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2016-06-16Tweak how R packages are built.Glenn Johnson5-10/+14
Add bzip2 as a dependency to base R. Switch from installing the R packages from tar files to installing from the extracted directory. This is more in line with a standard install and also allows installing from VCS. Use the Bioconductor version for BiocGenerics and future Bioconductor packages. Suffix the package with 'bioc-$version' to indicate which Bioconductor release the package is a part of. This is actually more important than the actual version attached to individual packages although those are subject to change within the Bioconductor branch.
2016-06-16Fix flake8 errorsGlenn Johnson2-3/+4
Use Bioconductor provided Short URL for homepage in BiocGenerics. Wrap description text for utf variant in pcre.
2016-06-16Update version of BiocGenericsGlenn Johnson1-1/+1
The BioConductor repositories only keep the most recent version so this has to be bumped.
2016-06-16Use configure_args rather than optionsGlenn Johnson1-8/+8
Replaced 'options' with 'configure_args'. That seems like a better name and is consistent with the packaging guide.
2016-06-16Add variant for UTF support to pcreGlenn Johnson1-1/+9
This will build PCRE with UTF support by default. That seems to be reasonable for most environments.
2016-06-16Clean up R extensionsGlenn Johnson4-8/+16
Run the existing R extension packages through autopep8 to clean up.
2016-06-16Add version 3.3.0 of RGlenn Johnson1-0/+3
This commit adds the 3.3.0 version of R and adds dependencies on curl and pcre.
2016-06-16Clean up R package filesGlenn Johnson1-25/+19
- remove unused imports - apply pep8 - reformat text strings
2016-06-16Merge pull request #1068 from epfl-scitas/fixes/flake8_no_f405Todd Gamblin1-1/+1
Flake8: ignore F405
2016-06-16Merge pull request #944 from adamjstewart/features/bertiniTodd Gamblin1-0/+50
Add bertini package
2016-06-16Merge pull request #962 from adamjstewart/features/hplTodd Gamblin1-0/+119
Add HPL benchmark package
2016-06-16Replace 2.6-incompatible skipIf with a conditional.Todd Gamblin1-4/+8
- skipIf doesn't work with Python 2.6.
2016-06-16remove dead code, cleanup.Todd Gamblin2-42/+26
2016-06-16simplify instance check.Todd Gamblin1-2/+1
2016-06-16rename Mac OS X to macosTodd Gamblin3-21/+19
2016-06-16flake8: ignore F405alalazo1-1/+1
2016-06-16Added str method to mac_osx so that whenever we try to access darwins ↵Mario Melara2-9/+8
different operating systems we can grab the name correctly. This avoids having to worry whether we have a version attached to it or not.
2016-06-16Merge branch 'features/newarch' into developTodd Gamblin68-516/+2350
Conflicts: lib/spack/spack/config.py var/spack/repos/builtin/packages/lua/package.py
2016-06-16Fixes #460: Do not show variants by default in spack find.Todd Gamblin3-11/+30
This does two things: 1. By default `spack find` no longer shows variants. You have to supply `-v` to get that 2. This improves the `colify` implementation so that it no longer pads the rightmost column. This avoids the issue where if one spec was too long in the output, *all* specs would have space padding added to that width, and it would look like the output of `spack find` was double spaced. This no longer happens -- the one bad line wraps around and the other lines are now single-spaced when you use `-v` with boost.
2016-06-16Just call old os "unknown"Todd Gamblin1-1/+1
2016-06-16fix up packages for new architecture.Todd Gamblin4-9/+9
2016-06-16Add libxcb dependencies. Fix up packages to get py-basemap and stat to build.Todd Gamblin8-6/+170
2016-06-16be more tolerant when parsing new specs.Todd Gamblin1-6/+13
2016-06-16Add `__contains__` to arch to satsify old packages.Todd Gamblin1-2/+9
2016-06-15two minor fixesGregory Becker2-9/+9
2016-06-15Two minor fixesGregory Becker2-8/+8
2016-06-15Merge pull request #1045 from eschnett/eschnett/openmpi-verbs-usrTodd Gamblin1-1/+1
Do not pass "/usr" or "/usr/local" as path to configure
2016-06-15Merge pull request #1058 from eschnett/eschnett/bloscTodd Gamblin2-0/+257
Add packages c-blosc and hdf5-blosc
2016-06-15Merge pull request #1028 from JRWynneIII/boost-graph-parallel-fixTodd Gamblin1-34/+43
Add variant for boost graph and parallel graph
2016-06-15Merge pull request #1040 from KineticTheory/pkg-trilinosTodd Gamblin1-84/+123
Make Boost an optional feature of Trilinos.
2016-06-15Merge pull request #1037 from KineticTheory/developTodd Gamblin1-3/+8
Package serf also depends on zlib.
2016-06-15Merge pull request #1031 from opoplawski/pcreTodd Gamblin2-0/+15
Add patch to compile pcre with Intel 16.0.3 compiler
2016-06-15Merge pull request #1051 from daboehme/developTodd Gamblin1-1/+1
Use https for github in Caliper package
2016-06-14Install shared libraries correctly on LinuxErik Schnetter1-10/+18
2016-06-14Correct Blosc install on DarwinErik Schnetter2-28/+153
2016-06-14Add packages c-blosc and hdf5-bloscErik Schnetter2-0/+124
c-blosc provides the Blosc compression filter, and hdf5-blosc provides a plugin for HDF5 to use that filter.
2016-06-13Use https for githubDavid Boehme1-1/+1
2016-06-12Update formatting to meet code style requirements.Kelly (KT) Thompson1-80/+113
2016-06-12Make Boost an optional feature of Trilinos.Kelly (KT) Thompson1-4/+10
I have been unable to build Boost with some toolset/platform combinations. The users I support don't need the Boost features in Trilinos, so I have been manually hacking trilinos/package.py to disable boost. I would like to propose that these changes be added to the released version. + Add boost as a variant, default to true so there is no change to existing behavior. + Move the CMake configure options related to Boost into a conditional block that is triggered by "if '+boost' in spec".
2016-06-12Merge pull request #1026 from epfl-scitas/packages/lmodTom Scogland5-155/+143
lmod : updated package and dependencies
2016-06-11Do not pass "/usr" or "/usr/local" as path to configureErik Schnetter1-1/+1
2016-06-11qa : fixed style and a bug reported by flake8alalazo1-45/+3
lib/spack/spack/test/versions.py:313: [F811] redefinition of unused 'test_union_with_containment' from line 306 Flake8 found errors.
2016-06-11versions : added unit tests for the new propertiesalalazo1-0/+8
2016-06-10I made a hash of that minor mergeGregory Becker5-131/+87
Merge commit '4eeb' into features/newarch
2016-06-10changed compiler yaml formatGregory Becker5-131/+87
2016-06-10Merge pull request #1020 from LLNL/bugfix/libdwarf_versionsTodd Gamblin1-4/+9
put older versions back + version-specific dwarfdump dir
2016-06-09Fix style issues.Kelly (KT) Thompson1-3/+5
2016-06-09Package serf also depends on zlib.Kelly (KT) Thompson1-2/+5
+ Add zlib as a required dependency. + Point scons build system to the spack provided zlib installation.
2016-06-08Add additional blank line for flake8Orion Poplawski1-0/+1
2016-06-08Add patch to compile pcre with Intel 16.0.3 compilerOrion Poplawski2-0/+14
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