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2018-05-31improve Advanced Compiler Configuration part of tutorial (#8325)Denis Davydov1-2/+21
2018-05-31latte: specify blas and lapack explicitly (#8327)Massimiliano Culpo1-0/+5
2018-05-30more-flexible user-specified dependency constraints (#8162)scheibelp3-17/+80
* allow user to constrain dependencies that are added conditionally * remove check for not-visited deps from normalize, move it to concretize. The check now runs after the concretization loop completes (so an error is only reported if the user-mentioned spec doesnt appear anywhere in the dag) * remove separate full_spec_deps variable; rename spec_deps to all_spec_deps to clarify that it merges user-specified dependencies with derived dependencies * add unit test to confirm new functionality
2018-05-30trimgalore: Use perl from env (#8318)Eric1-0/+2
2018-05-30fastqc: Add version 0.11.7 (#8319)Eric1-0/+1
2018-05-30config: add `spack config blame` command (#8081)Todd Gamblin5-10/+339
- `spack config blame` is similar to `spack config get`, but it prints out the config file and line number that each line of the merged configuration came from. - This is a debugging tool for understanding where Spack config settings come from. - add tests for config blame
2018-05-30Document specs with multiple version ranges (#8284)Adam J. Stewart1-0/+8
2018-05-30Update package: add info for emacs@26.1 (#8302)George Hartzell1-2/+7
* Update package: add info for emacs@26.1 In addition to the digest, it needs gnutls (perhaps there's a way to turn it off, but it seems like a Good Thing to encourage, so...). * Clean up tls variant handling - Don't to specify the dependency for @26.1:, just need to fix what's already there. - Don't assume that configure will DTRT w.r.t. gnutls when it's discovered in the environmnet, use explicit configure switches. - Clean up some unnecessary dependencies when +tls. Why would you need libxpm when building +tls? Will ask the original author about this. * Use append when adding configure switches * Add dependency on pcre When one builds +X, Spack's pcre is pulled into the build via the X dependencies. When one builds without it, the build discovers and links against the system library. We might as well just depend on it and have a consistent outcome.
2018-05-30paraview: set PARAVIEW_VTK_DIR in spack_env and run_env (#8308)Daryl W. Grunau1-0/+11
2018-05-29Add info for bedops@v2.4.35 (#8310)George Hartzell1-0/+1
2018-05-29new version: Phist 1.6.0 (#8312)jthies1-0/+1
* gmp: add oldish version 5.1.3 with checksum * new version phist 1.6.0
2018-05-29Add umpire package (#8229)David Beckingsale1-0/+61
* Add umpire package * Style fixes * Add package URL
2018-05-29perl: Fix build on Fedora 28 (#8305)Michael Kuhn1-0/+4
2018-05-29python: Update to 2.7.15 (#8306)Michael Kuhn1-1/+2
2.7.14 does not compile with GCC 8, see https://bugs.python.org/issue33374.
2018-05-29nasm: Fix compilation with GCC 8 (#8307)Michael Kuhn1-0/+4
2018-05-29Quantum espresso (#8183)nvarini3-9/+20
Changed the name from espresso to more appropriate quantum-espresso. Added github mirror.
2018-05-28py-pillow : update version and fix jpeg dependency (#8300)Sajid Ali1-14/+6
* modified: package.py * as requested.
2018-05-28Add far variant to openfst package (#8299)Jimmy Tang1-0/+11
* Add far variant * Append instead of extend
2018-05-28abinit: added version 8.8.2 (#8294)Massimiliano Culpo1-0/+1
2018-05-28nwchem: added version 6.8 (#8295)Massimiliano Culpo1-0/+2
It seems that the new versions on github don't require the patching that was needed in previous versions.
2018-05-28plumed: added versions 2.4.1 and 2.3.5 (#8297)Massimiliano Culpo1-0/+2
2018-05-28yambo: added versions 4.2.2 (#8298)Massimiliano Culpo1-0/+1
2018-05-26Add JasPer 2.0.14 (#8207)Adam J. Stewart1-14/+77
* Add JasPer 2.0.14 * Remove no longer necessary patch * Explicitly disable generation of documentation * Re-add support for JasPer 1.900.1, add GDAL patch * Remove GDAL patch
2018-05-26Add GDAL 2.3.0 (#8263)Adam J. Stewart2-46/+592
* Add GDAL 2.3.0 * Add missing dependencies, change default variants, and add links * GDAL requires old hacked version of JasPer * Move JasPer patch to GDAL
2018-05-26Fix compilation of FYBA with GCC 6 (#8273)Adam J. Stewart2-0/+22
2018-05-26Fix gettext: Problem with libxml2 (#8132)Elizabeth Fischer1-1/+3
* See https://github.com/spack/spack/issues/2882 * code review * Correctly access lib directory
2018-05-26Fix OpenCV JasPer disable (#8287)Corey McNeish1-10/+10
The recipe previously did not include -DWITH_JASPER Other edits: * BUILD_IPP_IW is BUILD instead of WITH; it was in a different section of the CMakeLists.txt. Move it to the top * Several options were missing :BOOL, add them * -DWITH_ZLIB doesn't actually exist as an option, at least in the latest version.
2018-05-25Added new package Camellia. (#8190)Nate Roberts1-0/+61
* Added new package Camellia. * Fixed an issue with a missing blank line. Added a couple more Trilinos packages (things I expect to depend on eventually). * Fixed a couple issues raised by @adamjstewart. * Specified 4.9.2 as the supported MOAB version. 5.0.0 causes build issues on Macs during the link of Camellia's drivers. The issue is that we end up with -framework -lAccelerate in the link line, where it should read -framework Accelerate, I believe. I'm not sure where this comes from, but 4.9.2 does not have this issue. * Trimmed slightly the Trilinos requirements. Also deleted a blank line that had spaces in it because the Travis-CI thing didn't like that. * Reduced length of MOAB description (Travis-CI complained). * Reduced the MOAB line further; didn't quite get there last time! This is to satisfy Travis-CI's requirement that the description be less than 80 characters long (E501). * Put in my GitHub handle, in place of an allusion to my email address. Also added a new argument for Camellia build, and made the MOAB description longer (thanks to @adamjstewart's note that long lines are allowed so long as they are not split). * Added MPI dependency. Added explicit OFF for MOAB enablement when ~moab. Swapped order of variant and version.
2018-05-25repeatmasker: fix bin location and dependency (#8286)Levi Baber1-1/+2
2018-05-25flang: add non-develop version (#8276)Andrey Prokopenko1-1/+2
2018-05-25perl-text-soundex: new package (#8279)Levi Baber1-0/+37
* perl-text-soundex: new package * perl-text-soundex: formatting
2018-05-25hdf5: add 1.10.2 (#8274)David Guibert1-0/+1
2018-05-24Add Tophat v2.1.2, fixes automake issues (#8266)George Hartzell1-1/+6
* Add Tophat v2.1.2, fixes automake issues The Tophat team merged the patch from https://github.com/spack/spack/pull/8244 and release v2.1.2 This change requires the old automake if you're building the older release and is relaxed about the automake it requires if you're building the v2.1.2 release. Building v2.1.1 and v2.1.2 works on a CentOS 7 system, I don't have the necessary bit to actually test the resulting binaries. Here's the commit note from the change that was ultimately merged upstream. Fixes #8025 > Tophat was failing to build with automake@1.16.1, it worked with the > older automake@1.15.1. This commit adds a patch to Tophat's > src/Makefile.am which cleans up a few things. The result builds > successfully with both automake@1.15.1 and automake@1.16.1. I have no > way to check that the resulting builds Do The Right Thing. > > It changes two things: > > the original Makefile.am had a rule for $(SAMPROG) with no > actions, and since there was a directory there with a tempting name > the newer automake was trying to do something with it, but lacked > the appropriate clues. Since that target is actually made as a side > effect of making the library (sigh...), it seems to work to just > give that rule something harmless to do (the Peter Principle > triumphs again...). > > a bunch of the targets need a libtophat.a and libgc.a; the older > automake was probably able to guess what to do given the list of > sources but the newer automake apparently won't make the necessary > assumptions. This patch wires up a simple rule and cleans up the > appropriate dependencies so that things work. > > While it may appear that I'm someone who understands automake, keep in > mind that I only play such a person on a TV reality show. YMMV. * Remove extraneous when constraint
2018-05-24Added gsl dependency to pnfft (#8255)Luca Heltai1-0/+1
2018-05-24Fix missing spack.compiler import (#8240)Michael Kuhn1-0/+1
Fixes: #8258 #8090 altered import behavior so that import spack no longer provides access to many other Spack modules. This addresses a case which depended on the prior behavior and was not updated as part of #8090. This particular import error only came up when users were setting compiler flags on specs. See also: #8194
2018-05-24kokkos: update kokkos spackage to add current host/gpu architectures. (#8226)Geoff Womeldorff1-1/+49
* kokkos: update kokkos spackage to add current host/gpu architectures. * kokkos: simplify host/gpu architecture selection and make intent of arg population logic more clear. * kokkos: mollify flake8. * Make strings and logic more pythonic. Add error for GPU arch without CUDA. * kokkos: simplify conflicts behaviour. make args population more pythonic. * kokkos: move gpu values to list for use in variant and conflicts checking. * kokkos: How fortunate the man with None. * kokkos: fix gpu_arch conflict loop error. add conflict to guard against +cuda and 2.5.00:develop versions, until kokkos issue #1296 is resolved. * kokkos: mollify flake8. * kokkos: add descriptive message to version conflict with +cuda.
2018-05-24Charm++: Add possibility to build git version (#8260)Matthias Diener1-1/+7
2018-05-24Add msgpack-c 3.0.1 (#8264)Sajid Ali1-1/+2
* new file: cpp-3.0.1.tar.gz modified: package.py * deleted: cpp-3.0.1.tar.gz * remove whitespace
2018-05-24trf: make executable (#8265)Levi Baber1-0/+2
2018-05-24openfoam-org: add v2.4.0 (#7850)Chris Hadjigeorgiou2-11/+118
Add 2.4.0 changes
2018-05-24Fix MD5 hash for opencv 3.2.0 and 3.1.0 release (#8241)jkelling1-2/+2
2018-05-23Add info for datamash@1.3 (#8261)George Hartzell1-0/+1
2018-05-23Add kealib 1.4.7 (#8235)Adam J. Stewart2-7/+83
* Add kealib 1.4.7 * Fix out-of-source builds * Remove username from kealib hg clone
2018-05-23Add PROJ 5.0.1 (#8233)Adam J. Stewart1-3/+22
* Add PROJ 5.0.1 * proj-datumgrid resource must be placed in nad directory
2018-05-23mvapich2: added a proper libs attribute (#8253)Massimiliano Culpo1-0/+12
2018-05-23Add pkgconf 1.4.2 (#8256)Adam J. Stewart1-3/+7
2018-05-23Add ncurses 6.1 (#8257)Adam J. Stewart1-1/+2
2018-05-23charm: Update install script (#7291)Edward Kim1-45/+94
* charm: Update install script * Addressed PR comments * Removed destination and suffix variants * Added back parallel support
2018-05-23gromacs: added version 2018.1 (#8251)Massimiliano Culpo1-0/+1
2018-05-23cgal: added version 4.12 (#8252)Massimiliano Culpo1-0/+1