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2019-01-09tutorial basics section: fix gcc install version (#10298)Greg Becker1-1/+1
2019-01-09petsc: fix petsc+debug to not reset COPTFLAGS - i.e use configure defaults ↵Satish Balay1-4/+6
'-g' (#10296)
2019-01-09eospac version bump to 6.4.0beta.4 (#10294)Daryl W. Grunau1-0/+2
2019-01-09elfutils: option to install elf.h header file (#10185)Mark W. Krentel1-3/+8
* elfutils: option to install elf.h header file Add variant 'elfh' (default False) to install the elf.h header file to the include directory. This provides access to a newer version of elf.h and allows an elf application to build with the same elf.h that libelf.so was built with. Add version 0.175. * Drop the variant 'elfh' and always install elf.h instead.
2019-01-09py-pyyaml: Add version 3.13 (#10293)Eric1-0/+1
2019-01-09R: add version 3.5.2 (#10292)Simon Flood1-0/+1
2019-01-09New package: git-fat-git (#10266)Andreas Baumbach1-0/+26
* new package: git-fat * backport of rsync -> older versions no longer available Change-Id: I3a41f17df0f88ca11e08ea6fd2f2d381435e0f09 * fix legal stuff and use new git attribute Change-Id: Ice156dfe8ad4137a861f7b2938ee92f4024142be * use date as version number rather than hash Change-Id: Ib537659e368f69124895306d6a6ac0c5e36061a7 * only use the date once Change-Id: I2592fa28aaa53fed949ddc82959d712ff3f6f752
2019-01-09gromacs: added simd and rdtscp variants + version 2019 (#9931)marvinbernhardt1-2/+24
2019-01-08OpenMPI: Add Development Version (#10257)Axel Huebl1-0/+14
Add the development version of OpenMPI from the git repo in `master`.
2019-01-08Updated fish to 3.0.0 (#10286)sknigh1-0/+1
2019-01-08bug fix: copy permissions when staging (#10285)Owen Solberg1-3/+3
Fixes #10284 #10152 replaced shutil.move with llnl's copy and copy_tree for resources. This did not copy permissions so led to later failures if an executable was copied (e.g. a configure script). This uses install/install_tree instead, which preserve permissions.
2019-01-08Armcompiler (#9840)Srinath Vadlamani6-27/+29
* Initial compiler support * added arm.py * Changed licence to Arm suggested header * Changed licence to the same as clang.py Main author of file is Nick Forrington <Nick.Forrington@arm.com> Minor changes by Srinath Vadlamani <srinath.vadlamani@arm.com> * compilers: add arm compiler detection to Spack - added arm.py with support for detecting `armclang` and `armflang` Co-authored-by: Srinath Vadlamani <srinath.vadlamani@arm.com> * Changed to using get get_compiler_version * linking to general cc for arm compiler * For arm compiler add CFLAGS to use compiler-rt rtlib. * Escape for special characters in rexep * Cleaned up for Flake8 to pass. * libcompiler-rt should be part of the LDFLAGS not CFLAGS * fixed m4 when using clang to used LDFLAGS. Fixed comments for arm.py to display compiler --version output with # NOAQ for flakes pass. * added arm compilers * proper linked names
2019-01-08r-ape: new versions (#10258)Owen Solberg1-3/+5
* updated versions for r-ape * added type=('build', 'run') to r dependency
2019-01-08r-cowplot: new versions, more specific dependencies (#10259)Owen Solberg1-4/+10
* updated versions for r-cowplot * depends_on: added type=('build', 'run') to r, and added r-scales
2019-01-08r-data-table: new versions (#10260)Owen Solberg1-5/+14
* updated versions for r-data-table * added type=('build', 'run') to r dependency
2019-01-08r-dbplyr: new versions (#10262)Owen Solberg1-9/+14
* added new versions, and tightened up depends_on() specs * added type=('build', 'run') to r dependency
2019-01-08New package: MGIS (#10273)thelfer1-0/+73
* add the tfel package * fix the tfel package * fix the tfel package * fix the tfel package * Taking Adam J. Steward' remarks into account * fixes trailing white spaces * Update description * Update dependencies following @adamjstewart adices * Style fixes * Style fixes * Add java optional support * add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice) * flake8 fixes * Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL) * Style fixes * Style fixes * Fix test on python version * Follow @adamjstewart advices: code is much cleaner and readable * Small fix * Small fix * Add comment * Small fix in cmake option * try again (trying to overcome Travis CI unstable build process) * Add support for the MFrontGenericInterfaceSupport project (MGIS) * Style fixes * Package documentation update * Package documentation update * Fix a typo thanks to Andreas Baumbach review * Follow Adam J. Stewart advices * Fix type
2019-01-08usearch: Make installed binary executable (#10269)Eric1-0/+2
* usearch: Make binary executable * usearch: remove join_path
2019-01-08Added bash 5.0 (#10282)sknigh1-0/+1
2019-01-08r-dt: new versions (#10261)Owen Solberg1-3/+7
* updated release and checksums, also tightened depends_on() * remove blank line at end of file * removing new version 0.5
2019-01-08updated versions (#10263)Owen Solberg1-6/+10
2019-01-08updated versions and depends_on() (#10264)Owen Solberg1-17/+18
2019-01-08added openpa package (#10265)dorier1-0/+19
2019-01-08libzip: Add zlib dependency (#10270)Eric1-0/+2
* libzip: Add zlib dependency * libzip: Add version limit
2019-01-08new version 1.0.1 for py-html5lib (#10278)Andreas Baumbach1-1/+6
Change-Id: I2837dc098fce142b152d2969687d1873e182bbc8
2019-01-08Check for ARM compiler in addition to clang (#10280)Ross Miller1-1/+2
Add "-rtlib=compiler-rt" to CFLAGS when building with either Clang or the ARM compiler. Refs #10279
2019-01-08salmon: Add version 0.12.0 (#10271)Eric0-0/+0
2019-01-08go: add 1.11.4 (#10272)Michael Kuhn1-0/+1
2019-01-08new package: py-webencodings (#10277)Andreas Baumbach1-0/+18
Change-Id: Icf20035367a34fa88acfef2d3fa3742c3f3901ac
2019-01-07For spec-file-based installs, store the initial spec read from the file as ↵Peter Josef Scheibel1-0/+1
the abstract spec
2019-01-07bowtie: new versions and %gcc@8.0.0: fix (#10232)George Hartzell2-3/+50
* bowtie: new versions and %gcc@8.0.0: fix Bowtie development shifted from Sourceforge to GitHub. This commit adds several versions from GitHub, using the archive tarballs. Note that the URL for 1.2.2 tarball is actually an '_p1' tag.... It leaves the old 1.2 release download info in place. Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and 1.2.0 are equivalent). Include a fix that enables %gcc@8.0.0: from: https://github.com/BenLangmead/bowtie/issues/87 But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for %gcc@6.0.0:. Feel free to tighten this. I know that: - 1.2 -> 1.2.2 work with %gcc@5.5.0; - 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and - 1.2.2 fails with %gcc@8.2.0 * Tighten to `conflicts('%gcc@8:', when='@1.2.2')` * Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
2019-01-07doxygen: URL and version hashes updated to project's GitHub home (#10250)Chad Wood1-7/+9
* Update package.py Doxygen has migrated from a private SVN to GitHub. This PR updates the URLs and adds versioned commit hashes from GitHub. It also includes version 1.8.15 as the latest option. * Update package.py
2019-01-04Multi-valued variants: better support for combinations (#9481)Massimiliano Culpo24-89/+585
This enforces conventions that allow for correct handling of multi-valued variants where specifying no value is an option, and adds convenience functionality for specifying multi-valued variants with conflicting sets of values. This also adds a notion of "feature values" for variants, which are those that are understood by the build system (e.g. those that would appear as configure options). In more detail: * Add documentation on variants to the packaging guide * Forbid usage of '' or None as a possible variant value, in particular as a default. To indicate choosing no value, the user must explicitly define an option like 'none'. Without this, multi-valued variants with default set to None were not parsable from the command line (Fixes #6314) * Add "disjoint_sets" function to support the declaration of multi-valued variants with conflicting sets of options. For example a variant "foo" with possible values "a", "b", and "c" where "c" is exclusive of the other values ("foo=a,b" and "foo=c" are valid but "foo=a,c" is not). * Add "any_combination_of" function to support the declaration of multi-valued variants where it is valid to choose none of the values. This automatically defines "none" as an option (exclusive with all other choices); this value does not appear when iterating over the variant's values, for example in "with_or_without" (which constructs autotools option strings from variant values). * The "disjoint_sets" and "any_combination_of" methods return an object which tracks the possible values. It is also possible to indicate that some of these values do not correspond to options understood by the package's build system, such that methods like "with_or_without" will not define options for those values (this occurs automatically for "none") * Add documentation for usage of new functions for specifying multi-valued variants
2019-01-04mvapich2: add missing zlib dependency (#10254)Michael Kuhn1-0/+1
2019-01-04Added package osmctools (#10249)Elizabeth Fischer1-0/+23
* Added package osmctools * Simplified Removed functions that did the same as existing defaults * flake8
2019-01-04Add tests for expanding/non-expanding resourcesPeter Josef Scheibel1-3/+92
2019-01-04stage: fix resources being deleted from local cache (#10152)Michael Kuhn1-4/+9
Non-expanded resources were being deleted from the cache on account of two behaviors: * ResourceStage was moving files rather than copying them, and uses "os.path.realpath" to resolve symlinks * CacheFetchStrategy creates a symlink to a cached resource rather than copying it This alters the first behavior: ResourceStage now copies the file rather than moving it.
2019-01-04Fix download path, the existing one has been removed from nvidia's site (#10253)Jimmy Tang1-1/+1
2019-01-03openssl: add location of system certificates for SUSE Linux (#10242)Neil Flood1-1/+3
2019-01-03Add missing code block (#10243)Ben Zwick1-0/+2
Otherwise the `--` in `--dot` is rendered as a single en-dash.
2019-01-02patch: split up fetch and clean into separate methods (#10150)Michael Kuhn5-50/+71
"mirror create" was invoking a package's do_patch method in order to retrieve and archive URL patches. If a package implements a "patch" method, this is also called as part of do_patch; this failed when the package-specific implementation referred to environment variables that are only available at the time the package is built (e.g. "spack_cc"). This change introduces fetch and clean methods for patches. They are no-ops for FilePatch but perform the appropriate actions for UrlPatch. This allows "mirror create" to invoke do_fetch, which does not call the package's patch method.
2019-01-02Catch2: v2.5.0 (#10237)Axel Huebl1-0/+1
Add the 2.5.0 release of catch2.
2019-01-02petsc4py: new versions (up to 3.10.0) and update website (#10238)Ben Zwick1-5/+15
2019-01-02slepc4py: new versions (up to 3.10.1) and update website (#10239)Ben Zwick1-3/+20
2019-01-01PARALLEL-NETCDF: Update new version and location (#10172)Greg Sjaardema1-6/+19
* PARALLEL-NETCDF: Update new version and location PnetCDF-1.11.0 is released. Also, the canonical download area has been changed and they are now using git, so can also provide a develop and master checkout. One issue is that they changed the name of the tar files, so 1.11.0 needs special handling (and future versions will also). All checksums at new location match the checksums from the old location. * Address concerns in review Added a `url_for_version` function to handle the name change in the tar files at version 1.11.0 and later. Updated description to match current shown on website. Updated `homepage` setting since it has recently moved. * Address issues in second review
2019-01-02Removed an extra comma after a dict literal (#10236)Massimiliano Culpo1-1/+1
The extra comma was turning a dict into a tuple, and caused errors during validation of the schema.
2019-01-01FEniCS: workaround concretization issue with PETSc (#10235)Ben Zwick1-1/+3
2019-01-01Add list_url for r-readr, finding old versions (#10231)George Hartzell1-0/+1
r-tidyverse needs r-readr@1.1.1, r-reardr needs a list_url so that it can find it.
2019-01-01README: LLNL release number and SPDX id don't need to be monospaced.Todd Gamblin1-2/+2
2019-01-01flake8: fix flake8 issues with invalid escapesTodd Gamblin22-148/+161
- in many files, regular strings were used in places where raw strings should've been used. - convert these to raw strings and get rid of new flake8 errors