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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 Hartzell6-0/+234
* 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
2017-10-09Fix setup for changes to dirty flag (#5592)becker332-3/+7
* Pass dirty arg through setup to setup_package
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
2017-10-06Don't check package.installed in _mark_concrete if value=True (#5634)scheibelp2-1/+18
* spec and spec.package.spec can refer to different objects in the database. When these two instances of spec differ in terms of the value of the 'concrete' property, Spec._mark_concrete can fail when checking Spec.package.installed (which requires package.spec to be concrete). This skips the check for spec.package.installed when _mark_concrete is called with 'True' (in other words, when the database is marking all specs as being concrete). * add test to confirm this fixes #5293
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
2017-10-05Fix formatting typo (#5622)Jimmy Tang1-1/+1
2017-10-05Don't change properties on already-installed packages (#5580)scheibelp5-0/+163
* 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
2017-10-04Identify the flag handlers feature as beta (#5609)becker331-0/+5
The flag-handling logic added in #4421 may change semantics, so this commit adds a warning to the documentation for this feature.
2017-10-04Fix module loads (#5599)becker331-10/+16
Fixes #5455 All methods within setup_package use an EnvironmentModifications object to control the environment. Those modifications are applied at the end of setup_package. Module loads for the build environment need to be done after the rest of the environment modifications are applied, as otherwise Spack may unset variables set by those modules (for example LD_LIBRARY_PATH).
2017-10-04module files: restricted token expansion + case sensitivity (#5474)Massimiliano Culpo8-22/+170
closes #2884 closes #4684 In #1848 we decided to use `Spec.format` to expand certain tokens in the module file naming scheme or in the environment variable name. Not all the tokens that are allowed in `Spec.format` make sense in module file generation. This PR restricts the set of tokens that can be used, and adds tests to check that the intended behavior is respected. Additionally, the names of environment variables set/modified by module files were, up to now, always uppercase. There are packages though that require case sensitive variable names to honor certain behaviors (e.g. OpenMPI). This PR restricts the uppercase transformation in variable names to `Spec.format` tokens.
2017-10-04spec.patches: fix dictionary reference (#5608)scheibelp1-2/+3
This fixes a loop that was iterating through the keys of a dictionary when it was intending to use the values.
2017-10-04extensions: create install prefixes (#5601)Ben Boeckel3-3/+3
Tests fail locally because the install prefix doesn't exist. Make them exist.