Commit graph

7962 commits

Author SHA1 Message Date
healther
cc5d5295bd add missing build dependency to py-pytest-runner (#6490) 2017-11-28 16:52:18 -07:00
Yan Grange
b5f3ecf3fa Update globus package version and hash (#6482) 2017-11-28 16:51:35 -07:00
Michael Kuhn
9adcb0b4b1 libmongoc: Fix pkg-config file not containing snappy and zlib paths (#6467) 2017-11-28 16:47:12 -07:00
healther
f7fda19f5d remove breaking version and cleanup of dependencies (#6494) 2017-11-28 16:46:23 -07:00
healther
8013996661 add conflicts to py-enum34 (#6496) 2017-11-28 16:45:08 -07:00
healther
2190ae43a5 Fix astroid dependency and mark broken version (#6493) 2017-11-28 16:43:43 -07:00
healther
cab07d2562 add package py-editdistance (#6492) 2017-11-28 16:43:00 -07:00
healther
82adc403ad add package py-isort (#6491) 2017-11-28 16:42:47 -07:00
healther
64b121fa87 add package: py-backports-functools-lru-cache (#6488) 2017-11-28 13:54:40 -08:00
Adam J. Stewart
e01a16b992 Remove spack md5 and sha256 commands (#6428) 2017-11-28 13:41:46 -08:00
healther
dc8f587b61 add path to package.py in case of a syntax error (#6458) 2017-11-28 13:32:21 -08:00
becker33
acd80b16a8
update scr package for cray (#6407)
* update scr package for cray

* added info on scr version 1.2.0
2017-11-28 10:33:45 -08:00
Massimiliano Culpo
f6ead27b5b spack spec: don't show normalize + no hash for non concrete specs (#6417)
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.
2017-11-28 09:03:32 -08:00
Denis Davydov
ddb55c2b26 py-numpy: add 1.13.3 (#6484) 2017-11-28 13:42:59 +01:00
Denis Davydov
fdb2386ba7 pi-scipy: add 1.0.0 (#6486) 2017-11-28 13:42:27 +01:00
Yifan Zhu
bec8ddcf81 r-classint: created new package (#6481) 2017-11-28 09:29:29 +01:00
Yifan Zhu
5cdf94233b r-rcppcctz: created new package (#6480) 2017-11-28 09:28:42 +01:00
lingnanyuan
8d64e192dc r-topgo: Create new package. (#6479) 2017-11-28 09:27:36 +01:00
Eric
6edd782d39 r-seurat: Create new package (#6477) 2017-11-28 09:27:14 +01:00
Eric
7f43411e59 Adding list_url to several R module packages (#6474) 2017-11-28 09:26:06 +01:00
Yifan Zhu
63a23b93c5 r-cli: new package (#6476) 2017-11-28 09:21:12 +01:00
Satish Balay
cd8da5a441 Xsdk 0.3.0 (#6277)
* 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 22:08:08 -08:00
peetsv
52f46d2bee ViennaRNA: adding version 2.4.3 + disable swig (#6408)
* 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
2017-11-27 16:45:43 -07:00
Mark Berrill
e2abebe8a5 Adding new package amp (#6471) 2017-11-27 14:43:03 -07:00
Quinn
1268bc8f45 Adding list_url to r-hms package (#6473) 2017-11-27 14:40:02 -07:00
Michael F. Herbst
3d4e51fad2 Add two test examples to bohrium (#6459) 2017-11-27 13:55:29 -07:00
Eric
dbb329637b r-rtsne: Create new package (#6470)
* r-rtsne: Create new package

* r-rtsne: add rcpp dependency
2017-11-27 13:54:53 -07:00
Eric
ebd796110d r-pcapp: Create new package (#6468) 2017-11-27 13:54:36 -07:00
Satish Balay
23bedc276c plasma: extract plasma changes from xsdk-0.3.0 (#6280)
* 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 11:38:10 -08:00
Adam Fidel
557309618f New Package: GAP Benchmark Suite (#6452) 2017-11-27 06:50:49 -07:00
Choong Jun Jin
45e1562162 fixed glog compilation for < 0.3.5 (#6463) 2017-11-27 06:50:26 -07:00
Massimiliano Culpo
eacaa1551e
r-rcpp: adds new versions, fixes failing download in Travis CI (#6464) 2017-11-27 10:15:47 +01:00
Eric
fcf331f176 r-tsne: Create new package (#6461) 2017-11-27 09:30:52 +01:00
Eric
0bb789eb23 r-rcpp: fix list_url to install archived versions (#6462) 2017-11-27 09:20:49 +01:00
peetsv
09eeb991a2 dialign-tx adding patch for gcc@5.4.0 (#6413) 2017-11-26 16:14:18 -07:00
Adam J. Stewart
257d968259 Use long flag in spack help message (#6429) 2017-11-26 06:14:47 -07:00
Michael F. Herbst
41eb496021 New Package: Add libcint to spack (#6456)
* Add libcint to spack

* Clearifying comment
2017-11-25 21:01:30 -07:00
Michael F. Herbst
178381edf9 Implement opencv libs property (#6457) 2017-11-25 21:00:18 -07:00
Eric
9b5e3434ad r-sn: Create new package (#6433)
* r-sn: Create new package

* r-sn: fix whitespace and depends_on
2017-11-25 12:50:13 -07:00
Axel Huebl
a465bf3bec pocl: fix link to libtool (#6440)
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
```
2017-11-25 11:55:08 -07:00
Gregory Lee
1f2867415a added intel 18.0.1 compilers (#6381) 2017-11-25 11:49:02 -07:00
Michael F. Herbst
25d7ef495c Expand bohrium package (#6438)
* GCC greater 4.7 required

* Add variant with opencv extmethods

* Fix and export the config path
2017-11-25 11:46:32 -07:00
healther
d7344d2987 add package py-linecache2 (#6448) 2017-11-25 11:42:16 -07:00
healther
8c5c46a7a2 add missing dependencies to py-pylint (#6445) 2017-11-25 11:41:45 -07:00
healther
835b1ff03d add missing build dependency to py-execnet (#6443) 2017-11-25 11:40:53 -07:00
Axel Huebl
ed685b0262 gearshifft: enable OpenCL (#6441)
With pocl builds fixed, we can now also use the OpenCL
implementations in gearshifft :)
2017-11-25 11:40:12 -07:00
healther
86e771bdb3 add missing dependency to py-scikit-image (#6446) 2017-11-25 11:39:16 -07:00
healther
ca90372f74 add missing dependency to py-unittest2 (#6447) 2017-11-25 11:38:42 -07:00
healther
65fd350eb4 add package py-setuptools-scm (#6449) 2017-11-25 11:38:10 -07:00
healther
0c7cf0c7a4 add package py-traceback2 (#6450) 2017-11-25 11:37:38 -07:00