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2018-01-04make nghttp2 optional for curl, as it does not build for older compilers. ↵Todd Gamblin1-4/+7
(#5977)
2018-01-04Adding Nek5000 to Spack (#6153)Thilina Rathnayake2-0/+154
* Start adding Nek5000 package * Add tools to install: genmap, prenek, postnek * Address comments by @davydden * Use install_tree (thanks @junghans) and polish * Update url * Fix flake formatting errors * Change F77 and CC compilers Apparently spack compilers can't be called outside spack and we have an underscore test in our Nek5000/core/makenek.inc file which calls F77 compiler. * Add support for visit and profiling options * Fix a typo * Fix a typo * Remove the C check * Add visit variant * Update the install of int_tp tool * Let MAXNEL to be set during installation
2018-01-04r-rgraphviz: Create new package. (#6316)lingnanyuan1-0/+38
2018-01-04Set SMPI library path in dependent packages (#6548)serbanmaerean1-0/+2
* Added magma package * Incorporated Serban's change * Remove deleted files * argparse.py * Sync forked Spack repo in github * Add spectrum-mpi lib path to LD_LIBRAY_PATH in spack_env. As a result of supporting alternate installation directories, spectrum-mpi does not use rpath anymore, so we need to set LD_LIBRARY_PATH in spack_env to allow MPI programs to run during dependent package configuration. * Fix flake8 error (blank line at EOF)
2018-01-04RNA-SeQC: Create new package (#6555)Eric2-0/+66
* RNA-SeQC: Create new package * RNA-SeQC: Fix flake8 error * RNA-SeQC: Fix Travis error
2018-01-04r-rgeos: Create new package. (#6592)lingnanyuan1-0/+42
2018-01-04qt: add 5.10.0, fix macOS build, clean-up comments/TODOs (#6766)Denis Davydov2-7/+57
* qt: add 5.10.0, fix macOS build, clean-up comments/TODOs * qt: fix pkgconfig files * qt: restore-pc-files.patch * add version constraint to the patch * qt: adjust url_for_version for 5.10.0
2018-01-04xios: I/O management for climate models (#6796)Milton Woods4-0/+289
* xios: XML-IO-SERVER library for IO management of climate models * xios: install to prefix directory * xios: add a test case * xios: define versions to use cache and mirror directories * xios: use proper svn URL for version 910 * xios: package url must be defined, otherwise uninstall fails * xios: add trunk version to allow building latest revision * xios: enable parallel build * xios: allow installation with mpif90 compiler wrappers * xios: use mpi variants of dependencies * xios: allow user to specify MPI launcher via MPIRUN environment variable * xios: prefer spack versions of blitz and boost (needed for gcc@7) * xios: enable builds with clang+gfortran on OSX * xios: use numeric versions for releases, @develop for trunk * xios: different patches required for @1.0 and @develop * xios: patch function for clang works across revisions * xios: link blitz library * xios: workaround bug 17782 in llvm * xios: whitespace adjustments for flake8 * xios: avoid bare except clause * xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
2018-01-04py-umi-tools: Create new package (#6823)Eric1-0/+45
* py-umi-tools: Create new package * py-umi-tools: fix dependencies
2018-01-03Update grackle (#6822)Loikki1-2/+3
2018-01-03package openfoam-com: add version 1712 and update patches (#6820)Mark Olesen12-906/+956
* combine all patches for 1612 into a single file, with additional comments to explain the rational. * Add kahip decomposition variant. * Add support for ARM64 architecture. * filter instead of patching etc/config.*/settings. This eliminates patch files for 1706, perhaps for the future as well. * URLs at or before version 1612 have a different structure, so provide a url_for_version implementation to handle this
2018-01-03package/r-rjags: create new package (#6804)Sinan1-0/+46
* package/r-rjags: create new package * fix typo fix typo * package/r-rjags small fix to pass flake8 tests * package/r-rjags: more fixes to satisfy flake8 tests
2018-01-03fltk depends on libx11. (#6816)健美猫1-0/+2
2018-01-03Add a new version and runtime dependency for MotionCor2. (#6817)健美猫1-0/+3
* Update motioncor2 to 1.0.4 and add libtiff dependency. * Add comments for libtiff dependency in MotionCor2.
2018-01-03Add libtiff@3. (#6818)健美猫1-0/+1
2018-01-03suite-sparse: support 64bit BLAS (#6767)Denis Davydov1-0/+6
* suite-sparse: support 64bit BLAS * use double quotes instead of escaped quotes
2018-01-03Flex v2.6.4 conflicts with gcc@7.2.0 (#6819)stefanosoffia1-0/+4
2018-01-02singularity - added master branch (#6631)Douglas Duckworth1-0/+1
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch * renamed to develop * added master branch properly
2018-01-02New Package: py-adios (#5686)Axel Huebl1-0/+78
The ADIOS1 numpy bindings depend on an installed, fully loaded ADIOS C library + its config tools to build properly.
2018-01-02Intel mkl dnn (#6268)Brian Van Essen1-0/+39
* Added a package for the MDAnalysis toolkit. * Added a package for the Intel MKL-DNN project. * Fixed flake8 errors. * Fixed Flake8
2018-01-02Fix HTML detection (#6394)Michael Kuhn1-1/+2
Some servers report a content-type header instead of Content-Type.
2018-01-02rsem: update version 1.3.0 md5sum (#6650)Eric1-1/+1
2018-01-02atom-dft: new package plus dependencies (#6653)Michael Kuron3-0/+156
* atom-dft: new package plus dependencies * Indentation fix * Use the compiler wrappers * Pass variables instead of using FileFilter
2018-01-02Install all the cli tools from all the sub-directories (#6705)Jimmy Tang1-1/+6
* Install all the cli tools from all the sub-directories * Satisfy pep8
2018-01-02py-lrudict: a LRU-based cache dictionary (#6734)Feiyi Wang1-0/+38
* add py-lrudict * style fix * style fix: add blank lines
2018-01-02py-scandir: a better directory iterator, backport to 2.7 (#6739)Feiyi Wang1-0/+37
2018-01-02gatk: boilerplate cleanup (#6744)Levi Baber1-15/+0
2018-01-02add OctavePackage (#6746)Denis Davydov9-49/+88
* add OctavePackage 1. remove import CudaPackage which is not needed anymore 2. mention CudaPackage and OctavePackage in packaging guide 3. adjust OctavePackageTemplate 4. add clue file for Octave build 5. sanity check on self.prefix * use setup_environment
2018-01-02py-xattr: a python interface to access extended file attribute (#6747)Feiyi Wang1-0/+38
* py-xattr: a python interface to access extended file attribute * py-xattr: style fix
2018-01-02Lbann update (#6751)Brian Van Essen1-2/+59
* Added a package for the MDAnalysis toolkit. * Updated the LBANN recipe to use the revised cmake environment being rolled out. * Flake8 errors
2018-01-02likwid: add stable 4.3.0 (#6761)Denis Davydov1-3/+2
2018-01-02mesa: disable binutils on macOS (#6763)Denis Davydov1-2/+2
2018-01-02jags: lapack fix (#6764)Levi Baber1-2/+4
* jags: fixing openblas thows a lapack error when compiling. atlas works. other lapack providers may work. also adding tags * changing blas/lapack reference * removing openblas conflict * jags: whitespace cleanup for flake8
2018-01-02Esmf fixes for Cray, OSX and mpich (#6768)Milton Woods2-3/+31
* esmf: put .mod files in the spack compiler search path * esmf: allow building with Cray mpi * esmf: create run-path dependent libraries on osx * esmf: link fortran interface libraries when building with mpich
2018-01-02Adding option to build Nalu with Hypre support. (#6782)Jon Rood1-1/+10
2018-01-02perl-xml-libxml: adding perl module (#6783)peetsv1-0/+35
* perl-xml-libxml: adding perl module * line length change
2018-01-02create perl-file-which package (#6800)Sinan1-0/+34
* create perl-file-which package * trivial edits for package.py so trivial edits for package.py so that flake8 will not complain
2018-01-02Updated 'nginx' from v1.12.0 to v1.13.8. (#6810)stefanosoffia1-0/+1
This fixes build issues with most recent gcc versions. See issue #6252.
2018-01-02py-pyani: Create new package (#6811)Eric1-0/+55
2018-01-02MinCED: Create new package (#6815)Eric1-0/+44
2018-01-02adding specific version url for augustus 3.3 due to old folder structure (#6813)Levi Baber1-1/+2
2018-01-02Tioga package: Explicitly list MPI compilers for Cmake (#6741)Jon Rood1-1/+4
2018-01-02paraview package: Explicitly specify MPI compilers in Cmake (#6738)Jon Rood1-1/+4
2018-01-02new package: Pfunit: unit testing framework for Fortran (#6795)Milton Woods1-0/+97
2018-01-02new package: DIAMOND (#6793)Eric1-0/+35
2018-01-02new package: tantan (#6792)Eric1-0/+38
2018-01-02Cython only needed for develop version of mpi4py (#6780)Adam J. Stewart1-1/+1
2018-01-02Add more unit tests for spack clean command (#6777)Adam J. Stewart1-3/+5
2018-01-02new package: py-rseqc (#6773)Eric1-0/+42
2018-01-02package py-biopython: remove py-mx dependency (#6772)Eric1-1/+0
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