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2017-05-25Packages/r adegenet (#4354)Tom Merrick13-1/+518
* Add mpi support to R * Add multiple precision math routines to R * Updated the URL to match the version * Remove duplicate packages * Add packages for r-ergm and it's dependents * Fixed depends-on types * Correct flake8 errors * Correct Build type * r-adegenet and dependent packages
2017-05-25Add info for bwa@0.7.12 (#4356)George Hartzell1-0/+2
2017-05-25Add ant@1.9.6 info (#4350)George Hartzell1-0/+1
2017-05-25Touch up string expansion. (#4344)George Hartzell1-1/+2
* Touch up string expansion. I'm chasing this: ``` $ (module purge; spack install perl %gcc/5.4.0) ==> Error: No installed spec matches the hash: '%s' ``` There's something deeper going on, but the error message isn't helpful. After this change it tells me this: ``` $ (module purge; spack install perl %gcc/5.4.0) ==> Error: No installed spec matches the hash: '5.4.0' ``` Which is weird because `5.4.0` is not a hash... Whatever is going on here, the error message needs to be fixed. * Flake8 whitespace
2017-05-25Add older version of CONVERGE (#4346)Adam J. Stewart1-0/+2
2017-05-25Add missing dependency to py-entrypoints (#4330)Adam J. Stewart3-11/+17
2017-05-25Trilinos: add DTK external package (#4304)Andrey Prokopenko1-3/+19
* trilinos: add DTK external package * Making +dtk and ~tpetra conflict
2017-05-24Fix issues parsing multiple anonymous specs (#4199)becker333-29/+32
* fix parser * Removed xfails * cleaned up debug print statements * make use of these changes in gcc * Added comment explaining unreachable line, line left for added protection
2017-05-24Add latest version of CONVERGE (#4337)Adam J. Stewart1-13/+21
* Add latest version of CONVERGE * Flake8 fixes
2017-05-24added new R package - r-rgl (#4335)Douglas Duckworth1-0/+54
2017-05-24Fix PGI version detection: 17.4-0 -> 17.4 (#4251)Adam J. Stewart1-1/+1
2017-05-23cairo: ensure that X support is disabled for variant "~X" (#4242)Milton Woods1-0/+4
* cairo: ensure that X support is disabled for variant "~X" * cairo: explicitly enable X support for +X variant * cairo: prefer "variant in spec" over spec.satisfies(variant)
2017-05-23Correct installation step for mummer (and dependency) (#4293)George Hartzell3-11/+121
* Trailing whitespace cleanup * Handcraft an install process for mummer (grumble) Mummer punts on an installation step, they just build in and run from the same directory. Mummer also has various hardcoded paths built into it that allow it to find other executables that it needs as well as its Perl library. This updates the package to deal with this approach. It patches the Makefile and scripts/Makefile so that the correct info is fed to sed when it munges the perl scripts. The install step is now finer grained and puts things where mummer relatively wants to find them. * Add perl dependency * perl should be build/run dependency * Fix whitespace * Delete stray u at top of file
2017-05-23new package virtualgl (#4297)Luigi Calori2-1/+48
* new package virtualgl, depends on mesa-glu but NOT on mesa, so added a variant to mesa-glu * add comment on mesa variant of mesa-glu
2017-05-23fix build command for caffe with openblas (#4299)Gregory Lee1-1/+2
2017-05-23opencoarrays: new version (#4271)Erik Schnetter1-0/+1
2017-05-23Add support for addl versions of bcl2fastq2 (#4328)George Hartzell1-1/+5
Two changes: - It seems that Illumina version numbers are dotted and that the dashed version in the 2.18... filename is an anomaly (based on the names for 2.17.1.14 and 2.19.0). `url_for_version` does the right thing for 2.18. It will need to be fixed when support for 2.19 is added. 2.17 is no longer generally available so it gets a pass. - Add version and hash for 2.17.1.14. 2.17.1.14 is no longer distributed. If you have a copy of the source tarball, you can drop it into a local mirror w/ the name mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
2017-05-23Add latest version of libpciaccess (#4325)Adam J. Stewart1-1/+2
2017-05-23Magics with eccodes variant (#4320)Milton Woods2-16/+15
* magics: use filter_file to avoid using system python in all versions * magics: add eccodes variant to switch between eccodes and grib-api
2017-05-23Packages/r ergm (#4314)Tom Merrick10-0/+384
* Add mpi support to R * Add multiple precision math routines to R * Add packages for r-ergm and it's dependents * Fixed depends-on types * Correct flake8 errors
2017-05-23plumed: fixed compilation on rhel6 (#4318)Massimiliano Culpo1-1/+11
* plumed: fixed compilation on rhel6 with mvapich2 and gcc@5.4.0 (#77) * plumed: prevent parallel compilation, as it breaks for the newest version
2017-05-22Add Microsoft's C++ Rest SDK (#4315)Robert D. French1-0/+41
2017-05-22magics: use spack perl instead of system perl (#4310)Milton Woods1-3/+3
2017-05-21qt: patch JavaScriptCore to favour internal pcre headers (#4270)Milton Woods2-0/+36
2017-05-21libdrm depends on pkg-config (#4308)Michael Kuhn1-0/+1
2017-05-21flex: create variant +lex that creates symlinks for lex and libl.{a,so} (#3894)Milton Woods1-0/+17
* flex: create variant +lex that creates symlinks for lex and libl.{a,so} * flex: enable variant +lex by default * flex: use dso_suffix for portability; replace repetitive code with a loop
2017-05-20spark: remove whitespaces from run_env variable (#4210)Massimiliano Culpo1-2/+7
2017-05-20Fix ncview with netcdf+mpi (#4305)Michael Kuhn1-0/+10
ncview has to be compiled using the same compiler as netcdf.
2017-05-20magics fixes for versions > 2.29.x (#4302)Michael Kuhn1-3/+9
2017-05-19julia: New version 0.5.2 (#4259)Erik Schnetter1-1/+2
2017-05-19hwloc: new version (#4272)Erik Schnetter1-0/+1
2017-05-19hpx5: new version (#4273)Erik Schnetter1-0/+1
2017-05-19cmake: new version (#4274)Erik Schnetter1-0/+1
2017-05-19gobject-introspection depends on pkg-build (#4301)Michael Kuhn1-0/+1
2017-05-19Mpifileutils (#4283)Adam Moody1-0/+81
* adding mpifileutils * mpifileutils: add +lustre variant * mpifileutils: add variant for xattr * mpifileutils: update to AutotoolsPackage * mpifileutils: simplify and eliminate redundant make * mpifileutils: drop unnecessary comments
2017-05-19Fix gcc not finding zlib (#4291)Michael Kuhn1-0/+9
2017-05-19added R 3.4.0, again (#4260) (#4294)Douglas Duckworth1-1/+2
2017-05-19Fix boost@:1.56.0%gcc@:5 (#4295)George Hartzell2-0/+59
I need boost@1.54.0 for bcl2fastq2. I tested bcl2fastq2 using the system compiler (gcc@4.8.5). My full build uses a spack-build gcc@5.4.0. boost@1.54.0 won't build. I found the answer [here](https://github.com/hashdist/hashstack/issues/802) with the details in [this upstream/boost ticket](https://svn.boost.org/trac/boost/ticket/10125). I've confirmed that these combo's build: boost version| compiler ------------ | ------------------ boost@1.54.0 | gcc@4.8.5 (system) boost@1.54.0 | gcc@5.4.0 (Spack) boost@1.64.0 | gcc@5.5.0 (system)
2017-05-19Add r-rmpfr and r-gmp to R (#4287)Tom Merrick2-0/+81
* Add mpi support to R * Add multiple precision math routines to R * Updated the URL to match the version * Remove duplicate packages
2017-05-18Add info for libxml2@2.7.8 (#4290)George Hartzell1-0/+1
bcl2fastq2 needs this older version.
2017-05-18added new version 7.900.1 (#4292)kothah1-0/+1
added new md5
2017-05-18add mpi support to meme (#4265)Douglas Duckworth1-0/+11
* added openmpi support to meme * openmpi is a link dependency which leverages r_path * openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used * added serial option and set mpi to not be default * modified meme
2017-05-18Add old version of ROOT 5 (#4288)Adam J. Stewart1-0/+1
2017-05-18Fix spec['python'].home (#4228)Adam J. Stewart1-0/+2
2017-05-18Add mpi support to R (#4286)Tom Merrick2-0/+93
2017-05-18Add the gnupg package and missing dependencies. Update versions of ex… (#4281)Patrick Gartung6-2/+171
* Add the gnupg package and missing dependencies. Update versions of existing dependencies. * this ended up in the wrong repo * put versions back, remove uneeded function * OK ;) * autopep8 * typo on npth line * whitespace
2017-05-18Add a new package for Open Babel (#4256)Adam J. Stewart3-0/+169
* Add a new package for Open Babel * Add post-installation tests, stolen from the fine folks at Homebrew * Add patch to fix Python 3.6 support * Add a more complete patch to get Python 3.6 support working * Add patch to convert tabs to spaces in test script testpdbformat.py contains mixed tabs and spaces causing the unit tests to fail. With this patch, all tests pass with flying colors.
2017-05-17benchmark: New package for the Google Benchmark library (#4194)Erik Schnetter1-0/+36
* benchmark: New package * benchmark: Remove empty function
2017-05-17Add info for miniconda[23]@4.3.14 (#4263)George Hartzell2-0/+2
2017-05-17Package for bcl2fastq2 (updates libxslt) (#4234)George Hartzell4-2/+131
* Add v1.1.26 and make crypto a variant I need 1.1.26 for bcl2fastq2. I also need to build it without crypto support. * Initial support for bcl2fastq2 * Clean up commentary, messages, names No substantial changes intended, just cleanup. * fix flake8 and extra import * The masked grammarian strikes again... * Be normal (messages don't end in periods) * When +crypto, add --with-crypto Add `--with-crypto` to configure args when user hasn't explicitly set `~crypto`. * self.spec.satisfies is unsatisfying, in is in instead See #4135, self.spec.satisfies has issues. @adamjstewart suggests simply using in.
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