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Bug 563264 - =sci-geosciences/grass-7.0.1-r1 fails to build with =sci-libs/cblas-reference-20110218-r1::science - configure: error: Unable to locate BLAS library
Summary: =sci-geosciences/grass-7.0.1-r1 fails to build with =sci-libs/cblas-reference...
Status: RESOLVED WONTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Sam Jorna (wraeth)
URL:
Whiteboard:
Keywords:
: 570078 (view as bug list)
Depends on: 563674
Blocks:
  Show dependency tree
 
Reported: 2015-10-16 17:45 UTC by Juergen Rose
Modified: 2017-10-06 23:26 UTC (History)
5 users (show)

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


Attachments
config.log (config.log,25.55 KB, text/x-log)
2015-10-16 17:45 UTC, Juergen Rose
Details
config.log wiht cblas-reference-20110218-r1 (config.log,26.00 KB, text/plain)
2015-10-19 14:57 UTC, Juergen Rose
Details
config.log with cblas-reference-20030223-r5 (config.log,25.83 KB, text/x-log)
2015-10-31 15:43 UTC, Juergen Rose
Details
build.log.bz2 with "ACCESS VIOLATION" (build.log.bz2,100.42 KB, application/x-bzip)
2015-11-04 17:13 UTC, Juergen Rose
Details

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Description Juergen Rose 2015-10-16 17:45:27 UTC
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
Comment 1 Sam Jorna (wraeth) gentoo-dev 2015-10-17 04:21:09 UTC
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.
Comment 2 Sam Jorna (wraeth) gentoo-dev 2015-10-19 11:26:26 UTC
This should now be resolved in sci-geosciences/grass-7.0.1-r1. If you still get this issue, please reopen this bug.
Comment 3 Juergen Rose 2015-10-19 14:55:57 UTC
(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
Comment 4 Juergen Rose 2015-10-19 14:57:56 UTC
Created attachment 414934 [details]
config.log wiht cblas-reference-20110218-r1
Comment 5 Ian Delaney (RETIRED) gentoo-dev 2015-10-19 15:18:18 UTC
portage has only

[I] sci-libs/cblas-reference
     Available versions:  20030223-r4 (~)20030223-r5


You have cblas-reference-20110218-r1
Comment 6 Juergen Rose 2015-10-20 17:26:57 UTC
(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?
Comment 7 Sam Jorna (wraeth) gentoo-dev 2015-10-20 22:43:12 UTC
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.
Comment 8 Ian Delaney (RETIRED) gentoo-dev 2015-10-21 06:02:31 UTC
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.
Comment 9 Sam Jorna (wraeth) gentoo-dev 2015-10-21 12:22:56 UTC
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.
Comment 10 Juergen Rose 2015-10-31 15:41:20 UTC
(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):
Comment 11 Juergen Rose 2015-10-31 15:43:13 UTC
Created attachment 415808 [details]
config.log with cblas-reference-20030223-r5
Comment 12 Sam Jorna (wraeth) gentoo-dev 2015-11-01 07:49:56 UTC
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.
Comment 13 Juergen Rose 2015-11-01 09:52:53 UTC
(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
Comment 14 Sam Jorna (wraeth) gentoo-dev 2015-11-01 10:40:16 UTC
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?
Comment 15 Juergen Rose 2015-11-01 18:59:06 UTC
(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?
Comment 16 Juergen Rose 2015-11-04 08:55:44 UTC
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.
Comment 17 Juergen Rose 2015-11-04 14:29:24 UTC
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
Comment 18 Juergen Rose 2015-11-04 17:10:47 UTC
(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 --------------------------------------------------------------------------------
Comment 19 Juergen Rose 2015-11-04 17:13:13 UTC
Created attachment 416076 [details]
build.log.bz2 with "ACCESS VIOLATION"
Comment 20 Jeremy Murphy 2015-12-10 05:04:38 UTC
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)?
Comment 21 Juergen Rose 2015-12-10 09:33:31 UTC
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)
Comment 22 Juergen Rose 2015-12-10 09:51:22 UTC
After deleting grass  'emerge --update --newuse --deep --with-bdeps=y --backtrack=30 @world' works again.
Comment 23 Sam Jorna (wraeth) gentoo-dev 2016-01-02 04:24:12 UTC
*** Bug 570078 has been marked as a duplicate of this bug. ***
Comment 24 Juergen Rose 2016-01-12 09:57:04 UTC
grass-7.0.2 fails to emerge with same error.
Comment 25 Juergen Rose 2016-08-08 07:16:35 UTC
sci-geosciences/grass-7.0.4 fails with the sanme error.