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2017-08-03New package for canu (#4937)George Hartzell1-0/+61
* Add package for canu There's a top-level perl script, which is touched up to use a spack-built perl instead of `#!/usr/bin/env perl`. It's self-contained, it uses `FindBin` to locate it's libaries. * Add dependency on gnuplot I noticed a hidden mention of the use of gnuplot in the docs. This adds the dependency. * Tighten dependencies, flake8 cleanup gnuplot is a run dependency. jdk is a run dependency. perl is a run dependency. Make flake8 happy.
2017-08-03Account for hyphens in package names when searching for libraries. (#4948)Sergey Kosukhin1-1/+12
2017-08-02Protobuf: CMake (#4846)Axel Huebl2-15/+71
* Protobuf: CMake This rebuilds protobuf to be build with CMake, so cmake config packages are created and installed, too. Unfurtunately, this drops support for protobuf < 3. * Protobuf CMake: Add .pc files * libprotobuf.a: -fPIC * Protobuf: Minor Updates Updates from upstream review and planned patch inclusion.
2017-08-01Fix color bug in Spec.format() introduced by #3013Todd Gamblin1-6/+3
2017-08-01Add `spack dependencies` command and tests for it and dependents.Todd Gamblin7-15/+261
2017-08-01document and make `display_specs` more versatileTodd Gamblin2-14/+48
2017-08-01Fix issue with case check and `spack -m`Todd Gamblin1-1/+5
2017-08-01Refactor installed_dependents -> installed_relativesTodd Gamblin4-15/+34
2017-08-01Package.possible_dependencies() descends into virtuals.Todd Gamblin1-1/+10
2017-08-01Add --transitive option to `spack dependents`Todd Gamblin2-8/+18
2017-08-01spack dependents lists possible dependencies by default.Todd Gamblin1-25/+37
2017-08-01Remove last vestiges of "special" deptypes.Todd Gamblin4-36/+64
- Remove `special_types` dict in spec.py, as only 'all' is still used - Still allow 'all' to be used as a deptype - Simplify `canonical_deptype` function - Clean up args in spack graph - Add tests
2017-08-01Remove unused code.Todd Gamblin1-4/+0
2017-08-01Add --all argument to `spack dependents`Todd Gamblin1-6/+56
--all causes spack dependents to list all possible dependents for a package, rather than actual dependents for an installed spec.
2017-08-01Fix xsdk build broken by petsc and trilinos (#4893)Alicia Klinvex2-3/+3
* Fix xsdk build broken by petsc and trilinos See #4891 for details * Fix version conflict in trilinos package Trilinos version 11 may conflict with superlu-dist. The version "xsdk-0.2.0" was conflicting with superlu-dist, even though it shouldn't. I added a lower bound to the comparison to fix this problem. Thanks for the help @davydden!
2017-07-31Clarify docs on using a hash in a spec (#4908)Adam J. Stewart1-7/+36
2017-07-31Fix preference for X.Y version when mixed with X.Y.Z versions (#4922)scheibelp3-1/+50
For packages which contain a mix of versions with formats X.Y and X.Y.Z, if the user entered an X.Y version as a preference in packages.yaml, Spack would get confused and favor any version A.B.Z where X=A and Y=B. In the case where there is a mix of these version types, this commit updates preferences so Spack will favor an exact match.
2017-07-31Add --color=[always|never|auto] argument; fix color when piping (#3013)paulhopkins14-45/+105
* Disable spec colorization when redirecting stdout and add command line flag to re-enable * Add command line `--color` flag to control output colorization * Add options to `llnl.util.tty.color` to allow color to be auto/always/never * Add `Spec.cformat()` function to be used when `format()` should have auto-coloring
2017-07-31Add latest version of SCons (#4929)Adam J. Stewart1-2/+7
2017-07-31ZeroMQ: C++ Headers (cppzmq) (#4841)Axel Huebl1-0/+40
Adds the cppzmq library, adding a C++ API to ZeroMQ (libzmq). In order to find the autotools-build libzmq, this requires the upcoming cppzmq release (or development branch).
2017-07-31Add missing dependencies to unixodbc (#4928)Adam J. Stewart1-0/+3
2017-07-31Add latest version of expat (#4930)Adam J. Stewart1-1/+3
2017-07-31Add latest version of apr (#4931)Adam J. Stewart1-9/+5
2017-07-31zsh: add variant that skips tcsetpgrp test (#4923)George Hartzell1-0/+16
zsh's configure script fails if there's it tries to test for terminal functionality if there's not a terminal (e.g. in a Jenkins build). The configure script has a switch that asserts that tcsetpgrp works and thereby avoids running that test. This commit adds a variant that invokes that switch, defaulting to True.
2017-07-31gBenchmark: v1.2.0 (#4935)Axel Huebl1-0/+3
Adds a the latest version of gBenchmark, release 1.2.0. This is the first gBenchmark version with proper [CMake config package installs](https://github.com/google/benchmark/issues/363). This is important for dependencies building against it, such as gRPC.
2017-07-28Initial Spackage for qmd-progress library (#4924)Robert Pavel1-0/+62
* Initial Spackage for qmd-progress library PROGRESS is a library is focused on the development of general solvers that are commonly used in quantum chemistry packages. * Removed LA-CC from description to fix formatting * Added Additional Formatting Requests Added requested formatting changes and also ensured that graphlib and mpi are disabled if not enabled
2017-07-28Fix for m4%clang (#4912)sknigh1-0/+3
* Fix for m4%clang * Restricted condition to not subsitute rtlib on OSX
2017-07-27Adding QWT package. (#4911)Jon Rood1-0/+50
* Adding QWT package. * Using builtin file filtering. * Formatting.
2017-07-27bml: fix homepage (#4918)Christoph Junghans1-1/+1
2017-07-27Added Proxy App tag (#4917)Akhil Reddy Patlolla1-0/+1
* Added Proxy App tag * NO changes except proxy app tag
2017-07-27New Package: lcals (#4792)pkondamudi1-0/+122
* New Pacakge: lcals * added logic for arch detection and compiler choice. * fixes for comments. * addressed comments. * removed LCALS_ARCH and added flags though spack. * addressed comments. * flake 8 fix. * reerted the changes along with comments.
2017-07-27Fix for Krell openspeedshop spack package bug. New multi-value variant for ↵Jim Galarowicz1-58/+40
GUI build. (#4880) * Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies. * Add libxml2+python depends on to get around issues with the libxml2 package file. * Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build. * Fix bad syntax in specifying the boost version range. * Update the version numbers for the krell institute components and tools: cbtf and openspeedshop. * Do not build glib for qt3, it is not needed and causes build problems at this time anyway. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Trim comments to fit more concisely. * Fix tabs versus spaces and swap if and else clause check from a negative to a positive check. * Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build. * Fix issues with the cbtf-argonavis package.py files related to comments. * Add changes for changing the krell packages from Package to CMakePackage. * Add better changes for changing the krell packages from Package to CMakePackage. * Add more modifications for changing the krell packages from Package to CMakePackage. * Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros * Fix new travis errors. * Fix new travis errors. * Add more changes for PR 4765. * Add more refinements to the conversion from Package to CMakePackage. * Fix new travis errors. * Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop. * Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue. * Fix more flake issues caused by last changes. * Fix a bug where openspeedshop will not build when no mpi variants are specified. Also switch to a multiple level variant for building the gui(s). Use none, qt3, and qt4 as the variants with qt3 being the default. * Add fix for spack issue #4843, where LTDL include files were not found. * Add the build_type variant back into the openspeedshop package file.
2017-07-27New Package: RSbench (#4752)pkondamudi1-0/+66
* New Package: RSbench * minor change * removed tags as per PR# 4749 * addressed comments and added gcc compiler. * added proxy app tags to description. * removed setting CC to pgicc through spec. * removed compiler as depedency * removed pgi variant. * flake 8 fix. * added mpi depedency with pgi compiler * added pgi compiler * removed PGI compiler as depedency. * added tags and addressed other code formattings. * added tags and addressed other code formattings. * addressed comments.
2017-07-27openblas: add 0.2.20 (#4915)Denis Davydov1-0/+1
2017-07-26snptest: new package (#4900)Audrey Thoma1-0/+39
* snptest: new package * fixed version things * fixed install phase
2017-07-26Improve version detection for URLs with dynamic after version (#4902)Adam J. Stewart2-1/+4
2017-07-26Updated Namespace of BML Repository (#4910)Robert Pavel1-4/+4
2017-07-26added MPI dependency to Nekbone package (#4903)pkondamudi1-0/+5
* removed the tags as per comment in PR# 4749 * addressed above comments * changed fortran compiler. * added proxy application tags. * added tags by removing them from description. * addressed comments * used join_path instead of path concat. * removed the tags as per comment in PR# 4749 * addressed above comments * changed fortran compiler. * added proxy application tags. * added tags by removing them from description. * addressed comments * used join_path instead of path concat. * added tags. * changes to use MPI as depedency. * removed MPI as variant. * changed pointer to filtered makenek file. * flake 8 fix.
2017-07-26shortstack: new package (#4905)Audrey Thoma1-0/+45
2017-07-25Add universal build_type variant to CMakePackage (#4797)Adam J. Stewart46-319/+68
* Add universal build_type variant to CMakePackage * Override build_type in some packages with different possible values * Remove reference to no longer existent debug variant * Update CBTF packages with new build_type variant * Keep note on build size of LLVM
2017-07-25tmux should not set PKG_CONFIG_PATH (#4901)Sam Bateman1-13/+3
* fixes #967 * Version bump to 0.9.1 - Bugfixes for spack find - 0.9.1 can read specs from current develop. * Don't assume spack is in the path when building docs. * Remove PKG_CONFIG_PATH from tmux configure * Change tmux to AutotoolsPackage * Correct link to libtinfo in tmux
2017-07-25fix callpath bug (#4659)becker331-1/+3
* fix callpath bug I found while testing env/cc * fix hanging indent for flake
2017-07-25transdecoder: new package (#4895)Audrey Thoma1-0/+50
* transdecoder: new package * fixed package structure
2017-07-25transposome: new package (#4896)Audrey Thoma1-0/+37
2017-07-25trimgalore: new package (#4899)Audrey Thoma1-0/+44
2017-07-25fix config.guess patch for ppc64le (#4858)Gregory Lee1-15/+3
* fix config.guess patch for ppc64le * explicit patch for config.guess not required
2017-07-25cleaveland4: new package (#4894)Audrey Thoma3-0/+150
* cleaveland4: new package * fixing return line in viennarna url_for_version
2017-07-25tabix: new package (#4886)Audrey Thoma1-0/+50
* tabix: new package * fixed docs location
2017-07-25sumaclust: new package (#4884)Audrey Thoma1-0/+42
* sumaclust: new package * tweaking url and make specs
2017-07-25Update zstd version (#4873)Jimmy Tang1-4/+2
* Update zstd version * Change order of versions * Use MakefilePackage
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