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2017-10-10ninja: add v1.8.2 (#5625)Christoph Junghans1-0/+1
2017-10-10plumed: reworked patching applications, added new version (#5680)Massimiliano Culpo1-47/+31
closes #5506 The application of patches to upstream executables has been reworked according to the suggestions of the main developer in #5506. In particular we are not maintaining a dictionary that maps plumed versions to the versions of patchable executables, and we are using a non-interactive command to patch applications. All the comments on substituting plumed at run-time do not apply here, since we use RPATH and we want to maintain a 1:1 relationship between the DAG hash and the plumed library used.
2017-10-10snap-korf: new package (#5589)Audrey Thoma1-0/+62
2017-10-09Adding openfast variant to nalu. (#5675)Jon Rood1-0/+9
2017-10-09r-adsplit: Create new package and update version for its dependencies. (#5640)lingnanyuan3-0/+47
* r-adsplit: Create new package. * r-rlang: Update version. * r-s4vectors: Update version.
2017-10-09switching downloads to git (#5659)Audrey Thoma1-7/+6
2017-10-09r-affycompatible: Create new package. (#5664)lingnanyuan1-0/+44
2017-10-09r-affydata: Create new package. (#5665)lingnanyuan1-0/+39
2017-10-09r-affycontam: Create new package. (#5668)lingnanyuan1-0/+40
2017-10-09strelka: new package (#5632)George Hartzell1-0/+88
* Add package for strelka@2.8.2 * Fix flake8 complaints
2017-10-09Add package for aspell and ass't dictionaries (#3890)George Hartzell4-0/+175
* Add package for aspell and ass't dictionaries Add a package definition for aspell. Add a handful of dictionaries to convince myself that the support for a bunch of dictionaries works. * Flake8 cleanup * Use six's version of urlparse `urlparse` is not python3 friendly. This works around it (stolen from `.../cmd/md5.py`). * Fix incorrect trimming regexp * Clean up dictionary build - more parsimonious use of `which` (`make()` has already been made) - use `sh` instead of `bash` * Use a helper method to generate info for variants I figured out my issues with static methods. I *think* that it this is pythonic. * Convert aspell to an extendable package Convert aspell to be extendable and rework the dictionaries to be extensions. As it stands, there's a great deal of cut and paste in the dictionaries, I'll abstract that out next. The {de,}activate methods copy a great deal of code out of package.py. Perhaps there's a better way.... * Create AspellDictPackage and use it for the dictionaries Reduce the repeated code, pull it into a base class. I'm confused about why 'from spack import *' wasn't more useful in the base class. * Oops, -de & -es should be AspellDictPackages too * Typo: pakcage -> package * Address some commentary * Update copyright dates, 2016->2017
2017-10-09Added mfem v3.3.1-rc1 to the mfem package. (#5644)Aaron Fisher1-1/+5
2017-10-09libpng: zlib flags more elegant (#5656)Axel Huebl1-2/+2
2017-10-08espressopp: added v1.9.5 (#5652)Christoph Junghans1-0/+1
2017-10-08Add PLASMA package (#5540)Piotr Luszczek2-0/+145
2017-10-08Fix node-js : requires openssl min 1.0.2 (#5650)Pramod S Kumbhar1-1/+1
2017-10-08hypre: add 2.12.1 (#5653)Denis Davydov1-2/+3
2017-10-07adding http2 support (#5628)George Hartzell1-0/+3
Requires nghttp2 libraries
2017-10-06r-affycomp: Create new package. (#5642)lingnanyuan1-0/+37
2017-10-06r-affxparser: Create new package. (#5641)lingnanyuan1-0/+42
2017-10-06r-genomeinfodbdata: created new package (#5639)Yifan Zhu1-0/+35
2017-10-06r-hms: created new package (#5638)Yifan Zhu1-0/+35
2017-10-06qmcpack: new package (#4907)William Scullin3-8/+253
This adds QMCPACK along with patches to Quantum Espresso for using Quantum Espresso in QMCPACK workflows.
2017-10-06Nghttp2 new package (#5627)George Hartzell1-0/+35
* nghttp2 library package Added for dependencies * Update package.py * Removed useless code * Flake8 fix
2017-10-06Add a package for VarDictJava@1.5.1 (#5626)George Hartzell1-0/+47
This is a simple package that drops their shell wrapper into prefix.bin and their jar files into prefix.lib. The approach comes from the picard package.
2017-10-06The silver searcher: new version (#5630)George Hartzell1-0/+2
* Updating ag to the latest version * Pretty by request * Restore url to previous value There *is* an https version available, but I've also been told to not just update the url when adding new version. I'm following the latter advice and trusting security to the digest.
2017-10-06git + luafilesystem: minor fixes (#5635)Massimiliano Culpo2-3/+12
* git: setup_dependent_environment won't fail for external packages * luafilesystem: relax the request on git (it seemed overly restrictive)
2017-10-06maven: new version (#5631)George Hartzell1-0/+1
* Adding maven v3.5.0 Updating package file to include later version of maven but still signifying a preference for the older * removing specific preference flag
2017-10-06ncl: Fix temp directory and depend on esmf (#5636)Michael Kuhn1-1/+4
* ncl: Fix temp directory Currently, ncl is configured using a transient temp directory. This leads to warnings such as this when executing ncl later on: warning:"/tmp/ncl_ncar_xxxxxx" tmp dir does not exist or is not writable: NCL functionality may be limited -- check TMPDIR environment variable As this also breaks some functionality, use the system temp directory instead (typically /tmp). * ncl: Depend on esmf esmf is required for some ncl scripts (such as ESMF_regridding.ncl).
2017-10-05Add link dependency on xproto to xau (recent dependency mechanics changes?) ↵George Hartzell3-4/+4
(#5624) * Add link dependency on xproto to xau The libxcb build was failing like so: ``` 1 error found in build log: [ ... ] 131 checking whether to build developer documentation... yes 132 checking for doxygen... /usr/bin/doxygen 133 checking for dot... /usr/bin/dot 134 checking for CHECK... no 135 checking for XCBPROTO... yes 136 checking for NEEDED... no >> 137 configure: error: Package requirements (pthread-stubs xau >= 0.99.2) were not met: 138 139 Package 'xproto', required by 'xau', not found 140 141 Consider adjusting the PKG_CONFIG_PATH environment variable if you 142 installed software in a non-standard prefix. 143 ``` This adds a link dependency on libxproto that allows the libxcb build to succeed. * Change more build deps to build, link These were also necessary for emacs+X to build. * Fix flake8 complaint
2017-10-05fsl: new package (#5605)Audrey Thoma1-0/+102
2017-10-05Don't change properties on already-installed packages (#5580)scheibelp3-0/+118
* edits to address issues where spack concretization attempts to set properties on already-installed specs * most added checks only need to check if the spec is concrete; they dont also need to check if the package is installed * add test to ensure that patches are not applied to an installed spec * add test to ensure that an error is detected when a dependent requests a dependency constraint which conflicts with a requested installed dependency
2017-10-05r-acme: Create new package. (#5620)lingnanyuan1-0/+45
2017-10-05r-acgh: Create new package. (#5619)lingnanyuan1-0/+42
2017-10-05r-cluster: Update version to 2.0.6. (#5618)lingnanyuan1-1/+3
2017-10-05r-absseq: Create new package. (#5617)lingnanyuan1-0/+40
2017-10-05r-acde: Create new package. (#5616)lingnanyuan1-0/+46
2017-10-05r-boot: Update version to 1.3-20 (#5615)lingnanyuan1-0/+2
2017-10-05esmf: Fix build (#5607)Michael Kuhn3-4/+266
- Use libs instead of lapack_libs (see #3364). - Add a patch to fix building with recent versions of gcc. - Add a patch to fix building with mvapich2.
2017-10-05r-abadata: new package. (#5611)lingnanyuan1-0/+41
2017-10-05r-abaenrichment: Create new package. (#5612)lingnanyuan1-0/+52
2017-10-05CMake: 3.9.4 (#5614)Axel Huebl1-0/+1
Adds the latest release of CMake.
2017-10-04Add the Sandbox package (#5595)Christoph Junghans1-0/+34
2017-10-04extensions: create install prefixes (#5601)Ben Boeckel3-3/+3
Tests fail locally because the install prefix doesn't exist. Make them exist.
2017-10-04r-tibble: added dependency r-rlang (#5536)Yifan Zhu1-1/+2
* pr-quantities: add version & py-numpy conflict (#5307) * r-tibble: Update version to 1.3.4 * r-tibble: added dependency r-rlang * r-tibble: changed r-lazyeval and r-rlang to be versioned dependencies * Update package.py * Update package.py
2017-10-04tassel: new package (#5583)Audrey Thoma1-0/+45
2017-10-04xerces-c: Fix url (#5597)Michael Kuhn1-1/+1
The main location only carries the latest release, while all previous (and current) ones are available at the archive location.
2017-10-04OpenSSL: Fix Zlib (#5584)Axel Huebl1-0/+2
Fix missing `-lz` on `make` of OpenSSL. Spotted on a system without a system-wide zlib installation.
2017-10-03r-edger: created new package (#5571)Yifan Zhu1-0/+44
2017-10-03Add package for multitail@6.4.2 (#5567)George Hartzell1-0/+62
* Add package for multitail@6.4.2 Lightly tested on CentOS 7. * Responde to feedback/comments Use `install_targets` to specify PREFIX= and DESTDIR= instead of hacking away at the Makefile. Expand commentary about "Why?". Use `headers.include_flags` and `libs.ld_flags` to avoid explicitly setting `-L` and `-I` when hacking away at the Makefile.