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2018-04-19Suite-sparse: provide patch to fix builts with clang@6.0.0. (#7811)Kelly (KT) Thompson2-0/+14
+ I am unable to build suite-sparse@5.2.0 with clang@6.0.0. The build fails with the error: ``` 2397 [ 99%] Linking C executable wildtype_demo 2398 make[4]: Leaving directory `/tmp/kellyt/spack-stage/spack-stage-w0XYhK/SuiteSparse/GraphBLAS/build' >> 2399 libgraphblas.so.2.0.1: undefined reference to `__fpclassify' >> 2400 clang-6.0: error: linker command failed with exit code 1 (use -v to see invocation) >> 2401 make[4]: *** [wildtype_demo] Error 1 ``` + This error appears because libgraphblas.so requires `-lm`, but that link dependency is not explicitly listed in GraphBLAS\CMakeLists.txt. + A patch file is provided to add this dependency. The patch is only applied when the compiler is `%clang`.
2018-04-19add variants and conflicts for curl (#7804)healther2-7/+61
* add variants and conflicts for curl * darwinssl - Apple's SSL/TLS implementation * libssh - use libssh implementation * add darwin conflict for libssh{,2} * add linux conflict for darwinssl * remove openssl when +darwinssl * Update package.py * Update package.py * Update package.py * Update package.py
2018-04-18freeglut: new package (#7820)Levi Baber1-0/+43
2018-04-18glew: adding gl dependency (#7817)Levi Baber1-0/+1
2018-04-18Simple updates to the Krell Institute OpenSpeedShop and CBTF components ↵Jim Galarowicz5-8/+10
build package files. (#7812)
2018-04-18xrandr: needs randrproto (#7814)Levi Baber1-0/+1
* xrandr: needs xrandrproto * xrandr: fix typo
2018-04-18ADIOS 1.13.1 & SZ 1.4.12.3 (#7808)Axel Huebl2-1/+4
* ADIOS 1.13.1 ADIOS 1.13.1 fixes several issues with zero-sized block reading and writing when compression transports are used. * SZ 1.4.12.3 Add the lastest SZ release used in ADIOS1.
2018-04-18bcl2fastq2: package update (#7794)Matteo Guglielmi1-9/+10
* bcl2fastq2: package update * package/bcl2fastq2: homepage fix * package/bcl2fastq2: glob fix * package/bcl2fastq2: code clean up * package/bcl2fastq2: code clean up #2
2018-04-18Add grackle 3.1 (#7805)Loic Hausammann1-2/+3
2018-04-17cmake: update version (#7802)Matthias Diener1-0/+1
2018-04-17DIAMOND: add zlib dependency (#7801)Eric1-0/+2
2018-04-17Add latest version of cURL (#7800)Adam J. Stewart1-1/+2
2018-04-17bismark: Create new package (#7795)Eric1-0/+54
* bismark: Create new package * bismark: fix dependency types
2018-04-17psmc: new package (#7773)Yifan Zhu1-0/+45
* psmc: new package * psmc: changed version number * psmc: overwrite build phase
2018-04-17perl-statistics-pca: Create new package (#7796)Eric1-0/+39
* perl-statistics-pca: Create new package * perl-statistics-pca: fix dependency types
2018-04-17r-biomart: package update (#7787)Matteo Guglielmi1-1/+5
2018-04-17r-delayedarray: package update (#7788)Matteo Guglielmi1-2/+5
2018-04-17DIAMOND: add versions 0.9.19, 0.8.38, 0.8.26 (#7789)Eric1-0/+3
2018-04-17r-summarizedexperiment: package update (#7790)Matteo Guglielmi1-3/+6
2018-04-17r-genomicalignments: package update (#7791)Matteo Guglielmi1-9/+13
2018-04-17r-bsgenome: package update (#7792)Matteo Guglielmi1-8/+12
2018-04-17r-topgo: package update (#7793)Matteo Guglielmi1-6/+7
2018-04-17r-s4vectors: package update (#7779)Matteo Guglielmi1-2/+4
* r-s4vectors: package update * r-s4vectors: dependencies fix
2018-04-17r-biobase: package update (#7785)Matteo Guglielmi1-2/+3
2018-04-17Package/r-iranges (#7780)Matteo Guglielmi1-3/+7
* r-iranges: package update * r-iranges: package update * r-iranges: dependencies fix
2018-04-17r-genomicranges: package update (#7782)Matteo Guglielmi1-5/+8
* r-genomicranges: package update * r-genomicranges: dependencies fix
2018-04-17Package/geopm (#7560)Matthias Maiterth3-0/+181
* geopm: Added initial files for package geopm and py-natsort dependency * geopm: Updated variants for hwloc and mpi defaults * geopm: Cleaned up unwanted hyphenation in description. * geopm: updates according to change request. * geopm: Updated minor change requests. Clarification for ruby-ronn dependency included as a TODO. This requires changes in the current configure and build process which will be changed in a future version. * geopm: changed to AutotoolsPackage and fixed hwloc The changes for hwloc required to add a specific version bc of a conflicting version of openmpi's hwloc dependency being below 1.99. This works but updates to this package should check if this restriction is still required. (Thus TODO added) * geopm: Added link dependencies (thanks for pointing this out). Also removed empty line below class definition. * geopm: Fixed depends_on according to package guide. Removed wrong type 'run' and removed types for numactl, mpi and hwloc to use default build & link type. * geopm: Fixed and updated +doc dependencies new pacakge ruby-ronn (package specified as in ruby-narray package) Updated second +doc dependency doxygen. * geopm: Changed args for Autotools specific feature. Added enable_or_disable and with_or_without instead of if cascade. Added overhead variant. Also added missing dependency (default: build&link) for json-c).
2018-04-17glvis@3.3: new package (#7166)Geoffrey Oxberry4-0/+163
* glvis@3.3: new package * mesa-glu: now provides 'glu' (GL Utility library) * openglu: add package, provides glu * [GLVis] Use MakefilePackage as base. Add 'develop' version. Small tweaks in the makefile arguments. * [GLVis] Locate the X11, GL and GLU libraries within their respective prefixes. Set the C compiler in the makefile arguments. * [GLVis] Fix a bug: the same variable was used for two different things. * [libx11] Add the libs property * [OpenGL] Add the libs property * [OpenGLU] Add the libs property * [GLVis] Use the libs properties of libx11, opengl, and openglu
2018-04-17r-biocgenerics: package update (#7778)Matteo Guglielmi1-1/+2
2018-04-17r-genomeinfodb: package update (#7781)Matteo Guglielmi1-1/+2
2018-04-17r-htmltable: package update (#7767)Matteo Guglielmi1-3/+5
* r-htmltable: package update * r-htmltable: dependency fix * r-htmltable: dependency fix #2 * r-htmltable: dependency fix #3
2018-04-16ospac: fix compiler usage and install (#7776)Christoph Junghans1-1/+10
2018-04-16miniasm: new package (#7772)Yifan Zhu1-0/+39
2018-04-16fermikit: new package (#7775)Yifan Zhu1-0/+39
2018-04-16r-limma: package update (#7763)Matteo Guglielmi1-1/+2
* r-limma: package update * r-limma: dependency fix
2018-04-16Add libcint version 3.0.11 (#7764)Michael F. Herbst1-0/+1
2018-04-16r-hmisc: package update (#7766)Matteo Guglielmi1-1/+2
2018-04-16r-data-table: package update (#7768)Matteo Guglielmi1-0/+1
2018-04-16r-matrix: package update (#7769)Matteo Guglielmi1-1/+2
2018-04-16r-deseq2: package update (#7770)Matteo Guglielmi1-1/+2
2018-04-16add version 2.0.9 to py-slurm-pipeline (#7771)healther1-0/+1
Change-Id: I6b597076b0740d65b8aeaebf95f459745b1b1503
2018-04-14votca-moo: removal (#7762)Christoph Junghans3-45/+0
votca-moo is now part of votca-ctp (see votca/ctp#93)
2018-04-14eospac: initial commit (#7761)Christoph Junghans1-0/+45
* eospac: initial commit * eospac: add stable version
2018-04-13perl-moose: Add versions 2.2007,2.2009,2.2010 (#7758)Eric1-0/+3
2018-04-13perl-devel-overloadinfo: Add version 0.005 (#7754)Eric1-0/+1
2018-04-13prank: Add version 170427 (#7755)Eric1-0/+1
2018-04-13tcl: Add version 8.6.8 (#7756)Eric1-0/+1
2018-04-13tk: Add version 8.6.8 (#7757)Eric1-0/+1
2018-04-13flux: changed default value for doc variant to False (#7749)Massimiliano Culpo1-1/+1
fixes #2095
2018-04-13libfabric: added v1.6.0 and v1.5.3 (#7742)Raghu Raja1-1/+3