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Author SHA1 Message Date
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
Andreas Baumbach
df172001cc fix numbering in build error template (#9030) 
The original numbering was not incorrect markdown but this is easier to read.
 2018-08-21 12:37:24 -04:00
Todd Gamblin
63004e3de1 yaml: use ruamel.yaml instead of pyyaml 
- ruamel.yaml allows round-tripping comments from/to files
- ruamel.yaml is single-source, python2/python3 compatible
 2018-08-20 16:36:04 -07:00
Adam J. Stewart
2e8a820afd Even better Makefile target parsing (#8819) 
#8223 replaced regex-based makefile target parsing with an invocation of
"make -q". #8818 discovered that "make -q" can result in an error for some
packages.

Also, the "make -q" strategy relied on interpreting the error code, which only
worked for GNU Make and not BSD Make (which was deemed acceptable at
the time). As an added bonus, this implementation ignores the exit code and
instead parses STDERR for any indications that the target does not exist; this
works for both GNU Make and BSD Make.

#8223 also updated ninja target detection to use "ninja -t targets". This does
not change that behavior but makes it more-explicit with "ninja -t targets all"

This also adds tests for detection of "make" and "ninja" targets.
 2018-08-20 17:42:28 -04:00