commit: 5e17effe61fea1a19ee87b9699f7d96306382874 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Sun Oct 26 16:16:03 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sun Oct 26 16:16:03 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5e17effe
Merge remote-tracking branch 'github/master' * github/master: (66 commits) sci-physics/root: Fix compilation with USE="mysql" wrt bug #523996; fix die_compiler message sync with gx86 net-libs/xrootd: version bump and fix bug 521496 travis.yml: use newer portage version fixed bash-comp (bug #526320) version bump sci-chemistry/pymol: Patch included upstream sci-chemistry/pymol: Fix broken plugin listing dev-python/ccdproc: Version bump to 0.2.1 Thanks to kiwifb for reporting https://github.com/gentoo-science/sci/issues/280 - Fix openblas: discrepancy between installed libraries and .pc file. Thanks to kiwifb for reporting https://github.com/gentoo-science/sci/issues/280 - Fix openblas: discrepancy between installed libraries and .pc file. sci-chemistry/pymol: Fix upstream buildsystem The fix for Bug 524612 failed in src_install building openblas from git. The fix is to move applying the patch to src_compile after building the library, then remove config.h and config_last.h; make config.h - ignoring the spurious warning; then cp config.h to config_last.h. Fix Bug 524612 - [science overlay] sci-libs/openblas-0.2.11 - Assembler messages: ../kernel/x86_64/gemm_kernel_8x4_barcelona.S:451: Error: missing ')', thanks to Juergen Rose, Jean-Francis Roy and Steven Trogdon for reporting. The problem was that applying the -0.2.11-openblas_config_header_same_between_ABIs.patch patch in src_prepare() causes build failures on assembler code as the assembler does not understand sizeof(float). So delay applying the patch until src_install(). Bump openblas to 0.2.12. dev-python/ccdproc: Version bump to 0.2.1 dev-cpp/eigen: version bump sci-chemistry/pymol: Import tree changes version bump sys-cluster/openmpi: bump sys-cluster/openmpi: bump ... .travis.yml | 10 +- ChangeLog | 10 + dev-cpp/eigen/ChangeLog | 5 + dev-cpp/eigen/Manifest | 2 + .../{eigen-3.1.4.ebuild => eigen-3.2.2.ebuild} | 0 dev-cpp/icnc/ChangeLog | 3 + dev-cpp/icnc/icnc-9999.ebuild | 5 +- dev-lang/ispc/ChangeLog | 3 + dev-lang/ispc/ispc-9999.ebuild | 1 + dev-lang/julia/ChangeLog | 5 + dev-lang/julia/julia-9999.ebuild | 59 ++-- dev-lang/julia/metadata.xml | 8 +- dev-python/ccdproc/ChangeLog | 9 +- dev-python/ccdproc/Manifest | 1 + .../{ccdproc-0.2.ebuild => ccdproc-0.2.1.ebuild} | 0 eclass/fortran-int64.eclass | 300 +++++++++++++++++++++ net-libs/xrootd/ChangeLog | 118 ++++++++ net-libs/xrootd/Manifest | 11 + net-libs/xrootd/files/cmsd.confd | 9 + net-libs/xrootd/files/cmsd.initd | 35 +++ net-libs/xrootd/files/frm_purged.initd | 35 +++ net-libs/xrootd/files/frm_xfrd.initd | 35 +++ net-libs/xrootd/files/xrootd-no-werror.patch | 11 + net-libs/xrootd/files/xrootd.confd | 21 ++ net-libs/xrootd/files/xrootd.initd | 33 +++ net-libs/xrootd/metadata.xml | 16 ++ net-libs/xrootd/xrootd-4.0.4.ebuild | 82 ++++++ profiles/arch/arm/use.mask | 10 + profiles/arch/m68k/use.mask | 10 + profiles/arch/sparc-fbsd/use.mask | 10 + profiles/arch/sparc/use.mask | 10 + profiles/arch/x86-fbsd/use.mask | 10 + profiles/arch/x86/use.mask | 10 + .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 6 +- sci-chemistry/gromacs/ChangeLog | 3 + sci-chemistry/gromacs/gromacs-9999.ebuild | 2 +- sci-chemistry/pymol/ChangeLog | 14 + sci-chemistry/pymol/files/pymol-9999-listing.patch | 17 ++ sci-chemistry/pymol/files/pymol-9999-options.patch | 15 ++ sci-chemistry/pymol/pymol-9999.ebuild | 6 +- sci-chemistry/votca-csg/ChangeLog | 3 + sci-chemistry/votca-csg/votca-csg-9999.ebuild | 6 +- sci-libs/blas-reference/ChangeLog | 9 +- ...16.ebuild => blas-reference-20131116-r1.ebuild} | 0 .../blas-reference/blas-reference-20131116.ebuild | 79 +++++- .../blas-reference/blas-reference-99999999.ebuild | 92 +++++-- sci-libs/blas-reference/metadata.xml | 3 + sci-libs/cblas-reference/ChangeLog | 7 + .../cblas-reference-20110218-r1.ebuild | 157 +++++++++++ sci-libs/cblas-reference/metadata.xml | 3 + sci-libs/dealii/ChangeLog | 7 + sci-libs/dealii/Manifest | 2 - sci-libs/dealii/dealii-8.0.0.ebuild | 1 - ...{dealii-8.1.0.ebuild => dealii-8.1.0-r1.ebuild} | 6 +- .../files/dealii-8.1.0-p4est1.0-support.patch | 271 +++++++++++++++++++ sci-libs/lapack-reference/ChangeLog | 50 ++++ .../lapack-reference/lapack-reference-9999.ebuild | 117 +++++--- sci-libs/lapack-reference/metadata.xml | 11 +- sci-libs/libsc/ChangeLog | 6 + sci-libs/libsc/Manifest | 2 +- sci-libs/libsc/libsc-0.7.3.ebuild | 79 ------ sci-libs/libsc/libsc-1.0.ebuild | 1 - sci-libs/libsc/libsc-1.1.ebuild | 1 + sci-libs/libsc/metadata.xml | 2 +- sci-libs/openblas/ChangeLog | 64 +++++ sci-libs/openblas/Manifest | 4 +- .../openblas/files/openblas-0.2.11-cpuid_x86.patch | 27 ++ ...-openblas_config_header_same_between_ABIs.patch | 21 ++ sci-libs/openblas/openblas-0.2.11.ebuild | 1 + sci-libs/openblas/openblas-0.2.12.ebuild | 1 + sci-libs/openblas/openblas-9999.ebuild | 277 +++++++++++++------ sci-libs/p4est/ChangeLog | 9 + sci-libs/p4est/Manifest | 2 + sci-libs/p4est/metadata.xml | 2 +- sci-libs/p4est/p4est-1.0.ebuild | 6 +- sci-libs/p4est/p4est-1.1.ebuild | 1 + sci-libs/pfft/ChangeLog | 36 +++ sci-libs/pfft/Manifest | 1 + sci-libs/{bliss => pfft}/metadata.xml | 0 sci-libs/pfft/pfft-1.0.7_alpha.ebuild | 54 ++++ sci-libs/pfft/pfft-9999.ebuild | 54 ++++ sci-libs/trilinos/ChangeLog | 6 + sci-libs/trilinos/Manifest | 1 + ...linos-11.4.2.ebuild => trilinos-11.10.2.ebuild} | 4 +- sci-libs/trilinos/trilinos-11.4.2.ebuild | 2 +- sci-libs/xblas/ChangeLog | 14 +- sci-libs/xblas/metadata.xml | 3 + sci-libs/xblas/xblas-1.0.248-r1.ebuild | 122 +++++++++ sci-mathematics/scilab/Manifest | 1 + ...on.patch => scilab-5.5.1-accessviolation.patch} | 0 ... scilab-5.5.1-fix-random-runtime-failure.patch} | 0 ...wlinks.patch => scilab-5.5.1-followlinks.patch} | 0 ....0-gluegen.patch => scilab-5.5.1-gluegen.patch} | 0 ...ava-heap.patch => scilab-5.5.1-java-heap.patch} | 0 .../scilab/files/scilab-5.5.1-missinglib.patch | 11 + ...-5.5.0-nogui.patch => scilab-5.5.1-nogui.patch} | 0 sci-mathematics/scilab/scilab-5.5.1.ebuild | 250 +++++++++++++++++ sci-physics/root/ChangeLog | 9 + sci-physics/root/files/root-6.00.02-tm_zone.patch | 22 ++ sci-physics/root/metadata.xml | 38 +-- sci-physics/root/root-5.34.18-r2.ebuild | 2 + sci-physics/root/root-6.00.01-r1.ebuild | 2 + sci-physics/root/root-6.00.02.ebuild | 13 +- sci-physics/root/root-9999.ebuild | 10 +- sys-cluster/openmpi/ChangeLog | 5 + sys-cluster/openmpi/Manifest | 1 + .../{openmpi-1.8.1.ebuild => openmpi-1.8.3.ebuild} | 0 virtual/blas/ChangeLog | 11 + virtual/blas/blas-2.1-r2.ebuild | 41 +++ virtual/blas/blas-2.1-r3.ebuild | 44 +++ virtual/blas/metadata.xml | 4 + virtual/cblas/ChangeLog | 13 +- virtual/cblas/cblas-2.0-r1.ebuild | 28 ++ virtual/cblas/cblas-2.0-r2.ebuild | 31 +++ virtual/cblas/metadata.xml | 4 + virtual/lapack/ChangeLog | 10 + virtual/lapack/lapack-3.5-r2.ebuild | 34 +++ virtual/lapack/metadata.xml | 4 + 118 files changed, 2850 insertions(+), 315 deletions(-)
