.1.tar.gz to /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work >>> Source unpacked in /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work >>> Preparing source in /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1 ... * Running autoconf ... [ ok ] * Fixing shebang in /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/lib/init/grass.py. * Fixing shebang in /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/lib/python/ctypes/ctypesgen.py. ... * Fixing shebang in /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/scripts/d.rast.leg/d.rast.leg.py. >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1 ... * Requested wxWidgets: unicode 2.8 * Using wxWidgets: gtk2-unicode-release-2.8 * econf: updating grass-7.0.1/config.sub with /usr/share/gnuconfig/config.sub * econf: updating grass-7.0.1/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --enable-shared --disable-w11 --with-cxx --with-tiff --with-png --with-postgres --with-mysql --with-mysql-includes=/usr/include/mysql --with-mysql-libs=/usr/lib64/mysql --with-sqlite --with-opengl --with-odbc --with-fftw --with-blas --with-lapack --with-cairo --with-freetype --with-freetype-includes=/usr/include/freetype2 --with-nls --with-readline --without-opendwg --with-regex --with-pthread --with-openmp --without-opencl --with-gdal=/usr/bin/gdal-config --without-liblas --with-wxwidgets=/usr/lib64/wx/config/gtk2-unicode-release-2.8 --with-netcdf=/usr/bin/nc-config --with-geos=/usr/bin/geos-config --with-proj-includes=/usr/include/libprojectM --with-proj-libs=/usr/lib64 --with-proj-share=/usr/share/proj/ --with-x loading site script /usr/share/config.site checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc ... checking for location of BLAS library... checking for cblas.h... yes checking for dnrm2_ in -lblas... no checking for dnrm2_ in -lblas... no configure: error: *** Unable to locate BLAS library. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/config.log * ERROR: sci-geosciences/grass-7.0.1-r3::gentoo failed (configure phase):
Created attachment 415808 [details] config.log with cblas-reference-20030223-r5
Can you show which version of sci-libs/blas-reference you have installed? I suspect this is due to sci-libs/blas-reference being installed from the science overlay as well.
(In reply to Sam Jorna (wraeth) from comment #12) > Can you show which version of sci-libs/blas-reference you have installed? I > suspect this is due to sci-libs/blas-reference being installed from the > science overlay as well. I assume, that I installed cblas-reference from the standard portage tree. Blas-reference is not installed. And it seems me that blas-reference is not a dependency of grass or cblas-reference. root@lynx:/root(18)# genlop -t cblas-reference | tail Sun Oct 18 07:04:29 2015 >>> sci-libs/cblas-reference-20110218-r1 merge time: 14 seconds. Thu Oct 29 14:53:56 2015 >>> sci-libs/cblas-reference-20110218 merge time: 1 minute. Sat Oct 31 12:48:03 2015 >>> sci-libs/cblas-reference-20030223-r5 merge time: 36 seconds. root@lynx:/root(19)# emerge -pvD cblas-reference These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/cblas-reference-20030223-r5::gentoo 0 KiB Total: 1 package (1 reinstall), Size of downloads: 0 KiB root@lynx:/root(20)# qlist -Iv blas app-doc/blas-docs-3.3 app-eselect/eselect-cblas-0.1 sci-libs/cblas-reference-20030223-r5 virtual/blas-2.1-r3 virtual/cblas-2.0-r3 root@lynx:/root(21)# emerge -pvuND world These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] dev-lang/ocaml-4.02.3:0/4.02.3::gentoo [4.02.1:0/4.02.1::gentoo] USE="X emacs latex ncurses ocamlopt -xemacs" 2,013 KiB [ebuild N ] cross-armv7a-hardfloat-linux-gnueabi/gcc-4.9.3:4.9.3::sage-on-gentoo USE="cilk doc nls nptl (-altivec) -awt -cxx -debug (-fixed-point) -fortran -gcj -go -graphite -hardened -libssp -multilib -multislot -nopie -nossp -objc -objc++ -objc-gc -openmp -regression-test -sanitize -vanilla" 0 KiB [ebuild R ] cross-armv7a-hardfloat-linux-gnueabi/glibc-2.20-r2:2.2::sage-on-gentoo USE="gd -debug -hardened -multilib -nscd -profile (-selinux) -suid -systemtap -vanilla" CROSSCOMPILE_OPTS="-headers-only*" 0 KiB [ebuild U ] dev-java/javacup-0.11b_beta20150326::gentoo [0.11a_beta20060608::gentoo] USE="doc -source -system-jflex%" 0 KiB [ebuild NS ] sci-geosciences/grass-7.0.1-r3:7::gentoo [7.0.0:6::local] USE="X blas cxx fftw geos lapack mysql netcdf nls odbc opengl openmp png postgres readline sqlite threads tiff truetype -debug -liblas -opencl" PYTHON_TARGETS="python2_7" 0 KiB [ebuild R ] dev-python/h5py-2.5.0::gentoo USE="doc examples mpi {-test}" PYTHON_TARGETS="python2_7 python3_4 -python3_3 -python3_5%" 0 KiB [ebuild U ] app-doc/root-docs-6.04.06::gentoo [6.02.05::science] USE="http math metric -api {-test}" 0 KiB [ebuild U ] sci-physics/root-6.04.06:0/6.04.06::gentoo [6.02.05-r2:0/6.02.05::gentoo] USE="R%* X afs doc emacs examples fftw fits graphviz http kerberos ldap math memstat mpi mysql odbc opengl postgres python qt4 sqlite ssl tiff xml -avahi -gdml -geocad -openmp -oracle (-prefix) -pythia6 -pythia8 -shadow -table -xinetd -xrootd" PYTHON_TARGETS="python2_7" 0 KiB Total: 8 packages (4 upgrades, 1 new, 1 in new slot, 2 reinstalls), Size of downloads: 2,013 KiB
Ah, may be missing dep then. Can you try installing sci-libs/blas-reference from the gentoo repository (not science overlay) and confirm if that allows it to build for you?
(In reply to Sam Jorna (wraeth) from comment #14) > Ah, may be missing dep then. Can you try installing sci-libs/blas-reference > from the gentoo repository (not science overlay) and confirm if that allows > it to build for you? If I mask >=sci-libs/blas-reference-20131116 and install blas-reference-20070226-r2::gentoo, 'emerge -v1 grass' fails with: checking for sgemm_ in -lf77blas... yes checking for cblas_dgemm in -lcblas... yes checking whether to use LAPACK... yes checking for location of LAPACK includes... checking for location of LAPACK library... checking for clapack.h... no checking for dsegv_... no checking for desgv_ in -llapack... no checking for dgesv_ in -llapack... no checking for dgesv_ in -llapack... no configure: error: *** Unable to locate LAPACK library. I assume there is a missing dependency on lapack-referenc. Is there not any chance that grass-7.0.1-r3 can work as before with sci-libs/atlas?
If I mask >=sci-libs/lapack-reference-3.4.2 (there is apack-reference-3.5.0 in science overlay) and manually emerge lapack-reference-3.2.1-r1, the subsequent 'emerge -uvDN grass' fails with file collisions. I would say. it is a file collision with the installed grass-7.0.0. After removing grass-7.0.0 I could emerge grass-7.0.1-r3. lapack-reference The next 'emerge -p --depclean' wants to remove blas-reference, lapack-reference, eselect-blas and eselect-lapack. Maybe someone should add blas-reference and lapack-reference as dependency to grass, if grass-7.0.1 does not work with the generic blas and lapack.
At the next system 'emerge -v grass' hangs at least longer than 10 minutes at: ... python2.7 -t -3 -m py_compile /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/etc/python/grass/lib/ctypes_loader.py Status: Processing description list. Status: Processing description list. Warning: Member "from" of Struct "DateTime" has been renamed to "_from" because it has the same name as a Python keyword. Warning: Member "in" of Struct "_tgisDataset" has been renamed to "_in" because it has the same name as a Python keyword. Warning: Could not parse macro "#define TGIS STR3DS i5" Status: Writing to OBJ.x86_64-pc-linux-gnu/temporal.py. Status: Wrapping complete. sed -f fix.sed OBJ.x86_64-pc-linux-gnu/temporal.py > /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/etc/python/grass/lib/temporal.py python2.7 -t -3 -m py_compile /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/etc/python/grass/lib/temporal.py Error: /usr/include/GL/gl.h:90: Syntax error at '\n' Error: /usr/include/GL/gl.h:93: Syntax error at '\n' Status: Processing description list. Error: /usr/include/GL/gl.h:90: Syntax error at '\n' Error: /usr/include/GL/gl.h:93: Syntax error at '\n' Status: Processing description list. ^C Exiting on signal 2 sandbox:stop caught signal 2 in pid 25722 sandbox:stop signal already caught and busy still cleaning up! ^Csandbox:stop signal already caught and busy still cleaning up! ^\Quit
(In reply to Juergen Rose from comment #17) > At the next system 'emerge -v grass' hangs at least longer than 10 minutes > at: > ... > python2.7 -t -3 -m py_compile ... > Status: Processing description list. > > ^C > > Exiting on signal 2 > sandbox:stop caught signal 2 in pid 25722 > sandbox:stop signal already caught and busy still cleaning up! > ^Csandbox:stop signal already caught and busy still cleaning up! > ^\Quit Maybe the hanging was a NFS problem. After Rebooting and changing the network 'emerge -v grass' fail with ACCESS VIOLATION: GRASS GIS 7.0.1 r00000 compilation log -------------------------------------------------- Started compilation: Wed Nov 4 16:55:26 CET 2015 -- Errors in: No errors detected. -- Finished compilation: Wed Nov 4 16:58:24 CET 2015 >>> Source compiled. [31;01m*[0m --------------------------- ACCESS VIOLATION SUMMARY --------------------------- [31;01m*[0m LOG FILE: "/var/log/sandbox/sandbox-23326.log" [31;01m*[0m VERSION 1.0 FORMAT: F - Function called FORMAT: S - Access Status FORMAT: P - Path as passed to function FORMAT: A - Absolute Path (not canonical) FORMAT: R - Canonical Path FORMAT: C - Command Line VERSION 1.0 FORMAT: F - Function called FORMAT: S - Access Status FORMAT: P - Path as passed to function FORMAT: A - Absolute Path (not canonical) FORMAT: R - Canonical Path FORMAT: C - Command Line F: F: open_wropen_wr S: S: denydeny P: P: /dev/dri/renderD129/dev/dri/renderD129 A: A: /dev/dri/renderD129/dev/dri/renderD129 R: R: /dev/dri/renderD129/dev/dri/renderD129 C: C: python2.7 ./ctypesgen.py --cpp x86_64-pc-linux-gnu-gcc -E -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -D__GLIBC_HAVE_LONG_LONG -lgrass_imagery.7.0.1 /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/imagery.h /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/defs/imagery.h -o OBJ.x86_64-pc-linux-gnu/imagery.py python2.7 ./ctypesgen.py --cpp x86_64-pc-linux-gnu-gcc -E -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -D__GLIBC_HAVE_LONG_LONG -lgrass_gproj.7.0.1 -I/usr/include/libprojectM -I/usr/include/gdal /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/gprojects.h /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/defs/gprojects.h -o OBJ.x86_64-pc-linux-gnu/proj.py F: open_wr S: deny P: /dev/dri/renderD129 A: /dev/dri/renderD129 R: /dev/dri/renderD129 C: python2.7 ./ctypesgen.py --cpp x86_64-pc-linux-gnu-gcc -E -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -D__GLIBC_HAVE_LONG_LONG -lgrass_gproj.7.0.1 -I/usr/include/libprojectM -I/usr/include/gdal /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/gprojects.h /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/defs/gprojects.h -o OBJ.x86_64-pc-linux-gnu/proj.py F: open_wr S: deny P: /dev/dri/renderD129 A: /dev/dri/renderD129 R: /dev/dri/renderD129 C: python2.7 ./ctypesgen.py --cpp x86_64-pc-linux-gnu-gcc -E -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -I/var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include -D__GLIBC_HAVE_LONG_LONG -lgrass_imagery.7.0.1 /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/imagery.h /var/tmp/portage/sci-geosciences/grass-7.0.1-r3/work/grass-7.0.1/dist.x86_64-pc-linux-gnu/include/grass/defs/imagery.h -o OBJ.x86_64-pc-linux-gnu/imagery.py ... F: open_wr S: deny P: /dev/dri/renderD129 A: /dev/dri/renderD129 R: /dev/dri/renderD129 C: v.perturb --interface-description F: open_w [31;01m*[0m --------------------------------------------------------------------------------
Created attachment 416076 [details] build.log.bz2 with "ACCESS VIOLATION"
FWIW, it also fails to configure in the same way if the selected blas implementation is science::sci-libs/openblas or science::dev-cpp/eigen, so the error is not specific to cblas-reference, and now that I think about it probably more likely related to blas than cblas (or both)?
grass-7.0.1 blocks if atlas is installed with its requirement of cblas-reference-20030223 'emerge -uvDN world': root@impala:/root(36)# emerge --update --newuse --deep --with-bdeps=y --backtrack=30 @world Calculating dependencies... done! [ebuild U ] app-dicts/myspell-en-20151201 [20081002] [ebuild U ] app-arch/rar-5.3.0 [5.2.1] [ebuild U ] dev-java/java-config-wrapper-0.16-r1 [0.16] [ebuild rR ] dev-ml/camlp4-4.02.1_p3 [ebuild rR ] dev-ml/camlidl-1.05-r1 [ebuild r U ] dev-lang/ocaml-4.02.3 [4.02.1] [ebuild U ] dev-lang/python-exec-2.1 [2.0.2] [ebuild U ] app-arch/arj-3.10.22-r5 [3.10.22-r4] [ebuild U ] net-misc/whois-5.2.11 [5.2.10] [ebuild U ] dev-java/antlr-2.7.7-r7 [2.7.7-r5] [ebuild U ] dev-java/mimepull-1.9.6-r1 [1.9.6] [ebuild U ] dev-java/glassfish-deployment-api-3.1.1 [1.2] USE="doc%*" [ebuild U ] dev-java/jacl-1.4.1-r1 [1.4.1] USE="-source%" [ebuild U ] dev-java/stringtemplate-3.2.1-r1 [3.2.1] [ebuild U ] dev-java/antlr-3.2 [3.1.3-r3] USE="doc%* {-test%}" [ebuild U ] app-text/tesseract-3.04.00-r3 [3.04.00-r2] USE="math%*" [ebuild U ] media-libs/libraw-0.17.1 [0.17.0] [ebuild U ] sci-biology/phylip-3.696-r1 [3.696] [ebuild U ] dev-ml/findlib-1.6.1 [1.5.6] [ebuild rR ] dev-ml/camlp5-6.14 [ebuild U ] dev-lang/python-2.7.11 [2.7.10-r10] [ebuild U ] dev-java/jaxme-0.5.2-r2 [0.5.2-r1] [ebuild U ] dev-lang/python-3.4.3-r4 [3.4.3-r2] [ebuild R ] dev-python/itsdangerous-0.24 PYTHON_TARGETS="-python3_5%" [ebuild R ] dev-python/blinker-1.4 PYTHON_TARGETS="-python3_5%" [ebuild U ] dev-python/rfc3986-0.3.1 [0.3.0] [ebuild R ] dev-python/markdown-2.6.5 PYTHON_TARGETS="-python3_5%" [ebuild U ] app-editors/nano-2.5.0 [2.4.3] [ebuild U ] app-pda/libplist-1.11-r1 [1.11] [ebuild U ] sci-libs/atlas-3.11.38-r1 [3.11.38] USE="deprecated%*" [ebuild U ] dev-lang/python-3.5.0-r3 [3.5.0-r1] [ebuild U ] app-eselect/eselect-python-20151117-r1 [20140125] [blocks b ] <app-eselect/eselect-python-20151117 ("<app-eselect/eselect-python-20151117" is blocking dev-lang/python-exec-2.1) [ebuild NS ] dev-java/eclipse-ecj-4.5.1 [4.4.2-r1] USE="ant doc -source" [ebuild NS ] dev-java/ant-eclipse-ecj-4.5.1 [4.4.2] USE="doc -source" [ebuild U ] net-misc/openvpn-2.3.8-r1 [2.3.8] USE="-libressl%" [ebuild U ] sys-apps/usbredir-0.7.1 [0.7] [ebuild U ] x11-libs/cairo-1.14.6 [1.14.4] [ebuild U ] dev-java/gnu-classpath-0.98-r4 [0.98-r3] USE="gjdoc*" [ebuild U ] dev-java/netbeans-java-8.0.2-r4 [8.0.2-r3] [ebuild U ] dev-java/icedtea-7.2.6.3-r2 [7.2.6.2-r1] [ebuild U ] dev-java/netbeans-enterprise-8.0.2-r1 [8.0.2] [ebuild U ] app-emulation/qemu-2.4.1-r1 [2.4.1] [ebuild R ] media-libs/gegl-0.3.4 USE="(-libav%)" [ebuild U ] app-doc/root-docs-6.04.06 [6.02.05] [ebuild U ] sci-physics/root-6.04.06 [6.02.05-r2] USE="R%*" [ebuild R ] dev-python/flask-0.10.1-r2 PYTHON_TARGETS="-python3_5%" [ebuild U ] www-plugins/adobe-flash-11.2.202.554 [11.2.202.548] [ebuild U ] kde-apps/kwalletmanager-15.04.3 [4.14.3] USE="-minimal%" [ebuild U ] kde-apps/okular-15.08.3-r1 [15.08.3] USE="kde%*" [ebuild U ] sci-geosciences/grass-7.0.1-r4 [7.0.1-r3] [ebuild U ] app-crypt/gnupg-2.1.10 [2.1.9-r1] USE="-tofu%" [ebuild U ] sys-apps/openrc-0.19.1 [0.19] [ebuild U ] gnome-base/gnome-core-libs-3.18.0 [3.16.0] [ebuild U ] sys-apps/gnome-disk-utility-3.18.3.1 [3.18.2] [ebuild U ] dev-lang/mono-4.2.1.102 [4.0.5.1] [ebuild U ] dev-cpp/gtkmm-2.24.4-r3 [2.24.4-r2] [ebuild U ] dev-cpp/eigen-3.2.7 [3.2.6] [ebuild N ] dev-cpp/antlr-cpp-2.7.7 USE="doc examples -static-libs" ABI_X86="(64) -32 (-x32)" [ebuild U ] sci-electronics/kicad-4.0.0 [4.0.0_rc2] [ebuild U ] dev-vcs/git-2.6.4 [2.6.3] [ebuild U ] media-gfx/inkscape-0.91-r1 [0.91] [ebuild U ] dev-db/sqlitebrowser-3.7.0-r1 [3.7.0] [ebuild U ] net-misc/ntp-4.2.8_p4-r1 [4.2.8_p4] USE="-libressl%" [ebuild U ] gnome-base/gnome-core-apps-3.18.0 [3.16.0] [ebuild U ] gnome-base/gnome-extra-apps-3.18.0 [3.16.0] [ebuild U ] gnome-base/gnome-3.18.0 [3.16.0] [ebuild U ] sci-biology/embassy-emnu-1.05.650-r1 [1.05.650] [blocks B ] app-eselect/eselect-cblas ("app-eselect/eselect-cblas" is blocking dev-cpp/eigen-3.2.7, sci-libs/atlas-3.11.38-r1) !!! Multiple package instances within a single package slot have been pulled !!! into the dependency graph, resulting in a slot conflict: dev-lang/ocaml:0 (dev-lang/ocaml-4.02.3:0/4.02.3::gentoo, ebuild scheduled for merge) pulled in by (no parents that aren't satisfied by other packages in this slot) (dev-lang/ocaml-4.02.1:0/4.02.1::gentoo, installed) pulled in by >=dev-lang/ocaml-4.02:0/4.02.1=[ocamlopt,X] required by (dev-ml/labltk-8.06.0:0/8.06.0::gentoo, installed) ^^^^^^^^^^ (and 4 more with the same problem) NOTE: Use the '--verbose-conflicts' option to display parents omitted above It may be possible to solve this problem by using package.mask to prevent one of those packages from being selected. However, it is also possible that conflicting dependencies exist such that they are impossible to satisfy simultaneously. If such a conflict exists in the dependencies of two different packages, then those packages can not be installed simultaneously. For more information, see MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook. * Error: The above package list contains packages which cannot be * installed at the same time on the same system. (app-eselect/eselect-cblas-0.1:0/0::gentoo, installed) pulled in by app-eselect/eselect-cblas required by (sci-libs/cblas-reference-20030223-r5:0/0::gentoo, installed) (sci-libs/atlas-3.11.38-r1:0/0::science, ebuild scheduled for merge) pulled in by >=sci-libs/atlas-3.10.1[lapack] required by (virtual/lapack-3.5-r3:0/0::science, installed) sci-libs/atlas required by @selected (dev-cpp/eigen-3.2.7:3/3::science, ebuild scheduled for merge) pulled in by dev-cpp/eigen:3 required by (media-libs/opencv-3.0.0:0/3.0::gentoo, installed) >=dev-cpp/eigen-3.2.0:3 required by (media-video/movit-1.1.3:0/0::gentoo, installed) dev-cpp/eigen:3 required by (media-gfx/freecad-0.15.4671:0/0::gentoo, installed) dev-cpp/eigen:3 required by (sci-chemistry/openbabel-2.3.2-r1:0/0::gentoo, installed) dev-cpp/eigen:3 required by (app-office/calligra-2.9.7:4/4::gentoo, installed) >=dev-cpp/eigen-3.1 required by (sci-libs/shogun-3.2.0:0/16::gentoo, installed) dev-cpp/eigen:3 required by (sci-chemistry/apbs-1.4.1-r2:0/0::gentoo, installed) dev-cpp/eigen:3 required by (media-gfx/digikam-4.14.0:4/4::x-portage, installed) For more information about Blocked Packages, please refer to the following section of the Gentoo Linux x86 Handbook (architecture is irrelevant): https://wiki.gentoo.org/wiki/Handbook:X86/Working/Portage#Blocked_packages The following packages are causing rebuilds: (dev-lang/ocaml-4.02.3:0/4.02.3::gentoo, ebuild scheduled for merge) causes rebuilds for: (dev-ml/camlp5-6.14:0/6.14::gentoo, ebuild scheduled for merge)
After deleting grass 'emerge --update --newuse --deep --with-bdeps=y --backtrack=30 @world' works again.
*** Bug 570078 has been marked as a duplicate of this bug. ***
grass-7.0.2 fails to emerge with same error.
sci-geosciences/grass-7.0.4 fails with the sanme error.