Commit graph

7709 commits

Author SHA1 Message Date
Adam J. Stewart
af8d84197d
Download GNU packages from mirrors (Part 2) (#10555) 2019-02-20 09:08:42 -06:00
Massimiliano Culpo
0a252eccc4
uvw: new package (#10645) 2019-02-20 13:53:07 +01:00
Ben Morgan
fb6a2b5cab xxhash: edit prefix in Makefile for macOS (#10606)
On macOS, the build of libxxhash is performed by a bare `make`
launched by `MakePackage`s default `build` phase. As `prefix`
is not set at this point, the library gets compiled with a hard-coded
install name of `/usr/local/libxxhash.dylib`. Downstream clients,
in the tested case Root, will then fail to build as the install name
is incorrect.

Move setting of `prefix` from `install` to `edit` so that it
propagates to subsequent `build` and `install` phases.
2019-02-20 10:55:09 +01:00
Isaac Whitfield
286da7f47b new package: libyaml (#10634) 2019-02-19 12:45:31 -06:00
Nichols A. Romero
7dd5bdcfa4 Quantum ESPRESSO: HDF5 update (#10607)
* QE hdf5 is now a multi-valued variant. Update conflicts accordingly.

* Update dependencies for hdf5 multi-valued variant. Bug fix:  high-level hdf5 library needs to be a hard dependecy.

* Support for HDF5 serial interface. Note that this is not supported in QE autoconf, but will be fixed in the next official release.
2019-02-19 17:07:27 +01:00
Tristan Carel
efc3406900 nix: new package added (#9171) 2019-02-19 15:27:39 +01:00
Rob Latham
2242b9f338 update IOR package (#10595)
- new GitHub home
- new 3.2 release
2019-02-19 12:10:17 +01:00
Andreas Baumbach
66bfad8d44 cquery: new package (#10636) 2019-02-19 11:30:41 +01:00
Andreas Baumbach
9e3d92692d connect-proxy: new package (#10635) 2019-02-19 11:30:09 +01:00
Michael Kuhn
bcee3efecd mvapich2: Improve package (#10642)
- Add support for nemesis:ofi netmod
- Add missing pkg-config and libxml2 dependencies
2019-02-19 11:02:02 +01:00
Elizabeth Fischer
ec4da14e2c Add comments and version (#10592) 2019-02-18 21:48:01 -06:00
Matthias Diener
aabd2be31a git-lfs: add version 2.7.0 (#10631) 2019-02-18 08:59:11 +01:00
Axel Huebl
899c83c215 openPMD-api: mpi4py support (#10616)
Refactor dependencies, increase new min versions, add
mpi4py variant.
2019-02-18 08:54:27 +01:00
Axel Huebl
e5dc5c173e NLohmann-JSON: v3.5.0 (#10615)
Add the latest bugfix release.
2019-02-18 08:53:50 +01:00
Axel Huebl
a4f9501a56 Catch2: v2.6.1 (#10613)
add the lastest bugfix release of Catch2
2019-02-18 08:53:33 +01:00
Nichols A. Romero
05269ad392 Update CUDA support in QMCPACK (#10587)
* Support in QMCPACK for CUDA_ARCH flag.

* No need to have explicit CUDA variant anymore.

* Internal QMCPACK CMake assumes a minimum GPU architecture if none is provided.
2019-02-17 08:17:58 -05:00
Hadrien G
a93581e8de Fix plural typo in ROOT package (#10614) 2019-02-16 21:22:23 +01:00
Cameron Smith
a06bf21610 new variant: simmodsuite for pumi (#8775) 2019-02-14 21:36:56 +01:00
Massimiliano Culpo
b3dd95bd62
cp2k is now a MakefilePackage (#10570)
* cp2k: archive the Makefile after a successful installation

* cp2k: all checksums are now sha256

* libint: all checksums are now sha256 + added versions 2.4.X

* libxc: all checksums are now sha256 + added version 4.3.2

* cp2k: os.path.join instead of join_path + simplified openmp flags

* cp2k: turned into a MakefilePackage

* cp2k: refactored edit method so that Makefile writing happens last
2019-02-14 07:11:20 +01:00
Chris Green
051c66335f pythia6: fix input verification issue and example data checksum. (#10563)
* pythia6: fix issue validating integer input.

* pythia6: account for apparent update of example data file.
2019-02-13 23:17:46 -06:00
Chris Green
24d7f0f0af xrootd: allow specification of C++ standard. (#10577)
* xrootd: add cxxstd variant.

* xrootd: support for recent and upcoming versions.
2019-02-13 23:17:10 -06:00
Ben Morgan
7e8b8d61a1 icu4c: Add cxxstd variant (#10552)
* icu4c: Add cxxstd variant

For versions supported in Spack, ICU4C defaults to the C++11.
Provide a variant to default to this, plus options for C++14
and 17 if dependees require for ABI compatibility.

* icu4c: cxxstd variant cannot be multi
2019-02-13 23:05:39 -06:00
Hadrien G
6e95e06bda Add Gaudi and RELAX packages (#9194)
* Add a RELAX package

* Add a Gaudi package
2019-02-13 23:04:38 -06:00
Hadrien G
54f94e5828 Add a DD4hep package (#9208) 2019-02-13 22:58:27 -06:00
Hadrien G
0e0e7d4137 Add new ROOT release, move to SHA-256 checksums (#10583) 2019-02-13 22:54:45 -06:00
Patrick Gartung
0748a32b2d
Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant (#10518)
* Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant so that it is applied consistently.

* Make standalone geant4 data packages that are used when data is not installed with geant4. This allows installing the data files are externals that can be common to many compiler version.

* move geant4 data package dependencies to umbrella package geant4-data
2019-02-13 22:51:26 -06:00
Peter Scheibel
8ca384875e
Dynamic library/include paths (#8136)
Fixes #7855
Closes #8070
Closes #2645

When searching for library directories (e.g. to add "-L" arguments to
the compiler wrapper) Spack was only trying the "lib/" and "lib64/"
directories for each dependency install prefix; this missed cases
where packages would install libraries to subdirectories and also was
not customizable. This PR makes use of the ".headers" and ".libs"
properties for more-advanced location of header/library directories.
Since packages can override the default behavior of ".headers" and
".libs", it also allows package writers to customize.

The following environment variables which used to be set by Spack
for a package build have been removed:

* Remove SPACK_PREFIX and SPACK_DEPENDENCIES environment variables as
  they are no-longer used
* Remove SPACK_INSTALL environment variable: it was not used before
  this PR
2019-02-13 17:38:14 -06:00
Peter Doak
1bf86292e1 add latest version of pixman (#10580) 2019-02-13 21:26:51 +01:00
Hadrien G
9374adb455 Eigen package: deactivate some dependencies (#10572)
Set defaults in eigen package to omit typically-unused dependencies
2019-02-13 13:33:01 -06:00
Brian Van Essen
406a242847 Update lbann sw stack dependencies (#10579)
* Added a package for the MDAnalysis toolkit.

* Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI
even when using CUDA.  Fixed small bugs within both LBANN and Hydrogen
packages.  Added requirements for breathe and cereal to LBANN.

* Update use case for doc dependencies.

* Cleaning up some of the LBANN software stack dependencies.
2019-02-13 11:19:15 -08:00
健美猞猁
2202579685 Cnvnator: a new package. (#8959) 2019-02-13 11:15:00 +01:00
健美猞猁
f9c27f52bd casacore: new package (#7471) 2019-02-12 17:22:48 +01:00
Ben Morgan
8fd4e9a9fa xerces-c: Add cxxstd variant (#10561)
Add variant to support compiling against main C++ standards if needed
for ABI compatibility. Use 'default' value as Xerces-C autoconf system
does not enforce a minimum, or set a default, C++ standard.
2019-02-12 09:40:59 +01:00
Brian Van Essen
dc12ca5c76 lbann: updated versions (#10568) 2019-02-12 09:05:32 +01:00
Matthias Diener
068eefb4f5 remove remaining lzma dependencies (#10553) 2019-02-12 09:03:50 +01:00
Matthias Diener
6e38423d1c openssl: add version 1.1.1a (#10562) 2019-02-12 08:58:50 +01:00
Javier Cervantes
36ebd7462c root package major update (#8428)
* Extend current recipe for root package
* Add removed old version
* Add dependency type for Python and R packages
* Add compiler variants
* Adding new root version: 6.14.00
* Add back the minimum cmake version required
* LZ4 and xxhash support for old (using builtin options) and new versions (external packages)
* Set PYTHONPATH in setup_environment
* Address typos and issues pointed by HadrienG2
* Add newer ROOT versions
* Solve support for asimage
* Define incompatible variants
* Organize old dependencies
* Add support for minuit
* Add support for pythia6
* Remove unneeded list_url
* Update license header
* Remove block of commented old dependencies
* Contrain Qt version
* Comment pythia8 variant/dependency, not supported by spack
* Force not to build pythia8
2019-02-08 09:17:07 -08:00
Matthias Diener
ff67009161 libarchive: remove lzma dependency (#10517)
lzma was last updated in 2008 and has compilation
issues on some platforms. The format has been superceded
by xz (see e.g. https://tukaani.org/xz/).
2019-02-08 16:33:13 +01:00
Robert Blake
a55fc5b963 Adding a package for cardioid. (#10448)
* Adding a package for cardioid.

* Changing package to pass flake8

* Removing template leftovers per @ax3l 's advice

* Adding a homepage so tests pass.

* Removing whitespace for flake8

* Changing the name of master branch to match spack standards.
2019-02-08 11:17:26 +01:00
Michael Kuhn
84bc2a4215 meson: add 0.49.1 and disable rpath stripping (#10463)
rpath stripping breaks (at least) the gtkplus build because at-spi2-atk's
dependencies can not be found.
2019-02-08 11:15:49 +01:00
Piotr Luszczek
f093515002 netlib-scalapack package: add CMake test patch (#10452)
Add patch to fix Fortran mangling in CMake test

This is a fix for builds with GCC 6/7/8 and CMake 2/3. It includes
a link to the issue where this is reported. For now, the Spack
package applies the patch to all releases >= 2.0.2
2019-02-07 20:58:27 -06:00
Justin Stanley
ec6de8326e repeatmasker package: add variant for cross_match engine (#10534) 2019-02-07 16:53:30 -06:00
wspear
76feb0205d New package: py-jupyterhub (#10461)
This package depends on both python 3.5+ and node-js which depends on
python 2.7/2.8 to build. Currently it can only be installed if the
node-js package's python dependency is manually removed, so node-js
will build with python found on the system rather than provided by
spack. Upcoming commits may allow spack to reconcile this
automatically.
2019-02-07 16:47:46 -06:00
Justin Stanley
ef89ae03bc mirdeep2 package: make sure bins are executable (#10515) 2019-02-07 13:05:19 -06:00
mathsen
570af0c313 Trilinos package: update superlu-dist dependency (#10511)
Trilinos master branch gets the latest superlu-dist (currently 6.1.0)
2019-02-07 12:58:45 -06:00
Satish Balay
b8684b318c
petsc: petscvariables is used from user makefiles - so it should not have spack compilers listed (#10365) 2019-02-07 09:09:23 -06:00
Satish Balay
1d71a5ea57
petsc4py and libensemble: add @develop dependencies (#10539)
* py-petsc4py: add @develop

* py-libensemble: add @develop dependency on py-petsc4py@develop
2019-02-07 09:06:31 -06:00
Satish Balay
0ad1b2a2c8
petsc@xsdk-0.2.0: fix sowing dependency (#10535) 2019-02-07 09:05:43 -06:00
Satish Balay
753fec39ae
xsdk@develop fixes (#10521)
* xsdk@develop: switch trilinos from @master to @develop

* xsdk@develop: dtk - fix trilinos dependency on dtk.
 - dkt-3.0 should be used with trilinos-12.4*
 - dtk/master should be used with trilinos@develop
2019-02-07 09:05:14 -06:00
Justin Stanley
09a884322f orthofiller: new package at 1.1.4 (#10373) 2019-02-07 10:22:36 +01:00
Gregory Lee
f0cb4580d1 fixed checksum (#10393) 2019-02-07 10:20:45 +01:00
Levi Baber
af7f1bb3ca new package: perl logger simple (#10509) 2019-02-07 10:19:07 +01:00
Levi Baber
07b5a6a512 perl-file-homedir: new package (#10533) 2019-02-07 10:09:20 +01:00
Levi Baber
4679c11098 py-biopython: new version (#10532) 2019-02-07 10:08:45 +01:00
Matthias Diener
d4d402586c cmake: add version 3.13.4 (#10538) 2019-02-07 09:15:32 +01:00
Justin Stanley
401d305f4e phrap-crossmatch-swat: new package at 1.090518 (#10529) 2019-02-06 19:13:44 -06:00
Owen Solberg
cdbaf8dfc5 mafft package: add version 7.407 (#10488) 2019-02-06 13:55:16 -06:00
Matthias Diener
6dbc1afe45 jdk package: add version 1.8.0_202 (#10536) 2019-02-06 13:54:02 -06:00
Levi Baber
0cf0fd47c8 New package: perl-object-insideout (#10508) 2019-02-06 13:53:33 -06:00
Matthias Wolf
5281403fb2 fmt package: fix cmake arguments (#10500) 2019-02-06 13:52:49 -06:00
Stephen Herbein
b028e99cac py-black: add new package 2019-02-06 13:50:04 -06:00
Stephen Herbein
4e92974ed1 py-toml: add latest version and update checksums to sha256
A version >= 0.9.4 required for py-black.  Added latest, which is
0.10.0.  Manually verified that the .tar.gz for v0.9.3 used to generate
the sha256 matched the previous md5.
2019-02-06 13:50:04 -06:00
Matthias Diener
bdabdb85ed curl package: add version 7.63.0 (#10516) 2019-02-06 13:48:36 -06:00
Douglas Duckworth
d053eac538 py-multiqc: add version 1.7 (#10520)
Added sha256 for py-multiqc as well as require py-matplotlib < v 3.0
2019-02-06 13:47:59 -06:00
Levi Baber
1a34bebe79 genemark et package: add version 4.38 (#10519)
Also add heu_dir to bin/
2019-02-06 13:46:35 -06:00
Jon Rood
11c52c3bf7 Paraview package: update PYTHONPATH for dependents (#10501)
Add vtkmodules directory to PYTHONPATH in Paraview for Trilinos
2019-02-06 12:45:14 -06:00
Daniel Topa
d9d75635c7 Add Python 3.7.2 updated (#10531)
Also add versions 3.7.1, 3.6.8, 3.6.7, 3.6.6. Does NOT alter preferred version (2.7.15).

Supplants PR 10491 "Add Python 3.7.2" (https://github.com/spack/spack/pull/10491).

Verification builds on LANL Darwin:

**Intel Xeon**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.2-d3p7vg6w2r563cpmwsmbgjbsiqc4j4fq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.1-ibom6qj2z64egyaqz5htkwp5tr362il6
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.8-rkifc3c7mjgdglw27upiap767ut4wpkz
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.7-meuesn43twttt756exyzqgdhohjgipjq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.6-qwnwme7otyuoqqudcglfmfy75t5npywl

**Arm**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.2-qj27kzs4ttdqudm3hsi3pt57kv7lshco
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.1-io5eneirgvpegy3tosvp6wq5ndf7yjis
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.8-ej3vnvta2hbtrh7p5hokfqkuewxeqgsa
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.7-l3qnue72ewppn2wxza3w6l62l7ijlque
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.6-b55pdoqsr5bie4k5djd4vokm3nywhm45

**Power9**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.2-cicayvl7ki4tswoqlljsmcetwqcnoh3x
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.1-7vej3zvnvyj2jvz5lnxhnts3ok2fcxbp
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.8-xijljmdanyrybcx2rv65qshycmbrfv6c
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.7-vqdhzg7c3xxxregqmzxsqqfzxt2hajvq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.6-jf4bnsdwk3qjhtmvjjhblnrcz5dztfdq

2019-02-05
Signed-off-by: Daniel Topa <dantopa@lanl.gov>

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-02-06 12:03:25 -06:00
Valentin Clement (バレンタイン クレメン)
548e6736c4 Update CLAW package with version 1.2.1 (#10528) 2019-02-06 15:51:52 +01:00
Levi Baber
881ce3a5c2 perl-yaml: new package (#10514) 2019-02-06 15:47:54 +01:00
simo-tuomisto
1be258a587 wordnet: new package (#10526) 2019-02-06 15:38:48 +01:00
Denis Davydov
871e7f525c xsdk: enable slepc in deal.ii (used to be a concretization error) (#10218) 2019-02-06 07:59:36 -06:00
Phil Carns
0b4a7dd04a New package: PMDK (#10453) 2019-02-05 16:53:16 -06:00
Justin Stanley
003ebf8bab r-wgcna: new package at 1.64-1 (#10392) 2019-02-05 09:00:25 -06:00
Axel Huebl
293e5c0781 MPark: Variant v1.4.0 (#10512)
Add the latest release of Michael Park's C++ Variant lib.
2019-02-05 15:18:19 +01:00
Phil Carns
de91d0badc mercury package: add 'udreg' variant (#10415)
Faster and/or more robust in some cases on Cray platforms
2019-02-04 19:51:04 -06:00
Levi Baber
c7ecb66a2f New package: perl-hash-merge (#10506) 2019-02-04 18:05:36 -06:00
Levi Baber
736a317e0c New package: perl-clone-choose (#10507) 2019-02-04 18:04:55 -06:00
Christoph Junghans
514cf0c1f4
votca*: add v1.5 (#10495)
* votca-tools: add v1.5

* votca-csg: add v1.5

* votca-xtp: add v1.5

* votca-ctp: add v1.5
2019-02-04 12:57:19 -07:00
Justin Stanley
478c3f5e8b augustus: fix bam2wig auxprog build (#10362)
* augustus: fix bam2wig auxprog build

* augustus: few more changes to make new versions work
2019-02-04 10:36:10 -06:00
Matthias Diener
bca72036a8 tar: add version 1.31 (#10485) 2019-02-04 11:02:13 +01:00
Axel Huebl
17cc4f208f Catch2: v2.6.0 (#10490)
Add the latest Catch2 release.
2019-02-04 10:52:47 +01:00
wspear
43fae5b807 New package: py-alembic (#10436) 2019-02-01 16:24:44 -06:00
wspear
ec7c7332c0 New package: py-prometheus-client (#10440) 2019-02-01 16:23:59 -06:00
Nicholas Labello
8c87a937e1 plumed package: add versions 2.4.4 and 2.5.0 (#10496) 2019-02-01 16:21:55 -06:00
Mark W. Krentel
a1969d9eec dyninst: add patch to work with new boost (#10454)
Add tribool.patch to add explicit casts from tribool to bool in two
places.  Boost, starting with version 1.69, turned on explicit
conversions for tribool, which breaks the build for dyninst.

This is merged into the current dyninst develop and is expected to be
part of the next release, so the version range uses the current
release as an upper bound.
2019-02-01 16:18:16 -06:00
wspear
c2b06c27ac New package: py-async-generator (#10439) 2019-02-01 12:40:19 -06:00
zschulte
a701c412bc gatk package: new versions, updated helper script (#10459)
Closes #10168

* Add versions 4.1.0.0 and 4.0.12.0
* Replace md5 checksums with sha256
* Logic to generate a helper script for versions earlier than 4 was
  not running. This corrects the branch which controls whether this
  script is generated.
* Constrain Java dependency to version 8 (GATK does not work with
  Java 11)
* Avoid adding scripts that have dependencies not handled by Spack
  such as gcloud and google-chrome. These scripts are good candidates
  for later extensions.
2019-01-31 16:10:06 -06:00
Ricardo Silva
cf754245fd py-pybigwig: fix build with python3, add numpy variant (#10444)
* added patch to correctly pick up non-system curl when building
  with Python 3
* added numpy variant
* add version 0.3.12
* update checksums to sha256
2019-01-31 14:50:10 -06:00
snehring
21afd258a4 New package: openjdk (#9861)
Closes #2622

This retrieves and installs the binary of Oracle's OpenJDK (an
open-source JDK implementation). The logic is largely based on the
Spack JDK package (Oracle's closed-source JDK implementation).

For now this is only supports Linux. If the download could be
customized based on OS (for the same version), binaries are also
available for MacOS and Windows.
2019-01-31 12:54:28 -06:00
Matthias Diener
ec78d362d2 git-lfs: add version 2.6.1, update build system (#10405)
Build system was changed to use a Makefile. Therefore older versions
(which don't support this) are removed. The new build system also
supports testing by default.
2019-01-30 21:21:08 -06:00
Tom Payerle
c42528fac2 fftw: fix include error for 2.x versions (#10039)
Fixes #7372

Added patch method which renames config.h in the fftw subdir of the
source tree. fftw 2.1.5 appears to ship with a copy of this file
with all defines commented out. This gets read by the #include
directives instead of the version in the build directory with the
correct defines. As a result, many C preprocessor macros left
undefined, including F77_FUNC_ which causes the bulk of fttwf77.c
to be skipped due to an #ifdef, so fftw_reverse_int_array et al
not included in library. Fixes #7372

Also fixed some inconsistencies with the handling of quad and
long_double in specs between the configure method and the build,
check, and install methods.
2019-01-30 21:18:10 -06:00
Axel Huebl
2aad75d98f HDF5: Add develop Version (#10382) 2019-01-30 21:04:24 -06:00
Phil Carns
36c46a7daf Mercury package: update libfabric dependency on Cray (#10408)
The Mercury package previously depended on libfabric@develop on
Cray platforms in order to pick up a fix for the GNI provider that
was only available in git. This is no longer needed now that the
libfabric package is at 1.7.0.
2019-01-30 20:57:31 -06:00
Justin Stanley
5a431eb408 r-pkgmaker: add 0.27, new dependencies (#10419) 2019-01-30 20:54:24 -06:00
Michael Kuhn
b1af6b43dc gobject-introspection: add 1.56.1 and fix download (#10462)
Define url_for_version, since Spack's default substitution is
not sufficient
2019-01-30 20:53:08 -06:00
Matthias Diener
3ce0fba036 go: fix directory structure issue for 1.11.5 (#10484) 2019-01-30 20:30:05 -06:00
Chuck Atkins
be38fded9b cmake: Fix linker errors on Darwin when using external dependencies (#10467)
Adds upstream patch for a missing framework. This is anticipated
to be fixed by CMake 3.13.4 so is only applied up to version 3.13.3
2019-01-30 20:24:20 -06:00
Matt Belhorn
2b6bf06150 libsodium: Updates source URL. (#10483)
The source URL for versions 1.0.15 and older is updated to reflect where
those archives are now hosted by the upstream libsodium developers.
2019-01-30 20:14:41 -06:00
Jon Rood
86747b39d4 ninja: Add kitware version with fortran capability (#10470) 2019-01-30 20:06:09 -06:00
G-Ragghianti
9630d732d6 New package: SLATE (#10434) 2019-01-30 19:59:26 -06:00
Jason Lee
c698384216 jemalloc: Add variant to prepend public api with "je_" prefix (#10356) 2019-01-30 19:16:33 -06:00
Justin Stanley
993745b919 redundans: add 0.14a (#10006)
Also update install to use globbing
2019-01-30 18:55:59 -06:00
Samuel Thibault
9bfcbcc155 New package: simgrid (#10076) 2019-01-30 18:39:59 -06:00
Cameron Smith
9d7f215e47 zoltan: detect metis int64 variant (#10051)
Configure zoltan depending on metis int64 support
2019-01-30 15:19:38 -06:00
dorier
477d3fb479 Package py-keras: add new versions and dependencies (#10353)
Add new versions for py-keras. Versions of py-keras at or after
2.2.0 require keras-processing and keras-applications packages.
Add these packages to Spack and add dependencies to the py-keras
package.
2019-01-30 14:32:37 -06:00
Jimmy Tang
47887499bf cudnn package: add version 7.2 (#10481) 2019-01-30 13:44:24 -06:00
sknigh
d4fbaa054f Update opa-psm2 package (#10344)
* Add version 11.2.68
* Add variant to disable AVX2 for older hardware
* Change the makefile so libraries and includes are not placed
  under $PREFIX/usr
* Updated URL and homepage
2019-01-30 13:38:48 -06:00
Justin Stanley
a3926620ee r-preprocesscore: add version 1.44.0 (#10389) 2019-01-30 13:30:06 -06:00
Justin Stanley
65429026af r-impute: add version 1.56.0 (#10390) 2019-01-30 13:29:09 -06:00
Abhinav Bhatele
5c99716160 codes package: add version 1.1.0 (#10414) 2019-01-30 13:27:56 -06:00
Justin Stanley
25d2ccfcc5 r-runit: new package at 0.4.32 (#10416) 2019-01-30 13:26:34 -06:00
Justin Stanley
2a28e6e6bb r-bibtex: new package at 0.4.2 (#10417) 2019-01-30 13:25:43 -06:00
Justin Stanley
9efeff6b1f r-rngtools: add 1.3.1 (#10418) 2019-01-30 13:25:10 -06:00
Abhinav Bhatele
16819a5b18 ROSS package: update homepage and git url (#10429) 2019-01-30 13:24:14 -06:00
Adam J. Stewart
f011c9976f Add JDK 11.0.2_9 (#10413)
Also add 11.0.1_13; remove 11.0.1, which is no longer available for
download.
2019-01-30 13:20:30 -06:00
Michael Kuhn
e338f2c2c1 ncl package: require cairo with pdf support (#10465)
Needed after #10135
2019-01-30 13:10:08 -06:00
Michael Kuhn
5ada4d9956 gtkplus: add gettext dependency (#10464) 2019-01-30 13:08:43 -06:00
G-Ragghianti
b114ec4e77 New package: lm-sensors (#10443) 2019-01-30 13:04:52 -06:00
Matthias Diener
28de435584 go: add version 1.11.5 (#10451) 2019-01-30 12:57:45 -06:00
Satish Balay
d8e9d7acbd py-petsc4py: add version 3.10.1 (#10457)
Also update dependency version ranges
2019-01-30 12:54:45 -06:00
Christoph Junghans
ccb3face64 py-espresso package: add version 4.0.1 (#10469) 2019-01-30 12:53:24 -06:00
Sajid Ali
a67995d66a py-dask package: add version 1.1.0 (#10475) 2019-01-30 12:51:56 -06:00
Sajid Ali
b34e2b8973 neovim package: add version 0.3.4 (#10472) 2019-01-30 12:51:17 -06:00
Matthias Maiterth
f50e91776d geopm package: new versions, dependency updates (#10480)
Added versions 1.0.0-rc1, 0.6.1, 0.6.0, 0.5.1

hwloc dependency was removed after 0.5.1, so the related configure
option is not specified after 0.5.1

Require py-matplotlib dependency version 2.2.3 (version was not
specified before)
2019-01-30 12:50:38 -06:00
Daniel Topa
1d4d2cff50 Add Open MPI 2.1.6 (#10478) 2019-01-30 12:45:46 -06:00
Sajid Ali
5992f508d3 py-numexpr package: add version 2.6.9 (#10477) 2019-01-30 12:45:19 -06:00
Sajid Ali
e0387ab1a1 modified: var/spack/repos/builtin/packages/libx11/package.py (#10473) 2019-01-30 12:44:03 -06:00
Sajid Ali
627ef75bb8 py-pyfftw package: add version 0.11.1 (#10474) 2019-01-30 12:43:23 -06:00
George Hartzell
f878c0cb5b Add configparser v3.5.1, fixes backports namespace (#10433)
Fixes #8343 #4154 #7370
Closes #4155 

All but one of the backports packages were using "pkgutil-style"
namespacing, but configparser was using "pkg_resource-style".
A namespace needs to be one style or another. This adds a new
configparser version which switches to using the pkgutil-style
namespace approach.

With this update, one can now install flake8 with Spack and use
it by loading modules.
2019-01-29 17:58:56 -06:00
Chuck Atkins
b7c31cb561 rhash: Fix broken RPATH info on darwin
The PREFIX variable in the makefiles is directly used to construct the
install name on the library metadata on darwin.  If not passed, the
default /usr/local is used and the resulting librhash.dylib contains
usage informaiton of /usr/local/lib/librhash.0.dylib.  This adds the
PREFIX= variable directly to the make command so the resulting usage
metadata contains the correct valid library path.
2019-01-29 16:31:15 -06:00
Stephen Herbein
67a1e56e4d add flux-core@0.11.0 and flux-sched@0.7.0 (#10447)
* flux-core: add v0.11.0 and updated dependencies

libuuid hasn't been a direct dependency of flux-core since 2015 (well
before any of the versions listed in the package).

The yaml-cpp dependency moved to flux-sched when we moved the jobpsec
library from core to sched.

Some python3 incompatibilities were found in 0.11.0, so bump the python3
support back a version.

* flux-sched: add v0.7.0 and make boost dependency more precise
2019-01-28 21:20:01 -07:00
Chuck Atkins
6535eae5c7 llvm: various updates (#10427)
* llvm: Bump version to 7.0.1

* llvm: Added perl-data-dumper build dependency for openmp

* llvm: Enable exception handling and RTTI

Useful to have turned on in general with RTTI but also necessary
to workaround some lldb stability issues with some versions of
libstdc++.
2019-01-29 00:32:30 +01:00
Ralph Castain
3b1fb7d9ff Update the PMIx package (#10442)
* Update the PMIx package

- Add latest releases to the list.
- Add dependency on hwloc for versions >= 3.0
- Flag preferred versions for libevent and hwloc
- Improve the description
- Point the project URL to the correct site

Signed-off-by: Ralph Castain <rhc@pmix.org>

* Only install the hwloc dependency for versions >= 3.0.0

Thanks to @ax3l for the suggestion

Signed-off-by: Ralph Castain <rhc@pmix.org>

* Add myself as a listed maintainer

Signed-off-by: Ralph Castain <rhc@pmix.org>
2019-01-26 21:25:18 +01:00
Cameron Smith
4e14752dd6 add variant for a debug build (#10409) 2019-01-26 18:42:24 +01:00
Nichols A. Romero
4ab89f4de1 QMCPACK Update - Jan 2019 (#10252)
* Add warnings for existing conflicts. New versions of QMCPACK require a compiler with C++14 support.

* QMCPACK now requires a newer release of CMake.

* Switch QMCPACK to using FFTW-api provider.

* Relax dependencies on QMCPACK +da variant.

* Add QMCPACK 3.6.0 release.

* QMCPACK compiler-CUDA conflicts.

* QMCPACK fix typo in expressing conflict.

* Conditional needed since these variables are only used when FFTW is a dependency to QMCPACK.

* QMCPACK QE variant dependency was underspecified. Must include MPI as a hard dependency on QE.

* Update QMCPACK dependencies for HDF5, CMake and Boost.

* QMCPACK clean-up, more consistent use of spec vs. self.spec.

* Add support for collective I/O variant of QMCPACK.

* Update QMCPACK conflicts for QE and PHDF5 variants.

* Use built-in install method for QMCPACK starting with 3.6.0

* QMCPACK compiler C++14 conflicts were off by one version.

* QMCPACK package needs to setup_environment method.

* In support of PR#10252, get rid of slashes in string.

* Migrate these to the CUDA package and make a seperate PR.

* In support of PR#10252, get rid of join_path for nexus.

* In support of PR#10252, work around concretizer limitation.

* In support of PR#10252, convert to conditionals to if-else clauses for compactness.

* In support of PR#10252, get rid of extra space and new line in warning messages.
2019-01-26 10:13:51 -06:00
Abhinav Bhatele
a307822fd9 laghos: update version (#10420) 2019-01-26 16:29:32 +01:00
Satish Balay
d071c6d341 petsc: configure works with python3 in current petsc@develop - and will work in future releases [3.11+] (#10380) 2019-01-26 16:28:20 +01:00
Matthias Diener
f299507fa9 diffutils: add version 3.7 (#10406) 2019-01-26 16:26:47 +01:00
Matthias Diener
2826d37a45 rust: add version 1.32.0 (#10407) 2019-01-26 16:26:16 +01:00
Ricardo Silva
3fc8203b93 bcftools: do not use bundled htslib (#10445)
* if the path to htslib is not specified the bundled one is built instead
* additionally this fixes the build with the intel compiler
2019-01-26 16:21:04 +01:00
Chuck Atkins
e867319ac3 perl-data-dumper: New package (#10425)
This package is added to satisfy a build time dependency for llvm-openmp
2019-01-26 16:16:03 +01:00
Chuck Atkins
76c757de22 libuv: Bump version to 1.25.0 (#10423) 2019-01-26 16:11:45 +01:00
Chuck Atkins
3266c69352 cmake: Use system libs by default (#10424)
This also fixes the libuv version dependency for 3.11+
2019-01-26 16:11:32 +01:00
wspear
68eb2a1418 Added the py-send2trash package as a pre-req for py-jupyterhub (#10441) 2019-01-26 16:10:02 +01:00
Piotr Luszczek
b94c8c2d53 magma: add version 2.5.0 (#10438) 2019-01-26 16:03:05 +01:00
Levi Baber
248452df4f capstone: new package (#10449) 2019-01-26 15:52:39 +01:00
sameershende
7d12ff6e16 Update ecp st tau pdt (#8192)
* Updated MPI and TAU versions in the TAU package
* Updated PDT versions
* Added support for Python (+python), default to `False`
* Cleaned up binutils, python, mpi usage.
* Updated binutils install to add additional header files to the include/extra directory.
* Resolving review problems with TAU and binutils packages.
  The binutils package was updated to include support for installing
  the ELF headers as a +headers variant.  The TAU package was updated
  to use all known Spack dependencies.
2019-01-23 20:40:58 -08:00
Justin Stanley
9252f7f957 trinotate: remove perl-dbd-mysql, move runtime files to HOME (#9850) 2019-01-22 14:26:31 -06:00
Justin Stanley
7baea68278 r-gamlss: new package (and data) at 5.1-2 (#10360)
* r-gamlss-data: new package at 5.1-0

* r-gamlss-dist: new package at 5.1-1

* r-gamlss: new package at 5.1-2

* r-gamlss: add mass, survival, nlme imports
2019-01-22 14:25:57 -06:00
Justin Stanley
bb942e1fc5 entrezdirect: new package (#10374) 2019-01-22 14:25:10 -06:00
Justin Stanley
4b7510ec38 py-whatshap: new package at 0.17 (#10377)
* py-whatshap: new package at 0.17

* py-whatshap: remove unused build_args
2019-01-22 14:24:45 -06:00
Justin Stanley
c1a1415e90 r-rrcov: new package at 1.4-7 (#10387) 2019-01-22 14:22:37 -06:00
Justin Stanley
e8014be017 r-robust: new package at 0.4-18 (#10391) 2019-01-22 14:22:24 -06:00
Justin Stanley
1bcc6e4d9c r-dynamictreecut: new package at 1.63-1 (#10388) 2019-01-22 14:22:09 -06:00
Peter Scheibel
c0972a3260
Exclude system mkl installs from numpy (#10383)
Fixes #10361
Fixes #6634

When mkl isnt in the spec, still write an explicit mkl entry to
prevent numpy from looking in system dirs and using a system install
of mkl. Do the same for openblas and atlas (although mkl was the only
system install reported to interfere with Spack's choice).
2019-01-22 12:18:54 -06:00
Justin Stanley
636d6007ba py-pyvcf: new package at 0.6.0 (#10375) 2019-01-22 17:11:19 +01:00
Justin Stanley
bb1f8b0e3e py-pyfaidx: new package at 0.5.5.2 (#10376) 2019-01-20 14:16:43 +01:00
Matthias Diener
ab00de9e81 cmake: add version 3.13.3 (#10397) 2019-01-20 14:14:37 +01:00
Jon Rood
e896ce7457 Update Nalu-Wind and dependencies (#10204)
* Updating nalu-wind, nalu, openfast, and tioga packages. Includes
  improved handling of +shared variant.
* Add fftw and catalyst support to nalu-wind.
* Restrict ParaView to use matplotlib versions before 3 (which
  require Python 3)
2019-01-18 18:43:59 -06:00
Owen Solberg
7a2315aa38 adding checksum for latest lmod release (#10381) 2019-01-18 08:49:26 +01:00
Hadrien G
3497098978 Update templight pseudo-release to remove need for patching (#10290)
* Update templight+LLVM combo

* Bring back old pseudo-release
2019-01-16 10:36:34 -06:00
Massimiliano Culpo
4bc3936004 Openblas: added version 0.3.5 (#10364) 2019-01-16 08:11:07 -06:00
sknigh
b31ecb0342 Added latest version of singularity 2.x (#10354) 2019-01-16 13:14:32 +01:00
George Hartzell
1f9fe02309 Add package for Hugo (static website generator) (#10358) 2019-01-16 13:11:15 +01:00
Tom Payerle
01bd67eb43 py-modred: New package (#10309)
* py-modred: New package

Parallelized python module for finding modal decompositions and
reduced order models.

* fix license
I think?

* Add dependency on py-numpy

and remove commented out code
2019-01-15 16:42:20 -06:00
sknigh
eaa340eba7 Added hpl 2.3 (#10345)
* Added hpl 2.3

* Added requested build fixes, added step to copy HPL.dat in 2.3+
2019-01-15 16:41:33 -06:00
Adam J. Stewart
d7fb3fd88e
r requires cairo+pdf (#10350) 2019-01-15 09:58:53 -06:00
Owen Solberg
2585c04b50 explicitly depend_on cairo with X **and** pdf variants (#10351) 2019-01-15 09:58:39 -06:00
Elizabeth Fischer
0628ebefd8 Add useful comment explaining why this is not needed for Python3. (#10326) 2019-01-15 07:31:20 -08:00
Axel Huebl
89a493522c openPMD-api: Dependency Update (#10314)
openPMD-api now only supports Python 3, needs a newer CMake and
ADIOS1 and also learned to read & write JSON :-)
2019-01-15 09:28:13 -06:00
Neil Flood
49dedb2443 vigra: new package (#10337)
* vigra: new package

* Better constraints and types on some depends_on. Use site_packages_dir variable for Python install dir. Explicit switch-offs where available. Change some local variables to suit style checks.

* Take care of lines too long

* Explicit WITH_HDF5=ON
2019-01-14 20:39:34 -06:00
Andrew Gaspar
04d4b07636 Add span-lite version (#10347) 2019-01-14 18:22:29 -06:00
sknigh
a1994d883c Added latest rust releases and develop branch (#10341)
* Added latest rust releases and develop branch

* Fixed spacing
2019-01-14 17:22:38 -06:00
Levi Baber
d1b7e560bd namd: fixing to reflect renamed charmpp per #9216 (#10342) 2019-01-14 17:22:03 -06:00
sknigh
43e6114db7 Added latest version of libfabric (#10343) 2019-01-14 17:21:33 -06:00
Geoffrey Oxberry
baf595351e feature: py-invoke: new python package (#10225) 2019-01-14 17:13:17 -06:00
George Hartzell
7abc2fb26d bugfix/gdk-pixbuf (#10312)
* docbook processing works correctly for gdk-pixbuf

1. The various bits of documentation in gdk-pixbuf include hardcoded
   references to dtd's and stuff at their canonical, Internet,
   locations.  BUT, gdk-pixbuf runs xslt-proc with the `--nonet`
   option, which forbids it from using the network.  Sadness ensues.

   Traditionally folks use XML Catalogs to map these to local copies.
   Our docbook-xsl package wasn't setting the appropriate env var in
   its dependents environments to use our catalog.

   Now it does.  Less sadness ensues.

2. If we're going to use these things, we should depend on them.

* Add gdk-pixbuf's bin to build environment

The "post-install.sh" script uses gdk-pixbuf-query-loaders, which was
installed earlier.

If py-psyclone can set its own bin on its PATH, so can we...

* Make gdk-pixbuf use recognizable docbook location

Our docbook-xsl package assumes that the canonical location is
`http://cdn.docbook.org/release/xsl/current/manpages/docbook.xsl`, but
the gdk-pixbuf's meson build script uses
`http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl`.

This means that our XML Catalog doesn't fix the reference and sadness
happens.

Just patch the build that we see what we want to see, then we can make
it all go away.

* Add commentary re docbook patch

* Make catalog helper a property

Thanks @adamjstewart!

* Run tests if/when run_tests is true

Thanks @adamjstewart!

* Tune up dependencies

Thanks @adamjstewart!

* Wordsmit commentary
2019-01-13 14:40:20 -06:00
Cyrus Harrison
9350db5665 update alpine ascent and friends (#10320)
This adds a lot of fixes and updates for alpine ascent and its dependencies:

* add support for static (via ~shared) and use vtk-m 1.2
* update vtkh package to output cmake configure file and pinning it to vtkm 1.2
* make conduit respect ~python
* fix ascent python logic
* consistant cmake usage
* conditionally add tbb in ascent if vtkh
* enable openmp
* more robust handling of variants
* update ascent and conduit for static builds
* add optional support for mfem in ascent
* enable mfem conduit support for ascent
* add optional adios dep to conduit
* remove ver req from conduit
* ascent: remove confusing comment
* tweaks to conduit and ascent pkg recipes
* fix typo in conduit package
* pref conduit master
* changing mfem to depend on conduit@master to get updated relay
* restore use of conduit 0.3.1 or greater for mfem
* set master as preferred conduit version
* allow mfem to use conduit master
* adding rover package and editing ascent
* updating vtkm cmake dep
* guard ascent python support on +shared
* removing rover to simply ascent package
* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified
* fix fortran compiler check so it can work on cray systems
* working towards cuda fix for vtkm lagrange filter
* update ascent package with more variants, and patch to avoid nvcc issue
* hdf5 flags fix for BGQ
* add post install test
* add testing to ascent
* add testing of the using-with-make example
* add ctest output on error for run_tests
2019-01-12 17:43:39 -08:00
Jiawei Zhuang
07d9d444ea Added osu-micro-benchmarks@5.5 (#10333) 2019-01-12 17:31:13 -08:00
George Hartzell
6c638600d7 Add libxslt v1.1.33 info (#10328) 2019-01-12 17:36:53 -06:00
Denis Davydov
09033e991e dealii: does not support sundials 4.x (#10324) 2019-01-12 15:28:57 -06:00
Neil Flood
04c1af0ee2 gdal: Add variant for GRIB driver (#10322) 2019-01-12 10:33:18 -06:00
Dan Ibanez
f9967d2f6f Omega_h changed its URL (#10315)
From https://github.com/ibaned/omega_h
To https://github.com/SNLComputation/omega_h
2019-01-11 13:29:56 -06:00
Satish Balay
4cbeec07a0 omega-h: fix CMAKE_BUILD_TYPE: breaks with spack deafult 'RelWithDebInfo' (#10297) 2019-01-11 10:08:28 -08:00
Denis Davydov
f4bda74b30 dealii: fix concretization of xsdk package (#10288)
* dealii: fix concretization of xsdk package

* tests: add concretization tests for deal.II and xSDK, which are often broken due to limitations in the concretizer

* use pytest.mark.parametrize
2019-01-11 10:07:28 -08:00
Brian Van Essen
9102cd5790 Updating LBANN and related packages (#10305)
Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI
even when using CUDA.  Fixed small bugs within both LBANN and Hydrogen
packages.  Added requirements for breathe and cereal to LBANN.
2019-01-10 17:10:11 -08:00
Mark W. Krentel
08c4b9d47a boost: fix the bjam build for Cray (#10295)
Fixes issues #9613 and #3209.

Remove the spack wrapper directories from PATH for the bootstrap step.
This was breaking the build for Cray (and other cross-compile) because
bjam was built for the BE and died on SIGILL on the FE.

This only affects building bjam.  The boost libraries are still built
the normal spack way with the spack wrappers.
2019-01-10 16:34:05 -08:00
Mark W. Krentel
7e8b17b177 hpctoolkit: variants to build for cray and blue gene (#10223)
Add variants 'cray' and 'bgq' to build for Cray and Blue Gene compute
nodes.  These systems need separate options to find the MPI compiler
for hpcprof-mpi.
2019-01-10 12:50:58 -08:00
Cody Balos
60a44d5155 sundials: add version 4.0.1 and remove 4.0.0-dev series (#10306)
The 4.0.1 release is the culmination of the SUNDIALS 4.0.0 preview releases,
i.e. the 4.0.0-dev versions. As such, the 4.0.0-dev releases are now
being removed.
2019-01-10 14:47:48 -06:00
Eric
b25f27d442 py-checkm-genome: Add version 1.0.13 (#10304)
* py-checkm-genome: Add version 1.0.13

* py-checkm-genome: Add missing py-backports-functools-lru-cache dependency

* py-checkm-genome: Fix missing whitespace
2019-01-10 12:28:07 -06:00
Jon Rood
12cf4eb734 Explicitly listing blas and lapack sections in site.cfg for numpy (#8708)
* Explicitly listing blas and lapack sections in site.cfg for numpy when using netlib-lapack so that scipy can find them as well.

* Reducing code to use a function call instead of copying and pasting.

* Fixing flake8 errors.

* Fixing python 3.6 error when site.cfg lists library_dirs multiple times.

* Formatting.

* Verifying blas and lapack are enabled before writing to site.cfg.

* Fixing flake8 errors.

* Fixing conflicts since this package file has been updated.

* Fixing flake8 stuff.

* Handling blas and lapack variants for netlib-lapack in site.cfg for py-numpy.

* Don't write netlib-lapack site.cfg file if no blas or lapack variants enabled in py-numpy.

* Removing redundant if statement.

* Fixing mistake in py-numpy site.cfg generation.

* Separating blas and lapack further in site.cfg for netlib-lapack in py-numpy.
2019-01-10 11:14:24 -06:00
Owen Solberg
586fe32166 update r-rcpp package with new versions (#10301) 2019-01-10 09:07:09 -06:00
Greg Becker
450b0e3059 Allow combinatorial projections in views (#9679)
Allow customizing views with Spec-formatted directory structure

Allow views to specify projections that are more complicated than
merging every package into a single shared prefix. This will allow
sites to configure a view for the way they want to present packages
to their users; for example this can be used to create a prefix for
each package but omit the DAG hash from the path.

This includes a new YAML format file for specifying the simplified
prefix for a spec in a view. This configuration allows the use of
different prefix formats for different specs (i.e. specs depending
on MPI can include the MPI implementation in the prefix).
Documentation on usage of the view projection configuration is
included.

Depending on the projection configuration, paths are not guaranteed
to be unique and it may not be possible to add multiple installs of
a package to a view.
2019-01-09 17:39:35 -08:00
Satish Balay
8ca674a574 petsc: fix petsc+debug to not reset COPTFLAGS - i.e use configure defaults '-g' (#10296) 2019-01-09 17:36:28 -06:00
Daryl W. Grunau
d1bb9caba4 eospac version bump to 6.4.0beta.4 (#10294) 2019-01-09 15:57:05 -06:00
Mark W. Krentel
1b991f9385 elfutils: option to install elf.h header file (#10185)
* elfutils: option to install elf.h header file

Add variant 'elfh' (default False) to install the elf.h header file to
the include directory.  This provides access to a newer version of
elf.h and allows an elf application to build with the same elf.h that
libelf.so was built with.

Add version 0.175.

* Drop the variant 'elfh' and always install elf.h instead.
2019-01-09 14:40:15 -06:00
Eric
b4dc73bed4 py-pyyaml: Add version 3.13 (#10293) 2019-01-09 13:39:34 -06:00
Simon Flood
0b2314bbc4 R: add version 3.5.2 (#10292) 2019-01-09 12:19:58 -06:00
Andreas Baumbach
730c629b09 New package: git-fat-git (#10266)
* new package: git-fat

* backport of rsync -> older versions no longer available

Change-Id: I3a41f17df0f88ca11e08ea6fd2f2d381435e0f09

* fix legal stuff and use new git attribute

Change-Id: Ice156dfe8ad4137a861f7b2938ee92f4024142be

* use date as version number rather than hash

Change-Id: Ib537659e368f69124895306d6a6ac0c5e36061a7

* only use the date once

Change-Id: I2592fa28aaa53fed949ddc82959d712ff3f6f752
2019-01-09 09:07:12 -06:00
marvinbernhardt
7571787a3a gromacs: added simd and rdtscp variants + version 2019 (#9931) 2019-01-09 10:39:05 +01:00
Axel Huebl
efe3e905a3 OpenMPI: Add Development Version (#10257)
Add the development version of OpenMPI from the git repo
in `master`.
2019-01-08 20:48:55 -06:00
sknigh
e3a2c94d60 Updated fish to 3.0.0 (#10286) 2019-01-08 20:47:52 -06:00
Srinath Vadlamani
4fdd3b6794 Armcompiler (#9840)
* Initial compiler support

* added arm.py

* Changed licence to Arm suggested header

* Changed licence to the same as clang.py
Main author of file is Nick Forrington <Nick.Forrington@arm.com>
Minor changes by Srinath Vadlamani <srinath.vadlamani@arm.com>

* compilers: add arm compiler detection to Spack

- added arm.py with support for detecting `armclang` and `armflang`

Co-authored-by: Srinath Vadlamani <srinath.vadlamani@arm.com>

* Changed to using get get_compiler_version

* linking to general cc for arm compiler

* For arm compiler add CFLAGS to use compiler-rt rtlib.

* Escape for special characters in rexep

* Cleaned up for Flake8 to pass.

* libcompiler-rt should be part of the LDFLAGS not CFLAGS

* fixed m4 when using clang to used LDFLAGS.  Fixed comments for arm.py to display compiler --version output with # NOAQ for flakes pass.

* added arm compilers

* proper linked names
2019-01-08 16:31:25 -08:00
Owen Solberg
ee64db4764 r-ape: new versions (#10258)
* updated versions for r-ape

* added type=('build', 'run') to r dependency
2019-01-08 18:15:03 -06:00
Owen Solberg
aa20724519 r-cowplot: new versions, more specific dependencies (#10259)
* updated versions for r-cowplot

* depends_on: added type=('build', 'run') to r, and added r-scales
2019-01-08 18:14:50 -06:00
Owen Solberg
7a816b9a66 r-data-table: new versions (#10260)
* updated versions for r-data-table

* added type=('build', 'run') to r dependency
2019-01-08 18:14:34 -06:00
Owen Solberg
2bd054adff r-dbplyr: new versions (#10262)
* added new versions, and tightened up depends_on() specs

* added type=('build', 'run') to r dependency
2019-01-08 18:14:19 -06:00
thelfer
d3caad4cd7 New package: MGIS (#10273)
* add the tfel package

* fix the tfel package

* fix the tfel package

* fix the tfel package

* Taking Adam J. Steward' remarks into account

* fixes trailing white spaces

* Update description

* Update dependencies following @adamjstewart adices

* Style fixes

* Style fixes

* Add java optional support

* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)

* flake8 fixes

* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)

* Style fixes

* Style fixes

* Fix test on python version

* Follow @adamjstewart advices: code is much cleaner and readable

* Small fix

* Small fix

* Add comment

* Small fix in cmake option

* try again (trying to overcome Travis CI unstable build process)

* Add support for the MFrontGenericInterfaceSupport project (MGIS)

* Style fixes

* Package documentation update

* Package documentation update

* Fix a typo thanks to Andreas Baumbach review

* Follow Adam J. Stewart advices

* Fix type
2019-01-08 15:07:47 -06:00
Eric
45882e1b6f usearch: Make installed binary executable (#10269)
* usearch: Make binary executable

* usearch: remove join_path
2019-01-08 14:20:13 -06:00
sknigh
d9c8d2f27b Added bash 5.0 (#10282) 2019-01-08 13:20:30 -06:00
Owen Solberg
0e50ff7339 r-dt: new versions (#10261)
* updated release and checksums, also tightened depends_on()

* remove blank line at end of file

* removing new version 0.5
2019-01-08 13:06:36 -06:00
Owen Solberg
76dd4ca9ae updated versions (#10263) 2019-01-08 13:00:12 -06:00
Owen Solberg
5c4156cd39 updated versions and depends_on() (#10264) 2019-01-08 12:54:55 -06:00
dorier
0a60cae516 added openpa package (#10265) 2019-01-08 12:53:37 -06:00
Eric
6ce6c79beb libzip: Add zlib dependency (#10270)
* libzip: Add zlib dependency

* libzip: Add version limit
2019-01-08 12:49:03 -06:00
Andreas Baumbach
a33d167c72 new version 1.0.1 for py-html5lib (#10278)
Change-Id: I2837dc098fce142b152d2969687d1873e182bbc8
2019-01-08 12:43:33 -06:00
Ross Miller
2934eda311 Check for ARM compiler in addition to clang (#10280)
Add "-rtlib=compiler-rt" to CFLAGS when building with either Clang or
the ARM compiler.

Refs #10279
2019-01-08 12:41:05 -06:00
Michael Kuhn
48db757be1 go: add 1.11.4 (#10272) 2019-01-08 13:57:25 +01:00
Andreas Baumbach
12b52baf7b new package: py-webencodings (#10277)
Change-Id: Icf20035367a34fa88acfef2d3fa3742c3f3901ac
2019-01-08 13:55:41 +01:00
George Hartzell
b984adb386 bowtie: new versions and %gcc@8.0.0: fix (#10232)
* bowtie: new versions and %gcc@8.0.0: fix

Bowtie development shifted from Sourceforge to GitHub.

This commit adds several versions from GitHub, using the archive
tarballs.  Note that the URL for 1.2.2 tarball is actually an '_p1'
tag....

It leaves the old 1.2 release download info in place.

Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and
1.2.0 are equivalent).

Include a fix that enables %gcc@8.0.0: from:

  https://github.com/BenLangmead/bowtie/issues/87

But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for
%gcc@6.0.0:.

Feel free to tighten this.  I know that:

- 1.2 -> 1.2.2 work with %gcc@5.5.0;
- 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and
- 1.2.2 fails with %gcc@8.2.0

* Tighten to `conflicts('%gcc@8:', when='@1.2.2')`

* Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
2019-01-07 11:30:59 -06:00
Chad Wood
3b59f70751 doxygen: URL and version hashes updated to project's GitHub home (#10250)
* Update package.py

Doxygen has migrated from a private SVN to GitHub. This PR updates the URLs and adds versioned commit hashes from GitHub. It also includes version 1.8.15 as the latest option.

* Update package.py
2019-01-07 10:38:32 +01:00
Massimiliano Culpo
c4521535e7 Multi-valued variants: better support for combinations (#9481)
This enforces conventions that allow for correct handling of
multi-valued variants where specifying no value is an option,
and adds convenience functionality for specifying multi-valued
variants with conflicting sets of values. This also adds a notion
of "feature values" for variants, which are those that are understood
by the build system (e.g. those that would appear as configure
options). In more detail:

* Add documentation on variants to the packaging guide
* Forbid usage of '' or None as a possible variant value, in
  particular as a default. To indicate choosing no value, the user
  must explicitly define an option like 'none'. Without this,
  multi-valued variants with default set to None were not parsable
  from the command line (Fixes #6314)
* Add "disjoint_sets" function to support the declaration of
  multi-valued variants with conflicting sets of options. For example
  a variant "foo" with possible values "a", "b", and "c" where "c"
  is exclusive of the other values ("foo=a,b" and "foo=c" are
  valid but "foo=a,c" is not).
* Add "any_combination_of" function to support the declaration of
  multi-valued variants where it is valid to choose none of the
  values. This automatically defines "none" as an option (exclusive
  with all other choices); this value does not appear when iterating
  over the variant's values, for example in "with_or_without" (which
  constructs autotools option strings from variant values).
* The "disjoint_sets" and "any_combination_of" methods return an
  object which tracks the possible values. It is also possible to
  indicate that some of these values do not correspond to options
  understood by the package's build system, such that methods like
  "with_or_without" will not define options for those values (this
  occurs automatically for "none")
* Add documentation for usage of new functions for specifying
  multi-valued variants
2019-01-04 19:02:34 -08:00
Michael Kuhn
051057caa3 mvapich2: add missing zlib dependency (#10254) 2019-01-04 20:52:00 -06:00
Elizabeth Fischer
f7b78412b1 Added package osmctools (#10249)
* Added package osmctools

* Simplified

Removed functions that did the same as existing defaults

* flake8
2019-01-04 20:51:44 -06:00
Jimmy Tang
5450303c97 Fix download path, the existing one has been removed from nvidia's site (#10253) 2019-01-04 18:13:11 -06:00
Neil Flood
3477d33751 openssl: add location of system certificates for SUSE Linux (#10242) 2019-01-03 10:02:25 -06:00
Axel Huebl
63e75c3972 Catch2: v2.5.0 (#10237)
Add the 2.5.0 release of catch2.
2019-01-02 08:59:36 -06:00
Ben Zwick
0c8fd8734d petsc4py: new versions (up to 3.10.0) and update website (#10238) 2019-01-02 08:59:14 -06:00
Ben Zwick
2577a5e686 slepc4py: new versions (up to 3.10.1) and update website (#10239) 2019-01-02 08:58:45 -06:00
Greg Sjaardema
9f40813004 PARALLEL-NETCDF: Update new version and location (#10172)
* PARALLEL-NETCDF: Update new version and location

PnetCDF-1.11.0 is released.

Also, the canonical download area has been changed and they are now using git, so can also provide a develop and master checkout.
One issue is that they changed the name of the tar files, so 1.11.0 needs special handling (and future versions will also).

All checksums at new location match the checksums from the old location.

* Address concerns in review

Added a `url_for_version` function to handle the name change in the tar files at version 1.11.0 and later.  Updated description to match current shown on website.  Updated `homepage` setting since it has recently moved.

* Address issues in second review
2019-01-01 19:55:29 -06:00
Ben Zwick
aca195367e FEniCS: workaround concretization issue with PETSc (#10235) 2019-01-01 10:39:07 -06:00
George Hartzell
60968a3fbf Add list_url for r-readr, finding old versions (#10231)
r-tidyverse needs r-readr@1.1.1, r-reardr needs a list_url so that it
can find it.
2019-01-01 08:05:53 -06:00
Todd Gamblin
5425a3dad4 flake8: fix flake8 issues with invalid escapes
- in many files, regular strings were used in places where raw strings
  should've been used.

- convert these to raw strings and get rid of new flake8 errors
2019-01-01 00:44:28 -08:00
Todd Gamblin
6f50cd52ed copyright: update license headers for 2013-2019 copyright. 2019-01-01 00:44:28 -08:00
George Hartzell
e6b2f0c179 express: new version, use tags and fix gcc@6.0.0: (#10230)
* express: new version, use tags and fix gcc@6.0.0:

Express fails to build with gcc@6.0.0:.

The debian project [has a
fix](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859) but
they don't seem to have pushed it upstream.

I've opened an issue and a PR in eXpress repo, but eXpress isn't
actively developed, so I'm fixing it here too.

Since the Spack package was created, the eXpress team tagged their
releases.  I've updated the package to use the tags.

Version 1.5.1 used to be known as 2015-11-29 (same commit).  1.5.2 is
new(er).

* Make flake8 happ{y,ier}
2018-12-31 20:28:15 -06:00
George Hartzell
fb52eb2a18 aspell builds with newer gcc's (#10227)
Apply fix from aspell issue (519) for a pointer dereference bug that
newer versions of gcc won't let slip past.

There hasn't been a release that includes the fix, this applies the
change to the latest release.
2018-12-31 16:13:03 -06:00
George Hartzell
51fbd315e9 fastx-toolkit builds with newer gcc's (#10228)
There's a missing break in a switch statement that newer gcc's
dislike.

Our #4696 simply disallowed newer gcc's.

This fixes the problem instead.

It's been [PR'ed upstream](https://github.com/agordon/fastx_toolkit/pull/22).

Tested with gcc@5.5.0 and gcc@8.2.0 on CentOS.
2018-12-31 16:12:51 -06:00
George Hartzell
7aeff18b6f bamutil builds with newer gcc's (#10229)
The most recent release of bamutil that we support uses an embedded
copy of libStatGen that has several issues that keep it from building
with newer releases of gcc.

They've all been fixed upstream and the latest release of bamutil
would pick them up if/when we support it.  The build process has
changed though, plus my team needs *this* version.

This commit backports those fixes.
2018-12-31 16:12:14 -06:00
Justin Stanley
7f528a5ed2 ds: new package at 9.8.0 (#9852)
* ds: new package at 9.8.0rc6

* ds: move patches to patch func

* ds: use built-in configure phase, remove autoreconf skip

* ds: revert to stable 9.8.0

* ds: remove unnecessary dep types

* ds: make url consistent with versions
2018-12-31 16:11:20 -06:00
Gary Klimowicz
a1d651e80f flang, llvm, pgmath: Add release for 2018-09-21 (#10224) 2018-12-31 11:50:04 -06:00
Geoffrey Oxberry
88417492f7 py-sphinxautomodapi: new python package (#10226) 2018-12-31 11:47:48 -06:00
Nichols A. Romero
54f76f7c51 Over specifying Quantum Espresso compiler variables causes problems in some corner cases. (#10216) 2018-12-30 11:29:28 -06:00
Sinan
70c5088a4c xgboost: make sure "libxgboost.so" is provided under prefix/lib (#10208) 2018-12-30 08:15:08 -08:00
Denis Davydov
309f70758b dealii: workaround concretization issue with PETSc (#10217) 2018-12-30 08:43:25 -06:00
Todd Gamblin
527ff860f0 patches: clean up patch.py, directives, and package class properties
- cleanup patch.py:
  - make patch.py constructors more understandable
  - loosen coupling of patch.py with package

- in Package: make package_dir, module, and namespace class properties

  - These were previously instance properties and couldn't be called from
    directives, e.g. in patch.create()

  - make them class properties so that they can be used in class definition

  - also add some instance properties to delegate to class properties so
    that prior usage on Package objects still works
2018-12-30 00:19:08 -08:00
George Hartzell
51cbc278aa Always build glib with iconv (#10219)
* Always build glib with iconv

My early PR, #10165, which added a variant to configure glib to use
libiconv and defaulted to false, seems to be causing more trouble than
the knob is worth.

This changes the glib package to always depend on and use libiconv.

* libiconv depends_on is no longer conditional
2018-12-29 16:01:08 -06:00
Adam J. Stewart
5f957920c4
Add GDAL 2.4.0 (#10215) 2018-12-28 21:20:13 -06:00
Eric
2c76e8feef salmon: Add version 0.12.0 (#10211) 2018-12-28 13:02:36 -06:00
Eric
ada8d5ce5c velvet: Add missing zlib dependency to fix installation errors (#10212) 2018-12-28 13:02:16 -06:00
Eric
722e7058f8 py-testinfra: Add version 1.18.0 (#10210) 2018-12-28 18:24:58 +01:00