summaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorFilesLines
2017-11-30Fix CGAL checksum and switch to more stable URL (#6511)Adam J. Stewart1-5/+6
2017-11-30add package py-lazy-object-proxy (#6489)healther1-0/+38
2017-11-30r-biomformat: Create new package. (#6517)lingnanyuan1-0/+48
2017-11-30r-phyloseq: Create new package. (#6518)lingnanyuan1-0/+53
2017-11-30r-nanotime: new package (#6519)Yifan Zhu1-0/+41
2017-11-30Flit package (#6260)Michael Bentley2-0/+93
Add initial build support for version 2.0-alpha.1
2017-11-29Improve docstring of spack.directives.extend (#6485)David Lukes1-2/+3
The original docstring had confusing wording re: what is going to symlinked and where when using the `extend` directive, and how exactly the symlinking is performed (not automatically on install, but using `spack activate`). See #5559.
2017-11-29travis: removed /usr/local/include/c++ before installing gcc on OSX (#6515)Massimiliano Culpo1-0/+1
"brew install gcc" fails for travis build because of an existing /usr/local/include/c++. This commit removes the offending file as suggested by brew.
2017-11-29Add new package nlopt (#6499)Stephen Hudson1-0/+80
2017-11-28add missing build dependency to py-pytest-runner (#6490)healther1-0/+1
2017-11-28Update globus package version and hash (#6482)Yan Grange1-2/+2
2017-11-28libmongoc: Fix pkg-config file not containing snappy and zlib paths (#6467)Michael Kuhn1-0/+12
2017-11-28remove breaking version and cleanup of dependencies (#6494)healther1-9/+13
2017-11-28add conflicts to py-enum34 (#6496)healther1-0/+1
2017-11-28Fix astroid dependency and mark broken version (#6493)healther1-3/+8
2017-11-28add package py-editdistance (#6492)healther1-0/+36
2017-11-28add package py-isort (#6491)healther1-0/+36
2017-11-28add package: py-backports-functools-lru-cache (#6488)healther1-0/+38
2017-11-28Remove spack md5 and sha256 commands (#6428)Adam J. Stewart3-160/+0
2017-11-28add path to package.py in case of a syntax error (#6458)healther1-1/+8
2017-11-28update scr package for cray (#6407)becker331-0/+7
* update scr package for cray * added info on scr version 1.2.0
2017-11-28spack spec: don't show normalize + no hash for non concrete specs (#6417)Massimiliano Culpo1-7/+2
Showing "Normalize" on output doesn't give users additional information, as this step is essentially an implementation detail of concretization. This PR skips it and shows just the input spec and the concretized one. Printing partial hashes for input spec has been disabled.
2017-11-28py-numpy: add 1.13.3 (#6484)Denis Davydov1-0/+1
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
2017-11-26Use long flag in spack help message (#6429)Adam J. Stewart1-1/+1
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