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Author SHA1 Message Date
Audrey Thoma
a97824df98 mrbayes: url now points to github + removed the deprecated sourceforge url (#6578) 2017-12-06 07:58:08 +01:00
Jon Rood
5c43090ceb Update CGNS and add CGNS capability to Trilinos (#6568) 
* Update CGNS to be able to be used in Trilinos.

* Updating Trilinos to be able to use CGNS.

* Fixing wrong cmake defines in trilinos for enabling cgns and cleaning up cgns package.

* Changing cgns parallel variant to mpi. Removing explicit dependence on parallel-netcdf in trilinos.
 2017-12-05 14:33:36 -07:00
nshtg
01ba69c635 Update gnupg to 2.2.3 (#6573) 
Updated dependencies:

* libassuan 2.4.5
* libgcrypt 1.8.1
* npth 1.5
 2017-12-05 14:29:20 -07:00
Axel Huebl
9e64fa53ed Add Maintainer (#6575) 
Add myself as maintainer to the packages we contributed
and/or maintain the mainline from.
 2017-12-05 14:27:56 -07:00
Jon Rood
67d7f3fc03 Add opennurbs package (#6570) 
* Adding OpenNurbs package.

* Fixing flake8 error.

* Removing unused os import from opennurbs.
 2017-12-05 10:33:55 -07:00
Axel Huebl
5a908a1c8a ADIOS 1.13.0: LZ4 & blosc support (#6572) 
Add additional transform libraries to ADIOS.
Also modifies existing transforms to the versions they were
introduced (otherwise this was resulting in unknown configure flags).
 2017-12-05 15:28:44 +01:00
Axel Huebl
e47d89a2ab ADIOS 1.13.0: Newer SZ Versions (#6561) 
The latest release of ADIOS needs a newer version of SZ due to an upstream library naming change.
 2017-12-05 12:50:22 +01:00
Axel Huebl
09e68c5c8a c-blosc: 1.12.1 (#6571) 
Adds a newer release of c-blosc, adds the new flags for external library builds, adds missing dependencies.
 2017-12-05 12:49:22 +01:00
Sergey Kosukhin
90c7bc7a24 OpenJPEG: all version tuples have the same length. (#6526) 2017-12-04 17:44:53 -07:00
Paschalis Korosoglou
b2c6306b94 Added package r version 3.4.3 (#6565) 2017-12-04 17:39:34 -07:00
Axel Huebl
9ad3b1a747 libpng: CPPFLAGS for -I (#6563) 
Recent versions of `libpng` (e.g. 1.6.34) warn/abort that includes
for `zlib` need to be passed properly via `CPPFLAGS`. This fixes it.
 2017-12-04 15:29:35 -07:00
Eric
6968777af7 bamtools: Add version 2.5.0 (#6553) 2017-12-04 10:38:30 -07:00
Denis Davydov
e9c66a76f0 dealii: add scalapack and various cleanups (#6552) 2017-12-04 08:02:05 +01:00
Chien-Chang Feng
f564e02301 py-h5py: fixed a typo in the name of a dependency (#6540) 2017-12-04 07:50:35 +01:00
Benedikt Riedel
6887107775 Adding zlib dependence to xrootd to resolve #6545 (#6550) 2017-12-03 16:22:44 -07:00
Eric
10ad2bc1bf py-multiqc: Add version 1.3 (#6554) 2017-12-03 16:21:27 -07:00
Yifan Zhu
1e702bfab0 r-fftwtools: new package (#6532) 2017-12-03 16:20:32 -07:00
Paschalis Korosoglou
79751729c9 Rename variant static to shared (#6543) 2017-12-03 16:19:32 -07:00
Denis Davydov
13dade60dd gcc: remove all variant (#5283) 2017-12-03 10:19:55 +01:00
Nils Deppe
07fcd0d115 Add Kvasir MPL (#6529) 2017-12-02 16:02:43 -07:00
Eric
6918ee3767 salmon: Add version 0.9.1 (#6516) 2017-12-02 12:45:10 -07:00
sknigh
80048ae4a9 Paraview expects qt to have opengl (#6520) 2017-12-01 13:46:39 -07:00
Axel Huebl
d6863a2940 ADIOS: 1.13.0 (#6539) 
New release of ADIOS: 1.13.0.
 2017-12-01 11:09:37 -07:00
Stephen Hudson
d5c96dbd94 Add new package py-libensemble (#6525) 2017-12-01 11:01:08 -07:00
Eric
fa32f8f914 py-dendropy: Create new package (#6528) 2017-12-01 11:00:45 -07:00
Paschalis Korosoglou
bd94be818a Added variant static for hwloc (#6538) 2017-12-01 06:25:23 -07:00
Yifan Zhu
e0264404b6 r-udunits2: new package r-udunits2 (#6533) 2017-12-01 11:16:35 +01:00
Yifan Zhu
4a55f81051 r-units: new package (#6531) 2017-12-01 05:26:05 +01:00
Adam J. Stewart
3dafbe901a Fix CGAL checksum and switch to more stable URL (#6511) 2017-11-30 09:18:54 +01:00
healther
130c56dbaa add package py-lazy-object-proxy (#6489) 2017-11-30 09:17:28 +01:00
lingnanyuan
5382279fa6 r-biomformat: Create new package. (#6517) 2017-11-30 09:14:12 +01:00
lingnanyuan
f9c820c39f r-phyloseq: Create new package. (#6518) 2017-11-30 09:13:31 +01:00
Yifan Zhu
86fbcc7140 r-nanotime: new package (#6519) 2017-11-30 09:12:58 +01:00
Michael Bentley
a097524281 Flit package (#6260) 
Add initial build support for version 2.0-alpha.1
 2017-11-30 09:05:40 +01:00
Stephen Hudson
02371d2ace Add new package nlopt (#6499) 2017-11-29 10:27:08 +01:00
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
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
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
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
健美猫
0d91f51a27 Python: add 3.6.3 . (#6454) 2017-11-25 11:34:24 -07:00
健美猫
086a1cfe7e r: add version 3.4.2. (#6455) 2017-11-25 11:34:05 -07:00
healther
7c174f11ec add new version to node-js (#6444) 2017-11-25 09:30:06 +01:00
Eric
be095fdb21 r-lars: Create new package (#6453) 2017-11-25 09:24:53 +01:00
Robert Cimrman
77bfda4da6 sfepy: Create new package (#6439) 2017-11-24 12:21:09 +01:00
健美猫
70adbaeeba Octave depends on qt+opengl. (#6437) 2017-11-24 09:40:48 +01:00
Massimiliano Culpo
cde5fdde20
Openblas needs FC, not F77 (#6435) 
fixes #5591
 2017-11-24 07:15:01 +01:00
Michael Kuron
ff4a4fcd9e siesta: add netcdf support (#6431) 2017-11-23 13:39:32 -07:00
George Hartzell
2a2670175d boost@1.54 alse needs the call_once patch (#6434) 2017-11-23 20:17:17 +01:00
Michael Kuhn
5bbbfe9446 Introduce virtual dependency pkgconfig (#5198) 
There are two providers, pkgconf and pkg-config, with the former being
the default provider.
 2017-11-23 08:05:38 -07:00
Sergey Kosukhin
7f0659f032 New version and patch for 'sqlite'. (#6303) 2017-11-23 08:04:41 -07:00
Audrey Thoma
cd7d812be9 express: new package (#6281) 2017-11-23 08:04:02 -07:00
Ondřej Čertík
7a2b3b2588 Add a patch for Intel 18.0.1 (#6392) 2017-11-23 07:28:35 -07:00
Michael F. Herbst
a955f63530 Add bohrium to spack (#6395) 
* Add bohrium package.py

* Changes suggested by @davydden

* Add +cuda guard

* Specify required environment setup
 2017-11-23 07:24:55 -07:00
Eric
1dba6435bd r-plotly: Create new package (#6423) 2017-11-23 07:17:17 -07:00
Denis Davydov
ddf10fa322 dealii: limit CMake to 3.9 as 3.10.0 is not supported yet (#6427) 2017-11-23 07:16:44 -07:00
sknigh
e2cf933ec1 gcc environment module will set CC, CXX, FC, F77, and F90 flags (#3954) 2017-11-23 12:44:55 +01:00
Cameron Smith
951679376e zoltan: add optional dependency on parmetis (#6387) 2017-11-23 09:03:02 +01:00
Eric
6fd1009081 r-mixtools: Create new package (#6421) 2017-11-23 09:01:10 +01:00
Eric
bdd8bb1fd9 r-ranger: Create new package (#6422) 2017-11-23 09:00:32 +01:00
Chien-Chang Feng
630d7e19db py-yt: Yt-project is moved. Add new version. (#6409) 2017-11-23 07:25:35 +01:00
Jon Rood
8b63cc6ad6 Using MPI environment compiler variables for pnetcdf. (#6424) 2017-11-22 21:34:21 -08:00
Massimiliano Culpo
0fc6611dc2
Changed every docs variant into doc as decided in #2663 (#6412) 
fixes #2663
 2017-11-22 15:06:59 +01:00
Sergey Kosukhin
d4ab511f73 Script for 'eccodes' is compatible with Python 3. (#6402) 2017-11-21 15:59:04 -07:00
Audrey Thoma
a0df5ae3e0 phantompeakqualtools: new package (#6403) 2017-11-21 15:58:20 -07:00
Eric
9e013ee036 r-pbapply: Create new package (#6377) 2017-11-21 13:45:12 -07:00
Eric
5a72d30816 r-ggjoy: Create new package (#6399) 2017-11-21 13:44:25 -07:00
Eric
60b50a7bd2 r-ica: Create new package (#6400) 2017-11-21 13:43:02 -07:00
Eric
d6a5310df5 r-cppprogress: Create new package (#6398) 2017-11-21 13:42:44 -07:00
Eric
d725904803 r-sdmtools: Create new package (#6397) 2017-11-21 13:42:28 -07:00
BenBrands
27b9d2614c CMake: add 3.10.0 (#6393) 2017-11-21 08:04:53 -07:00
David Poliakoff
003f83db50 gotcha: new package (#6391) 
* Initial stab at a package for Gotcha

* Commit with no boilerplate

* Flake8
 2017-11-21 08:04:43 -07:00
Audrey Thoma
c4613b8e1f mira: new package (#6385) 2017-11-21 08:04:08 -07:00
Michael F. Herbst
f0c0243cd4 Fix to allow installing pocl 0.14 again (#6372) 
* Resolve issue 4669

* Use prefix path magic attribute
 2017-11-21 08:03:36 -07:00
Yifan Zhu
5250c8eb0a r-broom: new package (#6282) 2017-11-21 10:49:09 +01:00
Yifan Zhu
e3abc7bfa4 r-haven: created new package (#6293) 2017-11-21 09:54:43 +01:00
Yifan Zhu
b7189ecf9e r-psych: created new package (#6286) 2017-11-21 09:40:10 +01:00
Yifan Zhu
ef8429c99c r-modelr: created new package (#6289) 2017-11-21 09:26:44 +01:00
Eric
0743c5bde6 r-crosstalk: Create new package (#6383) 2017-11-20 21:52:58 -07:00
Eric
cd5e6a14bb r-fnn: Create new package (#6384) 2017-11-20 21:52:39 -07:00
Audrey Thoma
8b2abfb28b masurca: new package (#6386) 2017-11-20 21:51:35 -07:00
Eric
70ce7e2099 meme: add version 4.12.0 (#6388) 2017-11-20 21:50:46 -07:00
Eric
035cce2b81 py-biopython: add version 1.70 (#6389) 2017-11-20 21:50:25 -07:00
Eric
17e0b81463 r-ggridges: Create new package (#6376) 2017-11-20 14:18:16 -07:00
Eric
30b794254f py-pysam: add version 0.13 (#6382) 2017-11-20 14:08:25 -07:00
BenBrands
93d5a91a56 dealii: fix HDF5 dependency (#6374) 2017-11-20 11:57:53 -07:00
BenBrands
83db25967e Atlas: add 3.11.39 (#6375) 2017-11-20 11:57:34 -07:00
Eric
9040f34aba r-tclust: Create new package (#6380) 2017-11-20 11:57:04 -07:00
Eric
1d69dbe7ae r-diffusionmap: Create new package (#6378) 2017-11-20 11:56:47 -07:00
Eric
012acdc7a2 r-chemometrics: Create new package (#6379) 2017-11-20 11:56:33 -07:00
Denis Davydov
4e878c21cd elpa: add 2017.05.002 and 2017.05.003 (#5306) 
* elpa: add 2017.05.002 and 2017.05.03
* add a variant for optimization flags
 2017-11-20 11:17:22 -07:00
Denis Davydov
34da07db9b dealii: add cuda_arch variant via CudaPackage (#6070) 2017-11-19 12:39:13 -07:00
Adam J. Stewart
acbdf516f7 Add a new package for rlwrap (#6371) 2017-11-19 06:45:25 -07:00
lingnanyuan
cf3df2a321 r-dose: Create new package. (#6355) 2017-11-18 12:54:14 -07:00
Eric
20092adb94 r-vgam: Create new package (#6363) 2017-11-18 06:39:55 -07:00
Eric
618f4dff6d r-bindrcpp: Create new package (#6366) 2017-11-18 06:36:39 -07:00
Eric
1c55a401b1 r-dtw: Create new package (#6365) 2017-11-18 06:35:47 -07:00
Eric
ebfc7bd7aa r-som: Create new package (#6364) 2017-11-18 06:35:21 -07:00
Michael Kuron
e2fea1e1e6 siesta: new package (#6346) 
* siesta: new package

* siesta: use libs instead of ld_flags everywhere
 2017-11-17 19:01:15 -07:00
Stephen Hudson
b2f0306c6f Mpi4py update (#6342) 2017-11-17 19:00:36 -07:00
Javier Cervantes
21da747a5d hepmc: fix hash and urls, add new version 3.0.0 (#6348) 2017-11-17 18:59:52 -07:00
健美猫
8bc024d2d9 Add cluster.2017.5 and cluster.2018.1. (#6349) 2017-11-17 18:59:18 -07:00
lingnanyuan
9647038f27 r-rvcheck: Create new package. (#6351) 2017-11-17 18:59:00 -07:00
lingnanyuan
eda91bebd7 r-gosemsim: Create new package. (#6352) 2017-11-17 18:58:43 -07:00
lingnanyuan
d836d7e7ea r-do-db: Create new package. (#6353) 2017-11-17 18:58:23 -07:00
lingnanyuan
c604638681 r-fgsea: Create new package. (#6354) 2017-11-17 18:58:01 -07:00
lingnanyuan
5c06255b24 r-clusterprofiler: Create new package. (#6356) 2017-11-17 18:57:40 -07:00
sknigh
1f8f593dd6 Added libhio 1.4.0.0 (#6357) 2017-11-17 18:57:17 -07:00
Brian Homerding
17debcb9b2 NuT: Add Installation of lib and demo app (#6341) 2017-11-16 16:30:42 -07:00
Matthias Vogelgesang
a62f8698c3 Add UFO and dependencies (#6337) 
* Add json-glib

* Add ufo-core

* Add ufo-filters
 2017-11-16 09:37:17 -08:00
healther
ef3c909701 add package py-numba (#6323) 
* add package py-numba

* Update package.py

* Update package.py

* Update package.py
 2017-11-16 10:13:20 -07:00
Audrey Thoma
e941f33eaf meraculous: new package (#6292) 
* meraculous: new package

* adding gcc version conflict

* Update package.py

* Update package.py
 2017-11-16 09:40:46 -07:00
lingnanyuan
bb3d5fd313 r-rhdf5: Create new package. (#6330) 2017-11-16 09:40:15 -07:00
lingnanyuan
e732a554ff r-shortread: Create new package. (#6332) 2017-11-16 09:30:18 -07:00
lingnanyuan
cca06422fa r-sva: Create new package. (#6333) 2017-11-16 09:28:59 -07:00
David Hows
d89b09493c Minor package fixes (#6334) 
* Add no-implicit-fallthrough to MsgpackC

* Add 0.2.1 of Neovim

* Lint
 2017-11-16 09:28:40 -07:00
Stephen Hudson
9d1224e5d8 py-petsc4py: Update version to 3.8.0 and add dependencies (#5792) 
* py-petsc4py: Update version to 3.8.0 and add dependencies

- Added explicit dependency on python and numpy

* Kept old version - and corrected minimal python version

* Update to 3.8.1
 2017-11-15 16:49:36 -07:00
baip
697f3ea71d cp2k: add dependency on smm and libxc & new version 5.1 (#6194) 
* cp2k: add libxsmm dependency

* cp2k: add libxc dependency

* cp2k: add smm variant to select from libxsmm or libsmm

* cp2k: add version 5.1
 2017-11-15 16:49:08 -07:00
Christoph Junghans
7da8a02cbf
git grep --files-with-matches github.com/llnl/spack | xargs sed -i '/github.com/s@llnl/spack@spack/spack@' (#6329) 2017-11-15 16:46:39 -07:00
Denis Davydov
cb5fd6035a intel: add 2018.1 (#6322) 2017-11-15 13:13:15 -07:00
Axel Huebl
d1a733bc86 xtensor, xtl, xsimd (#6315) 
Adds the QuantStack libs (C++, header-only) needed for
xtensor.
 2017-11-15 13:12:31 -07:00
Yifan Zhu
cde0570c56 r-janitor: created new package (#6313) 2017-11-15 13:09:24 -07:00
Yifan Zhu
0d9ab84ebb r-dbplyr: created new package (#6311) 2017-11-15 13:09:11 -07:00
Howard Pritchard
af1b93b3db Open MPI: add 2.0.4 release to package file (#6310) 
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2017-11-15 13:03:07 -07:00
健美猫
71f12597a7 Update pgi to 17.10 . (#6306) 2017-11-15 13:02:54 -07:00
Sergey Kosukhin
e77b11674f Update for 'magics' and 'libemos'. (#6275) 2017-11-15 13:01:23 -07:00
Benedikt Riedel
2eb7fabe62 Allow openblas to build on a VM (#6258) 
This adds a "virtual_machine" boolean variant which adds build
options that enable building openblas on a VM.
 2017-11-15 10:32:02 -08:00
Eric
9acf207023 picard: add versions and fix url format (#6309) 2017-11-14 16:41:27 -07:00
Michael Kuhn
ec5d366bcd likwid: Fix hash for 4.3.0 (#6307) 
Prefer 4.2.1 for now because 4.3.0's hash changes regularly.
 2017-11-14 16:41:05 -07:00
健美猫
d9a4e7a038 Update miniconda to 4.3.30. (#6233) 2017-11-14 12:11:53 -08:00
Adam J. Stewart
138e9d08c6 Add the latest version of Lmod (#6297) 2017-11-14 10:32:41 -08:00
koebbe
50957bd44f py-h5py: make sure to depend on the hl variant of hdf5 (#6304) 2017-11-14 09:26:58 -07:00
vishalkenchan
0692029273 update trilinos checksums (#6301) 2017-11-14 09:22:34 -07:00
Michael Kuhn
aa27432a1d ncl: Check for ncl binary after installation (#6298) 
ncl's build system will happily continue in case of errors, which might
result in the ncl binary not being built.
 2017-11-14 09:22:04 -07:00
Michael Kuhn
e31b997162 icu4c: Update to 60.1 (#6295) 
Previous versions try to include xlocale.h, which fails on glibc >= 2.26.
 2017-11-14 09:21:35 -07:00
Yifan Zhu
a8f9182ef3 r-forcats: created new package (#6291) 2017-11-14 09:21:21 -07:00
Michael Kuhn
93bca2f3a2 libbson, libmongoc: Update to 1.8.1 (#6290) 2017-11-14 09:21:05 -07:00
Eric
137a9e64ac trimgalore: add version 0.4.5 (#6288) 2017-11-14 09:20:20 -07:00
Yifan Zhu
392e25b7e6 r-mnormt: created new package (#6287) 2017-11-14 09:20:06 -07:00
Yifan Zhu
05eb287ed9 r-bindr: created new package (#6285) 2017-11-14 09:19:49 -07:00
Yifan Zhu
c042644b53 r-glue: created new package (#6283) 2017-11-13 16:25:52 -07:00
Douglas Duckworth
c7d2b4dbd6 relion 2.1 - update variant defaults (#6201) 
Default precision should be double for CPU. Generally users also want
to use GPUs so the +cuda variant is now also enabled by default.
 2017-11-13 12:29:43 -08:00
Christoph Junghans
bde727e187
mpibash: move to autotools (#6253) 2017-11-13 10:48:31 -07:00
Christoph Junghans
02335fa849
ucx: initial commit (#6265) 2017-11-13 10:47:58 -07:00
Eric
306aca812d ont-albacore: add version 2.1.2 (#6278) 2017-11-13 10:47:40 -07:00
Satish Balay
6fd92e4257 petsc: update to version 3.8.2 (#6244) 
Includes pkgconfig fix [for mfem static build failure]
 2017-11-11 07:16:03 -07:00
Brian Homerding
19f8940c01 Nekbone: Installing data files for example runs (#6243) 
* Nekbone: Installing data files for example runs

* Typo Fix
 2017-11-10 19:59:33 -07:00
Sergey Kosukhin
263126bc5d Create symlink for 'swig' binary after installation. (#6240) 2017-11-10 19:50:11 -07:00
Aaron Fisher
af06ea0e74 Fixed mfem mpi build issue. (#6254) 
* Fixed mfem mpi build issue.

* Fixed a non-mpi build issue and switched to the latest official MFEM release.
 2017-11-10 19:49:17 -07:00
Yifan Zhu
e38f31e773 feature/r-reprex: new package (#6257) 2017-11-10 19:47:21 -07:00
Cyrus Harrison
b079e1dbd5 add alpine ascent (#6224) 
* add ascent package and and deps

* proper use of site_packages_dir prop

* flake8

* add maitain, small updates

* flake8

* flake8

* fixs for docstrings for sphinx
 2017-11-10 17:00:47 -08:00
becker33
917d021997 Add version 1.04 (#6259) 2017-11-10 15:52:48 -08:00
becker33
a7b817b494 elfutils: add --no-as-needed flag for library ordering issue (#6256) 
* add --no-as-needed flag for library ordering issue libelf

* fix syntax error.
 2017-11-10 11:42:37 -08:00
Yifan Zhu
f6ed8d856a xclip: created new package (#6248) 2017-11-10 11:13:00 -07:00
Yifan Zhu
a872dc5927 r-clipr: created new package (#6249) 2017-11-10 11:11:45 -07:00
lingnanyuan
acc3817ffc r-purrr: Create new package. (#6241) 2017-11-09 14:51:30 -07:00
lingnanyuan
65a278c927 r-covr: Create new package. (#6239) 2017-11-09 13:19:53 -07:00
lingnanyuan
e43e29209d r-readxl: Create new package. (#6238) 2017-11-09 13:19:43 -07:00
lingnanyuan
0902f58f3d r-cellranger: Create new package. (#6237) 2017-11-09 13:19:25 -07:00
lingnanyuan
5e0e3092f6 r-rematch: Create new package. (#6236) 2017-11-09 13:19:12 -07:00
Satish Balay
2b07379831 petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configur… (#6189) 
* 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: 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
 2017-11-09 11:34:59 -08:00
Satish Balay
8d512ce9ae magma: cuda updates [from xsdk-0.3.0 branch] (#6160) 
- add gcc dependency per cuda versions
- Fix for cuda-9.0  as it does not support sm20

    nvcc fatal   : Unsupported gpu architecture 'compute_20'
 2017-11-09 11:34:40 -08:00
lingnanyuan
ee867db5de r-log4r: Create new package. (#6133) 2017-11-09 10:23:48 -07:00
Simone Bnà
c79a0fbbf2 mesa: fixed url for version (#5818) 2017-11-09 10:16:52 -07:00
Benedikt Riedel
266de67c24 ROOT needs to have a consistent version of binutils, as it is very sensitive to the version of libopcodes. You can't move the code from one system (with the same OS) as another. (#6226) 2017-11-09 06:49:27 -08:00
lingnanyuan
935a6b00d7 r-analysispageserver: Create new package. (#6135) 2017-11-09 07:23:10 -07:00
Levi Baber
74d38b3150 py-dlcpar (#6229) 
* py-dlcpar: new package

* py-dlcpar: whitespace
 2017-11-09 07:21:56 -07:00
baip
acf6653933 pexsi: add version 0.10.2 (#6232) 2017-11-09 07:21:39 -07:00
David Gardner
d9fc26b2a5 add sundials 3.1.0 (#6230) 2017-11-09 14:04:03 +01:00
Luigi Calori
24bb3c61de fix perl dependent modules, #5900 (#5937) 
*  FIX perl dependent environmwent setup to avoid void lines in generated modules as #5900

* remove debug prints

* fix flake8
 2017-11-08 22:10:50 -07:00
Alfredo Adolfo Gimenez
a754bd7eee Package/sosflow (#6122) 
* Added missing deps to libffs

* SOSflow spack package pointing to sos_flow feature/spack branch

* Using tag for spack build

* Change url to spack/spack
 2017-11-08 22:07:37 -07:00
David Gardner
a656bc300a add patch for building sundials (#6161) 
* add patch for building sundials on mac

* add upper limit on the patch
 2017-11-08 22:06:34 -07:00
Yifan Zhu
3159841e33 r-callr: created new package (#6223) 2017-11-08 21:59:21 -07:00
lingnanyuan
72bec9a7a0 r-rex: Create new package. (#6221) 2017-11-08 21:57:09 -07:00
Yifan Zhu
ca2ffd9299 r-rvest: created new package (#6220) 2017-11-08 21:56:50 -07:00
Levi Baber
ef126523f1 fastme: new package (#6219) 2017-11-08 21:56:32 -07:00
Yifan Zhu
edc1e6a0d8 r-selectr: created new package (#6218) 2017-11-08 21:56:02 -07:00
lingnanyuan
e57564e899 r-tseries: Create new package. (#6216) 2017-11-08 21:55:45 -07:00
sknigh
699748a2be Added missing build dependency to json-c (#6211) 2017-11-08 21:55:28 -07:00
lingnanyuan
e2004076b1 r-allelicimbalance: Create new package. (#6044) 2017-11-08 21:52:46 -07:00
Yifan Zhu
ac7f5a1af1 r-mzr: created new package (#6206) 2017-11-08 19:53:00 -07:00
Yifan Zhu
cd4b19ffa8 r-msnbase: new package (#6207) 2017-11-08 19:52:38 -07:00
lingnanyuan
912d39908d r-sqldf: Create new package. (#6208) 2017-11-08 19:52:08 -07:00
lingnanyuan
4585d6426a r-gsubfn: Create new package. (#6209) 2017-11-08 19:51:51 -07:00
Yifan Zhu
b110cd0b12 r-vsn: new package (#6210) 
* r-hexbin: updated md5

* r-vsn: created new package
 2017-11-08 19:51:35 -07:00
lingnanyuan
7848e0d4b6 r-quantmod: Update version to 0.4-11 (#6212) 2017-11-08 19:51:13 -07:00
Yifan Zhu
ecdaea1c8e r-xml2: created new package (#6217) 2017-11-08 19:50:53 -07:00
lingnanyuan
1c2292dcd4 r-timedate: Create new package. (#6215) 2017-11-08 19:50:37 -07:00
lingnanyuan
5558cce438 r-fracdiff: Create new package. (#6214) 2017-11-08 19:50:18 -07:00
lingnanyuan
2cd57876c7 r-forecast: Create new package. (#6213) 2017-11-08 19:49:58 -07:00
Christoph Junghans
b3f678c1c0
gasnet: add 1.30.0 (#6167) 
* gasnet: add 1.30.0

* gasnet: expose more options as variants

* gasnet: change defaults
 2017-11-08 19:43:13 -07:00
Audrey Thoma
877bee3cb5 guidance: new package (#6079) 
* guidance: new package

* not really fixed yet

* adding loop

* fixing url

* dang typos
 2017-11-08 14:07:13 -07:00
lingnanyuan
dd3a6d7f18 r-ampliqueso: Create new package. (#6132) 2017-11-08 14:05:53 -07:00
Yifan Zhu
96f70606e8 r-tiff: created new package (#6134) 2017-11-08 14:05:33 -07:00
lingnanyuan
f73b409968 r-anaquin: Create new package. (#6138) 2017-11-08 14:05:17 -07:00
lingnanyuan
2cba0d4d5f r-qvalue: Create new package. (#6137) 2017-11-08 14:05:00 -07:00
baip
4273ebac3c libxsmm: add libs property (#6193) 2017-11-08 14:04:26 -07:00
lingnanyuan
17b9a479b6 r-aneufinderdata: Create new package. (#6192) 2017-11-08 14:03:35 -07:00
lingnanyuan
bb619aa091 r-aneufinder: Create new package. (#6191) 2017-11-08 14:03:22 -07:00
Christoph Junghans
d8db861fec
flecsi: fix build (#6168) 2017-11-08 14:03:05 -07:00
lingnanyuan
04f32377b2 r-rhtslib: Create new package. (#6164) 2017-11-08 14:02:12 -07:00
Audrey Thoma
3fcc911737 kraken: new package (#6163) 2017-11-08 14:01:55 -07:00
Audrey Thoma
743a87abb3 fpc: new package (#6162) 2017-11-08 14:01:31 -07:00
lingnanyuan
6556a5c914 r-cowplot: Create new package. (#6190) 2017-11-08 13:58:57 -07:00
Yifan Zhu
5f70d578ec r-maldiquant: created new package (#6188) 2017-11-08 13:58:43 -07:00
lingnanyuan
860834e094 r-reordercluster: Create new package. (#6187) 2017-11-08 13:58:21 -07:00
Yifan Zhu
605c8e65b3 r-mzid: created new package (#6186) 2017-11-08 13:58:04 -07:00
Yifan Zhu
98baf49ba6 r-xde: created new package (#6185) 2017-11-08 13:57:46 -07:00
lingnanyuan
3943bc945b r-ggdendro: Create new package. (#6184) 2017-11-08 13:57:30 -07:00
lingnanyuan
241e1b56b5 r-dnacopy: Create new package. (#6183) 2017-11-08 13:57:15 -07:00
Yifan Zhu
92a582d5f8 r-mergemaid: created new package (#6182) 2017-11-08 13:56:59 -07:00
lingnanyuan
146db9adef r-bamsignals: Create new package. (#6181) 2017-11-08 13:56:34 -07:00
Yifan Zhu
87aafeb78a r-xmapbridge: created new package (#6180) 2017-11-08 13:56:15 -07:00
Sergey Kosukhin
c7a855ba57 Missing dependency for 'cdo'. (#6175) 2017-11-08 13:55:57 -07:00
baip
ed00757265 gcc: add 5.5.0 (#6171) 2017-11-08 20:27:08 +01:00
vishalkenchan
392929ba77 lammps: add more packages (#6174) 
* lammps : adding new varients and dependencies therein

* Update package.py

* removing trailing whitespaces
 2017-11-08 09:01:14 -07:00
Matthew Scott Krafczyk
00d48e60bf Fix for nghttp2 installation (#5904) 
nghttp2 depends on python, and requires the install directory to exist,
and contain the python module directory which it will eventually
install the python modules into.
 2017-11-07 15:59:15 -08:00
James Dickson
841d42b308 TyphonIO: new package + Updated MACSio package (#6177) 2017-11-07 13:13:06 -07:00
Audrey Thoma
8bae192d5c repeatmasker: new package (#6108) 2017-11-06 17:27:42 -07:00
Michael Kuhn
ca73103dac Introduce static_to_shared_library function (#6092) 
The static_to_shared_library function takes an existing static library
and produces a shared library based on it.
 2017-11-06 17:21:46 -07:00
Satish Balay
dc78e60c83 trilinos: update hdf5 dependency to use 'hdf5+hl' (#6025) 
* 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

* fix flake8 warning
 2017-11-06 13:03:06 -08:00
Luigi Calori
f0d33df3a9 some missing X11 "*proto" dependencies (#6158) 
* fix xinput deps

* adding other x11 proto missing deps, see #6157
 2017-11-06 13:02:05 -08:00
Satish Balay
436ebc4490 petsc: update petsc dependency on superlu-dist (#6159) 2017-11-06 12:52:10 -08:00
Yifan Zhu
cd4d26705e Bioconductor package url change (#5797) 2017-11-06 11:17:59 -07:00
Michael Kuhn
450f2fa034 likwid: Use external lua if possible (#6009) 2017-11-06 11:14:34 -07:00
Douglas Duckworth
47b15feec3 added new package - MotionCor2 (#6151) 2017-11-06 11:09:46 -07:00
Denis Davydov
f538b7ac3e dealii: make sure bundled libs are not used (#6106) 2017-11-06 12:38:59 +01:00
Besnard Jean-Baptiste
84c6fea32e Graphviz : Add a GTS variant (#6149) 
Enable support for the GNU Triangulated Surface Library

	- New variant +gts for graphviz
	- Optionnal dependency for GTS (already packaged)
 2017-11-05 16:55:44 -08:00
Douglas Duckworth
ccc51cea7d added relion v 2.1 (#6023) 
* added relion v 2.1

* relion 2.1 - misssed comma

* relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
 2017-11-05 15:01:21 -08:00
Ben Boeckel
22df09315f Re-add list_url for all R packages (#6110) 
* r-igraph: find old packages in the archive

Fixes #6104.

* r-irlba: find old packages in the archive

Fixes #6101.

* r-lazyeval: find old packages in the archive

Fixes #6102.

* packages: set list_url for all packages hosted on CRAN

* packages: consistently use the CRAN archive URLs
 2017-11-05 13:42:24 -08:00
Adam Moody
2a8c97d440 dtcmp: add v1.1.0 (#6146) 2017-11-05 09:25:03 -08:00
Satish Balay
d34d0d6cbc petsc: update to version 3.8.1 (#6150) 
* petsc: update to version 3.8.1

* petsc: add in conflict between petsc-3.8.0 & mkl
 2017-11-05 09:24:42 -08:00
Axel Huebl
5d9dd24daa ISAAC 1.3.3 (#6152) 
Add a new release of ISAAC.
 2017-11-05 09:24:18 -08:00
Todd Gamblin
05fa302655
Replace github.com/llnl/spack with github.com/spack/spack (#6142) 
We moved to a new GitHub org! Now make the code and docs reflect that.
 2017-11-04 17:08:04 -07:00
vishalkenchan
386e0af089 add rol variant (#6105) 2017-11-04 12:14:46 -07:00
Yifan Zhu
9d234c4f8e r-yapsa: created new package (#6121) 2017-11-03 14:21:00 -06:00
Yifan Zhu
fb1160d052 r-keggrest: created new package (#6120) 2017-11-03 14:20:36 -06:00
lingnanyuan
3921948b03 r-statmod: Create new package. (#6119) 2017-11-03 14:20:14 -06:00
lingnanyuan
b204c7e793 r-deseq: Create new package. (#6118) 2017-11-03 14:19:38 -06:00
lingnanyuan
f91c25ddee r-samr: Create new package. (#6117) 2017-11-03 14:19:16 -06:00
lingnanyuan
d54627659a r-impute: Create new package. (#6116) 2017-11-03 14:18:46 -06:00
lingnanyuan
95e290eaf3 r-altcdfenvs: Create new package. (#6115) 2017-11-03 14:18:17 -06:00
lingnanyuan
64689bdb01 r-makecdfenv: Create new package. (#6114) 2017-11-03 14:17:58 -06:00
lingnanyuan
b614c7970b r-hypergraph: Create new package. (#6113) 2017-11-03 14:17:36 -06:00
Axel Huebl
5a4544ab05 ISAAC 1.3.2 (#6129) 
Add a new release of ISAAC.
 2017-11-03 14:58:38 +01:00
Ben Boeckel
be01b2d5f0 aspell: refuse to work with non-global extensions 
Aspell compiles in the paths it looks for rather than looking relative
to its binary location. There are also no environment variables to
redirect it other than changing the path to the configuration file it
looks at.
 2017-11-02 18:45:40 -07:00
Ben Boeckel
a81485cb3f perl: support extensions in views 2017-11-02 18:45:40 -07:00
Oliver Breitwieser
643a28aac5 python: extensions support for easy-install.pth 2017-11-02 18:45:40 -07:00
Ben Boeckel
d5a3d9d20e view: test conflicting packages in views 2017-11-02 18:45:40 -07:00
Ben Boeckel
13b669de8e view: test that extension paths exist 2017-11-02 18:45:40 -07:00
Ben Boeckel
41dfba0ba1 extension1: add a second version 2017-11-02 18:45:40 -07:00
Ben Boeckel
a7925bb927 bdftopcf: require xproto and fontsproto at build time (#6112) 
These are technically "link" depends of libxfont, but they have no
actual libraries.

Fixes #5936.
 2017-11-02 15:47:18 -06:00
lingnanyuan
13f1781bea Add package r-reportingtools and update url for its dependencies. (#6071) 
* r-reportingtools: Create new package.

* r-go-db: Update url.

* r-gseabase: Update url.

* r-pfam-db: Update url.
 2017-11-02 14:21:32 -06:00
Michael Kuhn
d1db161aeb adios: Fix hdf5 and sz dependencies (#6016) 
- hdf5's +hl variant is required because the build uses libhdf5_hl.
- sz is only compatible up to version 1.4.10 because the library has
  been renamed to libSZ in 1.4.11.
 2017-11-02 13:41:25 -06:00
Brice Goglin
3a1b013291 hwloc: add version 1.11.8 (#6099) 
Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
 2017-11-02 13:40:46 -06:00
Audrey Thoma
f9341857c7 arlecore: new package (#6109) 2017-11-02 13:40:03 -06:00
Christoph Junghans
c4db3d384e gromacs: add develop version (#6098) 2017-11-02 15:16:21 +01:00
Adam J. Stewart
e47ceefc43 sundials+hypre depends on hypre (#6075) 2017-11-02 08:16:43 +01:00
Denis Davydov
11ba60413b the-silver-searcher: add missing dependency (#6095) 2017-11-02 08:10:40 +01:00
Michael Kuhn
61ed583266 xqilla: Use append instead of extend (#6094) 2017-11-02 08:09:24 +01:00
Brian Van Essen
932068d725 Update candle (#6097) 2017-11-01 23:58:55 -06:00
Yifan Zhu
7d0c6361ee r-getoptlong: created new package (#6069) 2017-11-01 19:09:54 -06:00
Yifan Zhu
f15969d624 r-gtrellis: created new package (#6088) 2017-11-01 19:09:20 -06:00
Brian Van Essen
86b7b84ddf LBANN flags and OpenCV variant (#5951) 
* Fixed the datatype flag in the LBANN package.
Fixed where the datatype flag should be set.

* Added variant to OpenCV to disable building DNN support

* Fixed a bug in how the elemental package tries to find its Fortran
library.  The current method does not work with Intel compilers.

* Added necessary paths for cuDNN and CUB.

* Addressed flake8 issues in Elemental package.

* Fixed several flake8 errors.  Added variant to build with or without
support for arbitrary-precision floating point arithmetic.

* Added the proper CMake flag when MPFR support is disabled.

* Fixed a bug in how the cudnn path was being set when there was no
cudnn requested.  Also requested that OpenCV is built without eigen
support.

* Fixed another bug where a dependency may not be there and thus should
not be always checked.
 2017-11-01 17:25:28 -07:00
Michael Kuhn
0d624eac55 lua: Build a shared library (#6008) 
Patch is inspired by Arch Linux and Homebrew.
 2017-11-01 17:10:14 -06:00
Yifan Zhu
f3af8272f5 r-circlize: new package (#6087) 2017-11-01 17:08:46 -06:00
lingnanyuan
ef240f59b8 r-alsace: Create new package. (#6064) 2017-11-01 17:04:56 -06:00
Yifan Zhu
26ade0c9ae r-globaloptions: new package (#6068) 2017-11-01 17:04:38 -06:00
lingnanyuan
a05cca49d8 r-affycoretools: Create new package and its dependency r-ff. (#6082) 
* r-ff: Create new package

* r-affycoretools: Create new package.

* r-ff: update url.
 2017-11-01 17:04:17 -06:00
lingnanyuan
541818ed06 r-agimicrorna: Create new package. (#6083) 2017-11-01 17:03:48 -06:00
Yifan Zhu
616a43b76d r-complexheatmap: created new package (#6084) 2017-11-01 17:03:30 -06:00
Yifan Zhu
ebff5086d7 r-shape: created new package (#6086) 2017-11-01 17:03:15 -06:00
Yifan Zhu
7fb6fbea54 r-pmcmr: new package (#6085) 2017-11-01 17:02:58 -06:00
Brian Van Essen
0c075b4923 Opencv eigen (#6014) 
* Added a package for the MDAnalysis toolkit.

* Changed dependency for the eigen library to not include support for
multiple-precision (arbitrary-precision) floating point arithmetic,
since OpenCV does not support these data types.

* Fixed incorrect implementation
 2017-11-01 13:50:06 -07:00
Mark Grondona
165e6bfe5f flux: update flux-core to v0.8.0 (#5914) 
* dockbook: remove update to dependent environment

Remove override of setup_dependent_environment in both docbook-xml
and docbook-xsl, which seems to generate a warning from spack about
"Suspicious requests to set or unset 'XML_CATLOG_FILES' found."

* flux: update version/dependencies to 0.8.0

Update flux-core to v0.8.0. Clean up dependencies and remove unneeded
extra invocation of ./autogen.sh when building from @master.

* flux: modify environment for Lua tests

Modify Spack environment to add `./?.lua` to LUA_PATH so that
fluxometer.lua can be found by tests during `make check` run
from `spack install --tests all flux`

* flux: fix broken flux version when on master

When building @master with spack, the flux version test from
`make check` fails because spack is using a shallow clone. Add
a setup section for @master that calls git pull --depth=50 --tags
to pull down tags and (hopefully) enough information for git-describe
to work properly.
 2017-11-01 08:53:37 -07:00
Satish Balay
445ffc46a1 mfem does not use cmake for builds [anymore] - so remove code corresponding to this dependency. (#6073) 
This enables mfem build on OSX [with xcode/clang compilers]
 2017-11-01 08:52:03 -07:00
Elsa Gonsiorowski
b53adc90f7 MACSio and JSON-CWX packages (#6018) 2017-10-31 19:07:00 -06:00
Patrick Gartung
8a812294e0 Preinstall some llvm shared libraries so tblgen will work. (#5988) 2017-10-31 18:34:33 -06:00
Yifan Zhu
0ecef7d7f8 r-somaticsignatures: created new package (#6065) 2017-10-31 18:31:06 -06:00
lingnanyuan
1ec8f6ea3f r-nloptr: Create new package. (#6063) 2017-10-31 18:30:49 -06:00
lingnanyuan
cfb685aa32 r-ptw: Create new package. (#6062) 2017-10-31 18:29:45 -06:00
lingnanyuan
aa1808c9a1 r-iso: Create new package. (#6061) 2017-10-31 16:17:53 -06:00
lingnanyuan
6af19477ef r-nnls: Create new package. (#6060) 2017-10-31 16:17:36 -06:00
lingnanyuan
77b29288e6 r-als: Create new package. (#6059) 2017-10-31 16:17:21 -06:00
Yifan Zhu
10fcd9382a r-ggbio: new package (#6058) 2017-10-31 16:17:07 -06:00
Bill Williams
f5e68879db Fix spack build for RAJA: master requires submodules (#6052) 
* Fix spack build for RAJA: master requires submodules

* Rename version: git to develop
 2017-10-31 15:08:32 -06:00
Scott Wittenburg
3cb2d5341d Fix incorrect checksum value for adios2 tarball (#6054) 2017-10-31 15:08:08 -06:00
lingnanyuan
6427406fc6 r-gviz: Create new package. (#6043) 2017-10-31 15:06:30 -06:00
Brian Homerding
8a86016bef Added fftw dependency (#6057) 2017-10-31 14:33:01 -06:00
Brian Homerding
180dcfc652 sw4lite: Added -lgfortran and set to serial build (#6055) 
* Added -lgfortran and set to serial build

* Update package.py
 2017-10-31 14:29:06 -06:00
Christoph Junghans
d98e337706
ecp-proxy-suite: add nekbone and candle-benchmarks (#6053) 2017-10-31 13:11:08 -06:00
Christoph Junghans
182c11dd92
nekbone: add v17 (#5978) 2017-10-31 10:47:24 -06:00
Christoph Junghans
178107699c
candle-benchmarks: initial commit (#6020) 2017-10-31 09:11:04 -06:00
Christoph Junghans
ea35f49cdd flang: fixed a typo (#6048) 2017-10-31 14:21:29 +01:00
Nils Deppe
4997291bf4 Add v3.2 of Blaze library (#5992) 2017-10-31 08:33:55 +01:00
George Hartzell
e69542c019 Fix tarball URL's for htslib (#5993) 
A recent update (#5907) to htslib added a different URL for an old
version of htslib.

Now the package is using that URL as the pattern for the newer
versions too.

I have a vague memory of running into this before, that it's a known
issue.

This fixes it by adding an explicit `url_for_version` routine.
 2017-10-30 22:49:52 -06:00
David Gardner
10b27ec788 sundials: update to v3.0.0 (#6004) 2017-10-30 22:49:13 -06:00
Jon Rood
50d932d9f1 Merging netcdf dependency lines in trilinos into one line for better coverage. (#5990) 2017-10-30 22:48:21 -06:00
Satish Balay
f5863d6708 superlu_dist: update to v5.2.2 (#6024) 2017-10-30 22:46:41 -06:00
Yifan Zhu
a31a1fef28 r-progress: new package (#6034) 
* r-progress: created new package

* added version
 2017-10-30 22:43:57 -06:00
Yifan Zhu
a97068a861 r-prettyunits: created new package (#6033) 2017-10-30 22:43:20 -06:00
lingnanyuan
6ddba08434 r-seqinr: Update version to 3.4-5 (#6032) 2017-10-30 22:42:51 -06:00
Yifan Zhu
8cc3bcb649 r-ggplot2: dependecy r-scales version should be 0.4.1: (#6031) 2017-10-30 22:42:31 -06:00
Yifan Zhu
fb072d1472 r-scales: added dependencies and version 0.5.0. (#6030) 
* r-scales: Update url.

* r-scales: added version 0.5.0 and dependencies
 2017-10-30 22:42:05 -06:00
lingnanyuan
7e4ac9a559 r-segmented: Update version to 0.5-2.2 (#6029) 2017-10-30 22:41:32 -06:00
Yifan Zhu
34c6ff10e9 r-ggally: new package (#6036) 
* r-ggally: created new package

* r-ggally: version modified
 2017-10-30 22:41:12 -06:00
lingnanyuan
65785cc3f5 r-speedglm: Create new package. (#6035) 2017-10-30 22:40:48 -06:00
lingnanyuan
a4138b6041 r-alpine: Create new package. (#6037) 2017-10-30 22:40:25 -06:00
Yifan Zhu
22f9125164 r-ensembldb: created new package (#6038) 2017-10-30 22:39:54 -06:00
Yifan Zhu
2a7027e2cc r-pcamethods: created new package (#6041) 2017-10-30 22:39:29 -06:00
Yifan Zhu
cbb433655c r-proxy: created new package (#6039) 2017-10-30 22:39:05 -06:00
lingnanyuan
8271434632 r-backports: Create new package. (#6040) 2017-10-30 22:38:35 -06:00
lingnanyuan
81d3c9fdc6 r-biovizbase: Create new package. (#6042) 2017-10-30 22:38:10 -06:00
Abhinav Bhatele
b37c8fef74 ecp-proxy-apps: release number changed to 1.0 (#6049) 2017-10-30 22:37:09 -06:00
Abhinav Bhatele
347c76b7a0 comd: update the git repo (#6027) 
git repo has moved from exmatex to ECP-copa
 2017-10-30 14:47:16 -06:00
George Hartzell
e6bc45a04a Add bowtie2@2.3.0, fix dependencies and sbangs (#5834) 
* Add bowtie2@2.3.0, fix dependencies and sbangs

Add support for bowtie2@2.3.0

- digest
- a patch for 2.3.0 that parallels the existing package.  Truth be
  told it builds (for me) without this, but I'm assuming that they're
  there for a reason...).
- tune up dependencies
  - need tbb
  - don't need readline or zlib

Several things were installed with sbang's that use `/usr/bin/env` to
fine perl or python.  Fix the dependency and clean up the sbang lines.

* Fix python exe name, avoid path banging

I'd cut and pasted the python bit from the perl bit and missed one
reference to perl.

While I'm there, use the cleaner `spec['perl'].command` instead of
banging together the path from its bits.

* Fix up the "when" constraints on the dependencies

Get the edge cases right.

- 2.2.5 doesn't need tbb, 2.3.[01] do.
- 2.3.1 needs readline and zlib.
 2017-10-29 15:40:00 -06:00
Denis Davydov
957ded209a add updated 2017 versions of Intel packages (#5957) 2017-10-29 15:38:10 -06:00
mmwolf
73fb02229a Changed from setting C compiler to setting C++ compiler (#6011) 2017-10-29 07:42:27 -06:00
Denis Davydov
f6a8ae230e dealii: remove bzip2 dependency for newer versions (#6022) 2017-10-29 07:39:51 -06:00
Yifan Zhu
56c7832789 r-iranges: changed url to git and added versioned dependency on r (#5971) 2017-10-28 12:14:33 -06:00
Audrey Thoma
f340333e6e r-geomorph and other r fixes (#5961) 2017-10-28 12:13:38 -06:00
lingnanyuan
57611397c9 r-e1071: Add list_url. (#5986) 2017-10-28 12:12:52 -06:00
Michael Kuhn
b43e2d2546 likwid: Update checksum (#6007) 2017-10-28 12:12:21 -06:00
Yifan Zhu
43c1bb5f30 r-organismdbi: new package (#5997) 2017-10-28 12:11:44 -06:00
lingnanyuan
3eab6ed4b2 r-aldex2: Create new package. (#6015) 2017-10-28 12:10:22 -06:00
Christoph Junghans
167f7d0cdd
legion: add v17.10.0 (#6019) 2017-10-28 12:09:39 -06:00
Audrey Thoma
edae3ceae7 fixing abyss (#5973) 2017-10-28 17:05:52 +02:00
Sergey Kosukhin
5ebddcd5e3 Bugfix: from_list_url(). (#5780) 
This fixes a bug in from_list_url where it was referring to a method
which no longer exists. This also adds a test for the from_list_url
function.
 2017-10-27 17:41:41 -07:00
Christoph Junghans
95c8ecb6f5
libaec: add v1.0.2 and generic url (#6017) 2017-10-27 18:22:27 -06:00
Matthias Diener
45bfcfa30a Byobu: new package (#5974) 2017-10-27 10:43:45 -07:00
Christoph Junghans
f9599c1772 ecp-proxy-apps: add more package (#6003) 2017-10-27 08:34:52 -06:00
Christoph Junghans
c97bf0486c SWFFT: initial commit (#5953) 
* SWFFT: initial commit

* swfft: fix build target

* swfft: add v1.0

* Update package.py
 2017-10-27 07:20:29 -06:00
Christoph Junghans
13b41cd53c comd: add v1.1 (#5994) 
* comd: add v1.1

* Update package.py

* remove serial variant, now ~mpi

* Update package.py
 2017-10-27 07:20:18 -06:00
lingnanyuan
222fee1cb3 r-graph: Create new package. (#5958) 2017-10-27 08:34:33 +02:00
lingnanyuan
f244653496 r-category: Create new package. (#5959) 2017-10-27 08:34:16 +02:00
lingnanyuan
715a679245 r-methodss3: Create new package. (#5960) 2017-10-27 08:32:20 +02:00
lingnanyuan
737f9eee5c r-oo: Create new package. (#5962) 2017-10-27 08:31:46 +02:00
lingnanyuan
f676d8f3d7 r-utils: Create new package. (#5964) 2017-10-27 08:31:26 +02:00
lingnanyuan
3bb4572e81 r-pfam-db: Create new package. (#5965) 2017-10-27 08:27:19 +02:00
lingnanyuan
95ece343c4 r-oligoclasses: Create new package. (#5966) 2017-10-27 08:26:25 +02:00
Yifan Zhu
3ea6a11043 r-interactivedisplaybase: created new package (#5967) 2017-10-27 08:26:02 +02:00
lingnanyuan
c672b2b191 r-annotationforge: Create new package. (#5968) 2017-10-27 08:25:12 +02:00
lingnanyuan
57528fddbb r-gostats: Create new package. (#5969) 2017-10-27 08:24:49 +02:00
Audrey Thoma
835e6107fe r-mcmcglmm: new package (#5970) 2017-10-27 08:24:28 +02:00
Yifan Zhu
7b0fd6510c r-annotationhub: created new package (#5972) 2017-10-27 08:23:25 +02:00
Denis Davydov
c2094a11e3 gnuplot: add 5.2.0 and 5.0.7 (#5979) 2017-10-27 08:20:34 +02:00
lingnanyuan
dc8a0e8410 r-deseq2: Create new package. (#5981) 2017-10-27 08:16:40 +02:00
lingnanyuan
1de2109a5a r-agdex: Create new package. (#5983) 2017-10-27 08:16:04 +02:00
lingnanyuan
82b1731ded r-agilp: Create new package. (#5984) 2017-10-27 08:15:39 +02:00
lingnanyuan
7c56318cb5 r-aims: Create new package. (#5987) 2017-10-27 08:14:55 +02:00
George Hartzell
55b79dca8c Add info for go@1.9.2 (#5989) 
The go team released 1.9.2 which includes fixes for some things
that 1.9.1 broke:

> ... include fixes to the compiler, linker, runtime, documentation, go command, and the crypto/x509, database/sql, log, and net/smtp packages. They include a fix to a bug introduced in Go 1.9.1 and Go 1.8.4 that broke "go get" of non-Git repositories under certain conditions.
 2017-10-27 08:13:33 +02:00
Yifan Zhu
3849401d85 r-annotationfilter: created new package (#5995) 2017-10-27 08:09:31 +02:00
Yifan Zhu
0c2a691b1b r-protgenerics: created new package (#5998) 2017-10-27 08:08:16 +02:00
Abhinav Bhatele
ad51e818a7 ecp-proxy-apps: add dependencies (#5999) 2017-10-26 19:54:40 -06:00
Christoph Junghans
0b3247c23d miniamr: bump to v1.4.0 (#5975) 2017-10-26 19:51:50 -06:00
Ondřej Čertík
0e464f86bb Exodus: skip the -G "Unix Makefiles" part (#5906) 
* Exodus: skip the -G "Unix Makefiles" part

The problem is that spack passes -G "Unix Makefiles" into cmake, which normally
works. But in the Exodus package, it is being passed into a bash wrapper
script. In there, the $@ then loses the information about "Unix Makefiles"
being just one argument, and in effect passes -G Unix Makefiles into the cmake
(without quotes), and so cmake only sees -G Unix, and then fails. This is a
known problem with bash with no simple solutions. As a workaround, this patch
skips the first two arguments, i.e., -G and "Unix Makefiles". This makes it
work.

Fixes #5895.

* Port exodusii to cmake

The cmake options were taken from the cmake-exodus bash script and ported to
spack directly.

* Use variant forwarding to forward the 'mpi'

Now instead of

    spack install exodusii~mpi^netcdf~mpi^hdf5~mpi

one can just use

    spack install exodusii~mpi
 2017-10-26 13:50:18 -06:00
Christoph Junghans
5c09176014 minife: version bump to v2.1.0 (#5985) 2017-10-26 11:45:40 -06:00
Abhinav Bhatele
0ff1fe90fa Laghos: new package (#5956) 2017-10-26 09:18:57 -06:00
Abhinav Bhatele
02744141e9 sw4lite: fix build errors and add variants (#5944) 
* sw4lite: fix build errors and add variants

* sw4lite: change linking against blas and lapack

* change order of blas and lapack

* satisfy flake8 requirements

* Update package.py
 2017-10-26 09:18:05 -06:00