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Author SHA1 Message Date
Massimiliano Culpo
8ecf5ae2ee Spack can guess lmod core compilers, if none is already present 
closes #8916

Currently Spack ends with an error if asked to write lmod modules files
and the 'core_compilers' entry is not found in `modules.yaml`. After
this PR an attempt will be made to guess that entry and the site
configuration file will be updated accordingly.

This is similar to what Spack already does to guess compilers on first
run.
 2018-08-27 14:49:50 -07:00
Sasha Nícolas
2fdfa46735 dyninst: add dependency on libiberty (#8806) 
* Adding dependency of libiberty to Dyninst package configuration.
* Now it depends on libiberty package and not binutils.
 2018-08-27 14:34:05 -07:00
Alan Williams
c56992587e Add line in trilinos/stk configuration to enable stk_ngp package. (#9082) 
The Trilinos/stk configuration is pretty Nalu specific right
now (and is acknowledged as such in a comment in package.py), and
this commit enables a module that Nalu will be needing.
 2018-08-26 19:49:35 -05:00
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