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2017-11-28pi-scipy: add 1.0.0 (#6486)Denis Davydov1-0/+1
2017-11-28r-classint: created new package (#6481)Yifan Zhu1-0/+39
2017-11-28r-rcppcctz: created new package (#6480)Yifan Zhu1-0/+41
2017-11-28r-topgo: Create new package. (#6479)lingnanyuan1-0/+48
2017-11-28r-seurat: Create new package (#6477)Eric1-0/+73
2017-11-28Adding list_url to several R module packages (#6474)Eric23-23/+23
2017-11-28r-cli: new package (#6476)Yifan Zhu1-0/+40
2017-11-27Xsdk 0.3.0 (#6277)Satish Balay3-2/+24
* xsdk: Added MFEM rc package. * xsdk: add version entry for xsdk-0.3.0-rc1 - and set it as preferred version * xsdk: remove 'xsdk' from version - recommended by Todd. Now the usage is: 'spack install xsdk@0.3.0-rc1' instead of the previous usage: 'spack install xsdk@xsdk-0.2.0' * xsdk: add petsc@3.8.0 as a dependency for xsdk-0.3.0-rc1 * mfem: fix dependency to use the corrected xsdk version * Updated the mfem version tags. * mfem: fix merge * fix flake8 warning * Modified xSDK scripts * fixing the default package.yaml * fix bad revert * revert changes to superlu-dist so that the 5.2.1 update can be merged * update xsdk to use superlu-dist-5.2.1 * update alquimia for xsdk * fix whitespace * update hypre for xsdk * update sundials for xsdk * update sundials for xsdk * Fix checking for MKL and extend range of GCC versions * pflotran: update to release branch * plasma: fix spec -> self.spec * Changes to enable mfem hooks into hypre, superlu-dist, and petsc. Sundials hooks may come in the future. * adding plasma with comment * Bumped the version of mfem up to handle integration with sundials3.0.0. Also enabled hypre in sundials. * Turn on the plasma package definition for testing * Fix conflict declaration to obey ordering rules * xsdk: udate superlu-dist dependency to v5.2.2 * plasma: change gcc dependency to workarround potential spack bug #5778 * trilinos: update hdf5 dependency to use 'hdf5+hl' Without this change - I get the following error [triggered by 161dca6d5 c9810f808 changes] $ ./bin/spack install trilinos+hdf5 ==> Error: An unsatisfiable variant constraint has been detected for spec: hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64 while trying to concretize the partial spec: netcdf+mpi ^m4 ^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64 ^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64 netcdf requires hdf5 variant +hl, but spec asked for ~hl * plasma: add in -lm dependency per #6046 * update sundials version to 3.0.0 * Add fixes to support Netlib LAPACK * mfem does not use cmake for builds [anymore] - so remove code corresponding to this dependency. This enables mfem build on OSX [with xcode/clang compilers] * mfem: update to v3.3.2-rc4 * add patch for building sundials on mac * xsdk: enable plasma for gcc-4.9+ - same as what plasma/package.py does. * magma: Fix for cuda-9.0 as it does not support sm20 nvcc fatal : Unsupported gpu architecture 'compute_20' * add in code for 'spack install xsdk+cuda' - which installs magma * fix flake8 warning * fix flake8 warnings * Updated to the latest MFEM RC. * alquimia: fix to use petsc-3.8.0+ versions * petsc: update to version 3.8.1 * petsc: add in conflict between petsc-3.8.0 & mkl * xsdk: update petsc to 3.8.1 to get MKL build fix * petsc: fix superlu_dist dependency * petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib * petsc: fix dependency [of zlib to be on hdf5 - and not on petsc] * petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build * petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code] recommended-by: @davydden * petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl https://github.com/spack/spack/issues/5846 * plasma: also detect -lgfortran * update sundials version to 3.1.0 * alquimia: xsdk-0.3.0-rc -> xsdk-0.3.0 * petsc: update to version 3.8.2 Includes pkgconfig fix [for mfem static build failure] * Revert "petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build" This reverts commit d1afa8c20d4313fdc42a27e5380573b035b32998. * xsdk: update to use petsc-3.8.2 * Fixed a problem with MFEM trying to use mpicxx instead of the spack defined compiler. * Minor changes to the mfem build and pointing at mfem's release branch that is currently undergoing internal testing. * Enabling shared build for Plasma * plasma: do not look for libgfortran on cray - spack finds the wrong one from the frontend '-L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64 -lgfortran' * Some changes to the mfem package that are in the process of being pulled into spack/develop. * xsdk: switch from 0.3.0-rc1 to 0.3.0 * fix flake8 warnings * plasma: extract plasma changes from xsdk-0.3.0 * plasma: cleanup per review - netlib-lapack: add support for spec['lapack:c'].libs, spec['blas:c'].libs - add getblaslapacklibs() to eliminate duplicate code in edit() and build_targets() - eliminate string manipulation of ld_flags - remove gfortran check (will check later) - remove build() (will check later) * netlib-lapack: fix tuple per review * netlib-lapack: use spec[lapack:c,fortran]
2017-11-27 ViennaRNA: adding version 2.4.3 + disable swig (#6408)peetsv1-1/+4
* Adding version 2.4.3 to ViennaRNA * Replaced tab indent with spaces Flake8 error correction * no swig for viennarna v2.4.3 only * correcting version/argument conditional syntax error
2017-11-27Adding new package amp (#6471)Mark Berrill1-0/+162
2017-11-27Adding list_url to r-hms package (#6473)Quinn1-0/+1
2017-11-27Add two test examples to bohrium (#6459)Michael F. Herbst3-9/+110
2017-11-27r-rtsne: Create new package (#6470)Eric1-0/+41
* r-rtsne: Create new package * r-rtsne: add rcpp dependency
2017-11-27r-pcapp: Create new package (#6468)Eric1-0/+42
2017-11-27plasma: extract plasma changes from xsdk-0.3.0 (#6280)Satish Balay3-11/+77
* plasma: extract plasma changes from xsdk-0.3.0 * plasma: cleanup per review - netlib-lapack: add support for spec['lapack:c'].libs, spec['blas:c'].libs - add getblaslapacklibs() to eliminate duplicate code in edit() and build_targets() - eliminate string manipulation of ld_flags - remove gfortran check (will check later) - remove build() (will check later) * netlib-lapack: fix tuple per review * netlib-lapack: use spec[lapack:c,fortran]
2017-11-27New Package: GAP Benchmark Suite (#6452)Adam Fidel1-0/+57
2017-11-27fixed glog compilation for < 0.3.5 (#6463)Choong Jun Jin1-4/+18
2017-11-27r-rcpp: adds new versions, fixes failing download in Travis CI (#6464)Massimiliano Culpo1-0/+1
2017-11-27r-tsne: Create new package (#6461)Eric1-0/+39
2017-11-27r-rcpp: fix list_url to install archived versions (#6462)Eric1-1/+1
2017-11-26dialign-tx adding patch for gcc@5.4.0 (#6413)peetsv2-0/+82
2017-11-25New Package: Add libcint to spack (#6456)Michael F. Herbst1-0/+74
* Add libcint to spack * Clearifying comment
2017-11-25Implement opencv libs property (#6457)Michael F. Herbst1-0/+7
2017-11-25r-sn: Create new package (#6433)Eric1-0/+46
* r-sn: Create new package * r-sn: fix whitespace and depends_on
2017-11-25pocl: fix link to libtool (#6440)Axel Huebl1-1/+1
libtool is also needed for linking, otherwise downstream dependencies such as clfft will fail linking against pocl's libOpenCL.so with errors such as: ``` >> 182 /usr/bin/ld: warning: libltdl.so.7, needed by /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so, not found (try using -rpath or -rpath-link) >> 183 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlinit' >> 184 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlerror' >> 185 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlopen' >> 186 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlsym' >> 187 collect2: error: ld returned 1 exit status ```
2017-11-25added intel 18.0.1 compilers (#6381)Gregory Lee2-0/+6
2017-11-25Expand bohrium package (#6438)Michael F. Herbst1-17/+57
* GCC greater 4.7 required * Add variant with opencv extmethods * Fix and export the config path
2017-11-25add package py-linecache2 (#6448)healther1-0/+37
2017-11-25add missing dependencies to py-pylint (#6445)healther1-0/+2
2017-11-25add missing build dependency to py-execnet (#6443)healther1-0/+1
2017-11-25gearshifft: enable OpenCL (#6441)Axel Huebl1-7/+7
With pocl builds fixed, we can now also use the OpenCL implementations in gearshifft :)
2017-11-25add missing dependency to py-scikit-image (#6446)healther1-0/+1
2017-11-25add missing dependency to py-unittest2 (#6447)healther1-0/+3
2017-11-25add package py-setuptools-scm (#6449)healther1-0/+36
2017-11-25add package py-traceback2 (#6450)healther1-0/+38
2017-11-25Python: add 3.6.3 . (#6454)健美猫1-0/+1
2017-11-25r: add version 3.4.2. (#6455)健美猫1-0/+1
2017-11-25add new version to node-js (#6444)healther1-0/+1
2017-11-25r-lars: Create new package (#6453)Eric1-0/+39
2017-11-24sfepy: Create new package (#6439)Robert Cimrman1-0/+50
2017-11-24Octave depends on qt+opengl. (#6437)健美猫1-1/+1
2017-11-24Openblas needs FC, not F77 (#6435)Massimiliano Culpo1-3/+4
fixes #5591
2017-11-23siesta: add netcdf support (#6431)Michael Kuron2-0/+27
2017-11-23boost@1.54 alse needs the call_once patch (#6434)George Hartzell1-1/+1
2017-11-23Introduce virtual dependency pkgconfig (#5198)Michael Kuhn297-296/+301
There are two providers, pkgconf and pkg-config, with the former being the default provider.
2017-11-23New version and patch for 'sqlite'. (#6303)Sergey Kosukhin2-0/+57
2017-11-23express: new package (#6281)Audrey Thoma1-0/+63
2017-11-23Add a patch for Intel 18.0.1 (#6392)Ondřej Čertík2-0/+15
2017-11-23Add bohrium to spack (#6395)Michael F. Herbst1-0/+182
* Add bohrium package.py * Changes suggested by @davydden * Add +cuda guard * Specify required environment setup
2017-11-23r-plotly: Create new package (#6423)Eric1-0/+53