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Author SHA1 Message Date
Levi Baber
bba5967dcc r-goseq: new package (#8939) 
* r-goseq: new package

* r-goseq: git not url

* r-goseq: adding packages needed at runtime

* r-goseq: package type

* r-goseq: dep types

* r-goseq: one more
 2018-08-26 19:45:23 -05:00
lingnanyuan
7c06492d94 braker: add new version 2.1.0 (#8946) 
* braker: add new version 2.1.0

* Set verison in descending order.

* Update URL.

* url

* braker: change url format.
 2018-08-26 19:44:53 -05:00
TZ
2ae1bfd283 patch for OF.com@18.06 to correctly find KAHIP (#8982) 
- OpenFOAM-v1806/wmake/scripts/have_kahip must check
  $KAHIP_ARCH_PATH instead of $METIS_ARCH_PATH to detect the KAHIB
  library
- use a local patch file until the issue is hopefully fixed upstream
 2018-08-26 19:44:06 -05:00
Adam J. Stewart
cc01e89d6b
Update to latest version of pytest and dependencies (#9087) 
* Update to latest version of pytest and dependencies

* Fix bug in installation tests
 2018-08-25 14:12:46 -05:00
Todd Gamblin
3c292de6bd bugfix: 'submodules' attribute should imply git fetch 
- 'submodules' wasn't properly declared as an optional attribute for git
  fetcher

- add it and add a test.
 2018-08-25 10:20:39 -07:00
Todd Gamblin
3f0e6d04e0 commands: add spack url stats command 
This command prints out stats about all package versions, like so:

$ spack url stats
==> 6070 total versions for 2827 packages:
------------------------------------
url                    5411    89.1%
  schemes
    https              3822    70.6%
    http               1527    28.2%
    ftp                  27     0.5%
    file                 35     0.6%
  checksums
    sha512                6     0.1%
    sha256              163     3.0%
    sha1                 81     1.5%
    md5                5161    95.4%
------------------------------------
svn                       3     0.0%
------------------------------------
hg                        5     0.1%
------------------------------------
go                        1     0.0%
------------------------------------
git                     650    10.7%
  security
    no commit           384    59.1%
    commit              266    40.9%
------------------------------------
 2018-08-25 10:20:39 -07:00
Todd Gamblin
82820efe37 Remove Python 3.3 from testing. 
- Support for Python 3.3 isn't really needed, as nothing uses it as the
  default system Python, and nearly everyone will have a newer Python 3
  version installed.
 2018-08-24 16:22:37 -07:00
Hadrien G
a7f3fa01d5 new package: GSL - C++ Guideline Support Library (#9091) 
Since "GSL" is a highly overloaded acronym, the package name is "cppgsl".
 2018-08-24 17:45:18 -04:00
Hadrien G
afff196a06 Update the pocl package (#9090) 
* Update the pocl package

* Use url_for_version

* Clarify hwloc version requirements

* Apply hwloc dependency suggestion
 2018-08-24 12:26:17 -05:00
Hadrien G
b7e4be4d29 Add new CLHEP releases and move to sha256 hashes (#9089) 2018-08-24 09:49:38 -05:00
Hadrien G
4fbcecd0cd range-v3 package (#9093) 
* Add first version of a Range-v3 package

* Add C++ standard variant to range-v3 package
 2018-08-24 09:41:25 -05:00
Matthias Diener
95ca99bbdd htop: add version 2.2.0 (#9086) 2018-08-23 18:50:01 -05:00
Matthias Diener
30cbca2c32 bison: add new version (#9085) 2018-08-23 17:00:26 -05:00
Christoph Junghans
ca2e1e9019 lammps: add v20180822 (#9081) 2018-08-23 12:17:27 -05:00
Brian Spilner
87c2214b02 add cdo releases 1.9.4 and 1.9.5 (#9079) 2018-08-23 10:27:35 -05:00
Adam J. Stewart
7f419d34ac Set DYLD_LIBRARY_PATH on macOS (#9073) 2018-08-23 15:39:44 +02:00
Michael Kuhn
983957f7c0 mvapich2: Use rdma-core for mrail and nemesis*ib* fabrics (#9072) 2018-08-23 07:32:46 -05:00
Adam J. Stewart
5e8a9ddaed More consistent colored messages from activate/deactivate (#9036) 
* More consistent colored messages from activate/deactivate

* Make 'activating' the default, make 'activated' the debug
 2018-08-22 22:09:51 -07:00
Daniel Topa
05c4ff4e92 Open mpi add v3.1.2 (#9078) 
* 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>

* Open MPI 3.1.2 built and tested

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2018-08-22 23:17:48 -05:00
Sam Gutiérrez
8c89e67669 libquo: Packaging updates. (#9076) 
* libquo: Packaging updates.

This commit accomplishes a few things:
* Changes distribution fetch source
* Removes a deprecated version (1.2.9)
* Changes dependencies based on version type
* Adds a custom autoreconf stage when using the 'develop' version,
  omitting this step when building from a distribution

* Reintroduce v1.2.9.
 2018-08-22 23:17:15 -05:00
Michael Kuhn
a6826a7a2d glib: Add 2.56.2 (#9071) 
This should finally fix build failures on RHEL6-based distributions.
Also fix the patch to apply to the correct versions and distributions.
 2018-08-22 14:21:54 -05:00
Sam Gutiérrez
66971f6ac8 libfabric: Add develop version option. (#9074) 
Add develop version option to libfabric, conditionally bringing in
additional build dependencies: m4, autoconf, automake, libtool.
 2018-08-22 14:21:30 -05:00
Michael Kuhn
0b2a4aea6d leveldb: Fix header installation (#9069) 
leveldb headers are typically included via <leveldb/c.h>. The migration
to install_tree in 73c978ddd9 caused the
headers to end up in prefix.include, which breaks existing applications.
 2018-08-22 09:46:11 -05:00
Levi Baber
8b092c242f r-genefilter: new version (#9063) 
* r-genefilter: new version

* r-genefilter: fix version in dep
 2018-08-22 09:45:56 -05:00
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
Massimiliano Culpo
85f84aabed Added a new target message to comply with newer versions of GNU Make (#9068) 
#fixes 9067

Unit tests were failing on a system with GNU Make v 4.1
 2018-08-22 09:32:25 -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
Adam J. Stewart
0b0887f48f Display warnings if no errors are found in build log 2018-08-21 21:21:53 -07:00
Adam J. Stewart
f97550e149 Fix error caused by missing spack-build.out build log 2018-08-21 14:16:50 -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