Commit graph

6525 commits

Author SHA1 Message Date
Levi Baber
0b47741400 r-annotate: new version (#9061) 2018-08-22 09:45:11 -05:00
Levi Baber
51b3edc4f4 r-geneplotter: new version (#9060) 2018-08-22 09:44:48 -05:00
Levi Baber
96913f1876 r-qvalue: new version (#9059) 2018-08-22 09:44:21 -05:00
Levi Baber
b474e0bdc9 r-rtracklayer: new version (#9056) 2018-08-22 09:43:25 -05:00
Levi Baber
bfe58cd4a9 r-genomicfeatures: new version (#9057) 2018-08-22 09:41:38 -05:00
Levi Baber
711c3d7d69 r-delayedarray: new version (#9053) 2018-08-22 09:39:52 -05:00
Levi Baber
9a98f45064 r-genomicranges: new version (#9052) 2018-08-22 09:39:23 -05:00
Levi Baber
c0aabecbb1 r-genomeinfodb: new version (#9051) 2018-08-22 09:38:28 -05:00
Levi Baber
a38e7c783d r-genomeinfodbdata: new version (#9050) 2018-08-22 09:37:56 -05:00
Levi Baber
b1a619fdeb r-rsamtools: new version (#9049) 2018-08-22 09:37:03 -05:00
Matthias Diener
6ca7654df9 intel-parallel-studio: add version 2018.3 (#9047)
* intel-parallel-studio: add version 2018.3

* update intel package too
2018-08-22 09:36:33 -05:00
Denis Davydov
3a041b3fea dealii: patch boost 1.68.0 (#9070)
* dealii: patch boost 1.68.0

* indent for readability
2018-08-22 09:34:47 -05:00
Levi Baber
2f6a6a45a9 r-biostrings: new version (#9048) 2018-08-22 12:21:43 +02:00
Todd Gamblin
c0855d9bd5 tests: add tests for warnings in build output
- add tests for build warnings and error messages
- simplify some code in build environment with plural() function
2018-08-21 21:21:53 -07:00
Levi Baber
db508a8f89 r-iranges: new version (#9041)
* r-iranges: new version

* r-iranges: typo
2018-08-21 15:02:52 -05:00
Levi Baber
db09b71be1 r-biobase: new version (#9038)
* r-biobase: new version

* r-biobase: reordering versions
2018-08-21 14:15:42 -05:00
Levi Baber
1340abf1bc r-biocgenerics: new version (#9039)
* r-biocgenerics: new version

* r-biocgenerics: reordering versions
2018-08-21 14:15:30 -05:00
Levi Baber
2c92d50495 r-annotationdbi : new version (#9040)
* r-annotationdbi: new version

* r-annotationdbi: dep type

* r-annotationdbi: reordering versions
2018-08-21 14:15:17 -05:00
Sam Gutiérrez
c9fdb610f2 Add 1.6.1 release. (#9042) 2018-08-21 14:14:17 -05:00
Levi Baber
c62c9257d7 r-s4vectors: new version (#9043) 2018-08-21 14:14:05 -05:00
Levi Baber
efbb2c0733 r-zlibbioc: new version (#9044) 2018-08-21 14:13:52 -05:00
Levi Baber
eb74f49363 r-xvector: new version (#9045) 2018-08-21 14:13:39 -05:00
Levi Baber
af2dc7f3d3 r-biocparallel: new version (#9046) 2018-08-21 14:13:27 -05:00
Denis Davydov
271633ee93 dealii: add constraint on suite-sparse for old gcc (#9026) 2018-08-20 10:43:30 -05:00
Denis Davydov
5aa126d850 dealii: blacklist boost 1.68.0 due to segmentation fault in serialization lib (#9023) 2018-08-20 09:40:10 -05:00
Denis Davydov
4ba8c0cb58 update Intel packages (2018.u5 for TBB and 2018.u3 for the others) (#8928) 2018-08-20 07:56:53 -05:00
Daniel Topa
11d94f4c4f Open MPI: add v2.1.5 (#9021)
Final fix for v2.1 (hopefully)
Test build on LANL CCSCS4, Desktop

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-08-18 22:44:14 -05:00
Daniel Topa
31380204c9 Openmpi add v2.1.4 (#9006)
* Add latest release 3.0.2
https://www.open-mpi.org/software/ompi/v3.0/:x

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* 1. Added correct md5 sum for Open MPI v3.1.1 (https://www.open-mpi.org//software/ompi/v3.1/)
2. Made v3.1.1 the default version
3. Added libmpiso versions for v3.1.1 and 3.0.2

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* Added Open MPI v2.14 to version list; Tested build; Added libmpi.so version

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-08-18 20:34:05 -05:00
Abhinav Bhatele
9628181bd4 chatterbug: new spack package (#8994) 2018-08-18 16:18:50 -07:00
Nichols A. Romero
f4ee07527c QMCPACK Spack Package Update (Summer 2018) (#9008)
* QMCPACK now supports QE 6.3. Dropped QE 5.3 due to incompatibilities.

* QMCPACK general clean-up of depends_on.

* Add QMCPACK 3.5.0

* More robust support of MKL detection in QMCPACK.
2018-08-18 11:26:17 -05:00
Abhinav Bhatele
412832159b scorep: make optional packages variants (#9011)
* scorep: make optional packages variants

add packages for cube sub-components: cubew, cubelib

* fix style errors
2018-08-18 11:25:05 -05:00
Adam J. Stewart
d14991a261
Fix missing makefile variable in clapack package (#9016) 2018-08-18 11:19:40 -05:00
Adam J. Stewart
879bdec285
CBLAS: Don't hardcode BLAS library name (#9017) 2018-08-18 11:19:24 -05:00
Michael F. Herbst
ce68216574 Update bohrium version (#9020) 2018-08-18 09:22:16 -05:00
scheibelp
638cc64571
install_tree: symlink handling and add 'ignore' option (#9019)
Fixes #9001

#8289 added support for install_tree and copy_tree to merge into an existing
directory structure. However, it did not properly handle relative symlinks and
also removed support for the 'ignore' keyword. Additionally, some of the tests
were overly-strict when checking the permissions on the copied files.

This updates the install_tree/copy_tree methods and their tests:

* copy_tree/install_tree now preserve relative link targets (if the symlink in the
  source directory structure is relative, the symlink created in the destination
  will be relative)
* Added support for 'ignore' argument back to copy_tree/install_tree (removed
  in #8289). It is no longer the object output by shutil.ignore_patterns: you pass a
  function that accepts a path relative to the source and returns whether that
  path should be copied.
* The openfoam packages (currently the only ones making use of the 'ignore'
  argument) are updated for the new API
* When a symlink target is absolute, copy_tree and install_tree now rewrite the
  source prefix to be the destination prefix
* copy_tree tests no longer check permissions: copy_tree doesn't enforce
  anything about permissions so its tests don't check for that
* install_tree tests no longer check for exact permission matching since it can add
  file permissions
2018-08-17 22:08:38 -04:00
Jim Galarowicz
a7a6745120 qtgraph and cbtf-argonavis create proper library paths in modules (#8797) 2018-08-17 15:58:08 -07:00
Adam J. Stewart
99492dc910
Specify Python executable in VTK package (#9000) 2018-08-17 14:51:49 -05:00
Michael Kuhn
e04fb382b1 libmongoc: Fix build (#9012)
libmongoc requires pkg-config to detect several of its dependencies.
2018-08-17 08:22:30 -05:00
Mark W. Krentel
c06c02bce5 libunwind: add version 1.3-rc1 and variant xz (#8989)
* libunwind: add version 1.3-rc1 and variant xz

Version 1.3-rc1 is the latest published snapshot from libunwind.

Variant xz adds spack-built support for reading compressed symbol
tables, or else disables this feature.  Without the variant, libunwind
will look for liblzma in /usr/lib.

* Add preferred=True to version 1.2.1 as the last official stable
release.
2018-08-17 08:22:04 -05:00
Geoffrey Oxberry
e92e14e330 gperftools@2.7: new version; homepage, URL, hash updates (#9010)
* gperftools@2.7: new version

* gperftools: update homepage & url

The URL in the homepage field of the gperftools package redirects to
its GitHub repo, and the URL for version 2.3 returns a 404 error. This
commit updates both fields to the most recent sensible values.

* gperftools: update commit hashes to sha256

This commit deletes the url field for all listed versions because it
is no longer needed as a result of updating the package url field. In
addition, all commit hashes are updated to SHA256.
2018-08-16 19:38:02 -05:00
Tom Merrick
f5b4209543 Packages/atk (#9002)
* initial atk update

* Add coreqs

* Fixed flake8 errors

* corrected gnome's version URLs

* Added correct list_url's

* Changed list_depth
2018-08-16 18:11:52 -05:00
Geoffrey Oxberry
e8e672972a binutils@2.31.1: new version (#9007) 2018-08-16 18:10:08 -05:00
Michael F. Herbst
f838b5e8c0 libcint: New version 3.0.12 (#9003) 2018-08-16 15:59:26 -05:00
rvinaybharadwaj
2f8168c778 fix for issue #8845 (#8988) 2018-08-16 13:22:44 -06:00
Sajid Ali
cde5116bb2 Add blis package (#8925) 2018-08-16 11:26:43 -05:00
Douglas Duckworth
be11608732 added relion version 3 (beta) (#8872)
* added relion 3 beta - WIP

* added relion 3 beta - WIP

* more relion changes - still WIP

* more changes for relion

* more changes

* now correctly handling cuda_arch

* now correctly handling cuda_arch

* fixed flake8 syntax errors

* fixed flake8 syntax errors

* merge

* fixed flake8 errors again

* relion 3 finished

* added print message to cuda_arch exception

* relion - shortened explination

* still need tag=2.0.3 for v 2.0.3 - removed @develop since it no longer exists

* correct cuda versions now used properly

* relion 3 done

* added tags back

* fixed exception message

* relion - added develop back as master
2018-08-16 10:51:58 -05:00
TZ
cd446a9668 openfoam-com: correctly use foam_add_lib() (#8969)
- foam_add_lib() must be used instead of the undefined foamAddLib()
  for adding VTK
2018-08-16 08:44:30 -07:00
Tom Merrick
d099eba8c4 glib: patch for rhel6, centos6, and sl6 (#8947) 2018-08-16 08:43:56 -07:00
Andreas Baumbach
ead9363bee add patch for gcc@8 for python 2.7.14 (#8990)
* add gcc8 patch for python 2.7.14

Change-Id: I48cb5e717577d8158d1f7f1fe270156a01940d8a

* add explaining comment

Change-Id: Ia46168e2269d7de47d7ec8d0bf9e3b7696ea8e31

* remove unnecessary part of the patch

Change-Id: Iee763effe2439f0f160c1547640eca4bb9451a68
2018-08-16 07:51:09 -05:00
Adam J. Stewart
5be5c486ac Download GNU packages from mirrors (#8992) 2018-08-15 23:27:21 -07:00