Commit graph

10711 commits

Author SHA1 Message Date
Eric Müller
f5afc98cc2 libXi requires pkgconfig and fixesproto (#7480) 2018-03-21 19:51:58 -05:00
Levi Baber
b0ecd0fd0b py-pybedtools: fix hash for 0.6.9 (#7492) 2018-03-21 19:51:34 -05:00
Levi Baber
383c2aa2d6 Singularity: new version (#7551)
* singularity: new version

* singularity: hash
2018-03-21 19:50:53 -05:00
Eric
81dcd1b33a perl-module-implementation: Create new package (#7549) 2018-03-21 17:16:24 -05:00
Julien Adam
a81ebfc2ba New Package: jchronoss (#7207)
* New Package: jchronoss

* jchronoss: Fix flake8 errors

* jchronoss: Fix according to recommendations

* jchronoss: Remove FIXME

* jchronoss: Fix another flake8 error
2018-03-21 16:56:20 -05:00
lingnanyuan
a2b885d0ba r-dirichletmultinomial: Create new package. (#7227)
* r-dirichletmultinomial: Create new package.

* Change description.

* Change description.
2018-03-21 16:55:35 -05:00
scheibelp
6548f2db5c Enable creation of mirrors for systems with different compilers (#5153)
* Create mirror for system with different compilers

Spack concretizes the spec provided by the user in
"spack mirror create" to ensure downloading the right
dependencies. Under normal circumstances concretization
requires that the chosen compiler exists on the system,
but this is not required when creating download mirrors
for other systems, so this requirement is removed in that
case.

* Add test for disabling compiler existence check

* Update compiler existence checking logic

* improve test for disabling compiler existence check
2018-03-21 14:55:26 -07:00
Eric
88fb67768d py-python-levenshtein: Create new package (#7426)
* py-python-levenshtein: Create new package

* py-python-levenshtein: fix flake8 errors

* py-python-levenshtein: Use pypi.io per packaging guide
2018-03-21 16:54:51 -05:00
Eric
08f3ebf859 perl-cairo: Create new package (#7432)
* perl-cairo: Create new package

* perl-cairo: Add cairo dependency
2018-03-21 16:54:25 -05:00
Levi Baber
5e8370e093 bamutil: needs zlib (#7444) 2018-03-21 16:53:55 -05:00
Sinan
6c23b82d6b package/JAGS: new version (4.3) (#7456)
* package/JAGS: new version (4.3)

* fix typo

fix typo
2018-03-21 16:53:11 -05:00
Levi Baber
720a4854c2 pandaseq: needs bzip and libtool as link (#7465) 2018-03-21 16:52:46 -05:00
Jon Rood
de52c175de Using self.prefix in Trilinos to avoid global name prefix undefined bug (#7478)
* Using self.prefix in Trilinos to avoid global name prefix undefined bug during module refreshing.

* Fixing flake8 errors.
2018-03-21 16:52:08 -05:00
Howard Pritchard
f59a447f71 Open MPI: add 2.1.3 (#7535)
note the libmpi.so itself didn't have changes, only other
components of the package had updates.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-03-21 16:49:31 -05:00
Denis Davydov
75c9083139 suite-sparse: add cmake dependency (#7538) 2018-03-21 16:49:01 -05:00
健美猫
71055a8ef4 Generate spack docset for Dash. (#6981) 2018-03-21 16:37:26 -05:00
Gregory Lee
7504e9997d make py-setuptools a run-time-only dep for py-basemap and patch pytho… (#6989)
* make py-setuptools a run-time-only dep for py-basemap and patch python package to only apply setuptools flag for build deps

* py-qtconsole does not require setuptools
2018-03-21 16:34:27 -05:00
Yifan Zhu
55f4bbb111 snphylo: new package (#7045)
* pushing partially done recipe for snphylo

* r-snphylo: try

* phylip: added version 3.697

* snphylo: updated package.py

* snphylo: flake8 error fixed
2018-03-21 16:21:55 -05:00
scheibelp
e8a0637606 Support MD5 with a warning when OpenSSL is compiled in FIPS mode (#7531)
* This allows Spack to work with MD5 hashes on machines with openssl in FIPS mode.
* We are still using MD5 for validation in many places, and a later PR will replace all uses of MD5 with SHA256.
* This is a quick fix until that happens.
2018-03-21 14:11:54 -07:00
Geoffrey Oxberry
6127b02324 elfutils: document conflict with clang (#7096) 2018-03-21 16:00:49 -05:00
Mark W. Krentel
154401de76 intel-xed: new package (#7106)
* intel-xed: new package

The Intel X86 Encoder Decoder library for encoding and decoding
x86 machine instructions.

* intel-xed: style fixes for flake8.

* intel-xed: better style fix

* intel-xed: update to version 2018.02.14, add PYTHONPATH for
building with python 3, cleanup the opt flag.
2018-03-21 14:39:06 -05:00
lpoirel
9d2fce4544 scotch%intel: remove restrict (#7148)
The restrict compilation option with icc causes deadlock when multithreading is used. This issue has already been reported to the Scotch development team, but for current versions it is more reliable not to use the restrict compilation option.
2018-03-21 14:22:50 -05:00
Geoffrey Oxberry
935cc30c17 librom: new package (#7180)
* libtool: actually do symlinking correctly on darwin

Version 4 of the libtool/darwin debacle:

AutotoolsPackage hardcodes libtool & libtoolize into the autoreconf
stage, so the commands `libtool` and `libtoolize` MUST be present, and
shimming in glibtoolize into AutotoolsPackage when sys.platfrom ==
'darwin' does not work.

join_path(spec['libtool'].prefix.bin, 'libtool') still shadows system
BSD libtool (in apple-cctools, see PR #7177), but this shadowing could
be okay, depending on the combination of dependent specs.

* librom: new package
2018-03-21 14:16:36 -05:00
Eric
e07ed2ab97 py-backports-functools-lru-cache: add version 1.5 (#7206)
* py-backports-functools-lru-cache: add version 1.5

* py-backports-functools-lru-cache: fix conflicts
2018-03-21 14:09:55 -05:00
Jon Rood
3d7930a379 Adding unzip package. (#7446)
* Adding unzip package.

* Removing bzip2 dependency in unzip and raising an error when on Cray.

* Fixing error.

* Using conflicts statement for Cray detection in unzip package.
2018-03-21 13:59:39 -05:00
lingnanyuan
011d407132 Xorg-server: Add dependencies and fix installation. (#7220)
* xorg-server: Add several dependencies.

* libepoxy: Add dependendies mesa and meson.

* mesa: Add dependencies for hwrender.

* mesa: undo some changes.
2018-03-21 13:53:26 -05:00
Eric Müller
647c4a1507 py-py{gobject,gtk} require pkgconfig for build (#7380) 2018-03-21 13:22:08 -05:00
scheibelp
849078e95a remove cray-specific path modifications from pkgconfig providers (now handled in cray platform) (#7406) 2018-03-21 13:20:40 -05:00
Gregory Lee
500ac793bc patch config.guess for ARM (aarch64) (#7427) 2018-03-21 13:13:38 -05:00
Levi Baber
29e429e525 orfm: needs zlib (#7466) 2018-03-21 12:55:47 -05:00
Eric
64f15957ce new package: perl-module-runtime (#7494) 2018-03-21 10:35:28 -07:00
peetsv
71802a57cf VMD-python v2.0.10 - new package (#7490)
* VMD-python v2.0.10 - new package

* removing extraneous comments

* flake8 error - trailing blank lines removed
2018-03-21 11:08:58 -05:00
Leonhard Reichenbach
8c9a5a95d8 Add latest version of patch (#7539) 2018-03-21 08:16:41 -05:00
健美猫
9b1d69c934 A new package: wcslib. (#7463) 2018-03-20 22:16:55 -05:00
jthies
35e7b9ac44 Ghost as cuda package (#7501)
* add headers  property to netlib-lapack and intel-mkl

* ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())

* fix flake8 errors

* ghost: remove unnecessary query parameter

* fix flake8 errors

* ghost: make it a CudaPackage (as suggested by @davydden, thanks!)

* ghost: missing whitespace
2018-03-20 11:23:45 -05:00
Denis Davydov
ed4640c75b alglib: fix on Darwin (#7534) 2018-03-20 08:33:14 -05:00
Peter Scheibel
6458b15bb1 spec: support "full" hashes
This hash includes the content of the package itself as well as the DAG
for the package.
2018-03-20 00:29:54 -07:00
Peter Scheibel
3501f2f4b5 package: add a content_hash method for packages
This calculates a hash which depends on the complete content of the
package including sources and the associated `package.py` file.
2018-03-20 00:29:54 -07:00
Peter Scheibel
e97c28e5b3 package: ensure patches are applied in-order
This helps to ensure that patches are applied consistently and will also
be used as the source for the patch part of full package hashes.
2018-03-20 00:29:54 -07:00
Peter Scheibel
2379ed54b9 package_hash: add code to generate a hash for a package file
This will be included in the full hash of packages.
2018-03-20 00:29:54 -07:00
Peter Scheibel
db81d19ddd PackageBase: add a list of metadata attributes
These attributes are ignored when doing a content hash of a package.
2018-03-20 00:29:54 -07:00
Peter Scheibel
39cb9d0397 fetch_strategy: add a source_id to fetches
This will be included in the full hash of packages.
2018-03-20 00:29:54 -07:00
Adam J. Stewart
6058cc1770 Add latest version of py-setuptools (#7523) 2018-03-20 07:18:20 +01:00
Adam J. Stewart
c11b46ae99 Add DSDP package (#7526) 2018-03-20 07:08:18 +01:00
Veselin Dobrev
ae795d8184 [MUMPS] Various improvements in the package.
* Fix a bug when checking for 'xl' or 'xl_r' compiler.
* Add support for parallel build - the 's', 'c', 'd', and 'z' targets
  are build separately allowing parallel builds.
* When build '+shared', inject all dependencies into the link lines of
  the mumps libraries.
* Run the examples only when installing with the '--test' Spack option.
2018-03-19 15:57:03 -07:00
Axel Huebl
106827db03 pocl: fix spec (#7461)
It seems there has been a change in concretization that resulted in
a request for a llvm latest (5.0.1) while not satisfying the later
more precise request for a version.

Remove the first line and only rely on the last.
2018-03-19 16:44:01 -05:00
Eric
4ea0c16f36 picard: Add version 2.18.0 (#7528) 2018-03-19 16:21:04 -05:00
Adam J. Stewart
869cb69985
Add latest version of SuiteSparse (#7525) 2018-03-19 16:19:44 -05:00
Massimiliano Culpo
c14c0d8e74
python: dbm module + version 3.6.4 (#7520)
A build of python@3.X had the following in the logs:
```
The necessary bits to build these optional modules were not found:
_dbm                  _gdbm                 _tkinter
```
As Tkinter is already a variant, we adopt the same strategy for dbm.
2018-03-19 22:19:26 +01:00
Adam J. Stewart
3874871512
Add latest version of py-six (#7524) 2018-03-19 16:19:19 -05:00