Commit graph

10826 commits

Author SHA1 Message Date
Javier Cervantes
9b1690641b Fix bug getting specs from build caches (#9600) 2019-02-15 13:33:49 -06:00
Scott Wittenburg
75487dca44 CDash: allow installing from spec.yaml (#10565)
If the -f <specyamlfile> argument to install is used (rather than
providing package specs on the command line), CDash throws an exception
due to missing the installation command (the packages targeted for
install).  This fixes that behavior so CDash reporting succeeds in
either case.
2019-02-14 17:43:53 -06:00
Cameron Smith
a06bf21610 new variant: simmodsuite for pumi (#8775) 2019-02-14 21:36:56 +01:00
Massimiliano Culpo
1ec0d4feb3 Removed pkg.headers.directories from the include list (#10604)
fixes #10601

Due to a bug this attribute is wrong for packages that use directories
as namespaces. For instance it will add "<boost-prefix>/include/boost"
instead of "<boost-prefix>/include" to the include path.

As a minor addition a few loops in the compiler wrappers have been
simplified.
2019-02-14 08:35:41 -08:00
Massimiliano Culpo
b3dd95bd62
cp2k is now a MakefilePackage (#10570)
* cp2k: archive the Makefile after a successful installation

* cp2k: all checksums are now sha256

* libint: all checksums are now sha256 + added versions 2.4.X

* libxc: all checksums are now sha256 + added version 4.3.2

* cp2k: os.path.join instead of join_path + simplified openmp flags

* cp2k: turned into a MakefilePackage

* cp2k: refactored edit method so that Makefile writing happens last
2019-02-14 07:11:20 +01:00
Chris Green
051c66335f pythia6: fix input verification issue and example data checksum. (#10563)
* pythia6: fix issue validating integer input.

* pythia6: account for apparent update of example data file.
2019-02-13 23:17:46 -06:00
Chris Green
24d7f0f0af xrootd: allow specification of C++ standard. (#10577)
* xrootd: add cxxstd variant.

* xrootd: support for recent and upcoming versions.
2019-02-13 23:17:10 -06:00
Ben Morgan
7e8b8d61a1 icu4c: Add cxxstd variant (#10552)
* icu4c: Add cxxstd variant

For versions supported in Spack, ICU4C defaults to the C++11.
Provide a variant to default to this, plus options for C++14
and 17 if dependees require for ABI compatibility.

* icu4c: cxxstd variant cannot be multi
2019-02-13 23:05:39 -06:00
Hadrien G
6e95e06bda Add Gaudi and RELAX packages (#9194)
* Add a RELAX package

* Add a Gaudi package
2019-02-13 23:04:38 -06:00
Hadrien G
54f94e5828 Add a DD4hep package (#9208) 2019-02-13 22:58:27 -06:00
Hadrien G
0e0e7d4137 Add new ROOT release, move to SHA-256 checksums (#10583) 2019-02-13 22:54:45 -06:00
Patrick Gartung
0748a32b2d
Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant (#10518)
* Updated Geant4 and dependencies clhep and vecgeom to use cxxstd= variant so that it is applied consistently.

* Make standalone geant4 data packages that are used when data is not installed with geant4. This allows installing the data files are externals that can be common to many compiler version.

* move geant4 data package dependencies to umbrella package geant4-data
2019-02-13 22:51:26 -06:00
Phil Carns
6971f8ae32 make SPACK_SHELL detection more robust (#9712)
Spack shell detection in setup-env.sh was originally based on
examining the executable name of $$ (from "ps"). In some cases this
does not actually give the name of the shell used, for example when
setup-env.sh was invoked from a script using "#!". To make shell
detection more robust, this adds a preliminary check for shell
variables which indicate that the shell is bash or zsh; the
executable name of $$ is retained as a fallback if those variables
are not defined.
2019-02-13 19:52:18 -06:00
Peter Scheibel
8ca384875e
Dynamic library/include paths (#8136)
Fixes #7855
Closes #8070
Closes #2645

When searching for library directories (e.g. to add "-L" arguments to
the compiler wrapper) Spack was only trying the "lib/" and "lib64/"
directories for each dependency install prefix; this missed cases
where packages would install libraries to subdirectories and also was
not customizable. This PR makes use of the ".headers" and ".libs"
properties for more-advanced location of header/library directories.
Since packages can override the default behavior of ".headers" and
".libs", it also allows package writers to customize.

The following environment variables which used to be set by Spack
for a package build have been removed:

* Remove SPACK_PREFIX and SPACK_DEPENDENCIES environment variables as
  they are no-longer used
* Remove SPACK_INSTALL environment variable: it was not used before
  this PR
2019-02-13 17:38:14 -06:00
Peter Doak
1bf86292e1 add latest version of pixman (#10580) 2019-02-13 21:26:51 +01:00
Hadrien G
9374adb455 Eigen package: deactivate some dependencies (#10572)
Set defaults in eigen package to omit typically-unused dependencies
2019-02-13 13:33:01 -06:00
Brian Van Essen
406a242847 Update lbann sw stack dependencies (#10579)
* Added a package for the MDAnalysis toolkit.

* Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI
even when using CUDA.  Fixed small bugs within both LBANN and Hydrogen
packages.  Added requirements for breathe and cereal to LBANN.

* Update use case for doc dependencies.

* Cleaning up some of the LBANN software stack dependencies.
2019-02-13 11:19:15 -08:00
abernede
89727ba4e7 Bug Fix in permission setter (#10584)
* fix permission setter

Fix a typo in islink test when applied to files.

* os.walk explicitly set not to follow links

The algorithm strongly rely on not following links.
2019-02-13 11:18:36 -08:00
sknigh
a76c50d1ee Allow tty output to be timestamped (#10554)
* Spack debug output now includes microsecond-granularity timestamps.
* Timestamps can also be enabled with the `--timestamp` command line argument.
2019-02-13 10:14:35 -08:00
健美猞猁
2202579685 Cnvnator: a new package. (#8959) 2019-02-13 11:15:00 +01:00
Matthias Wolf
861dd06bd1 enh: allow time like HH:MM in date strings. (#10034) 2019-02-13 11:05:00 +01:00
George Hartzell
f65a1155e1 Enhancement to module autoload documentation (#10310)
* Note that `none` is the default for lmod autoload

Save a bit of confusion by *explicitly* pointing out that `none` is
the default value for autoload in the lmod module file generator.

* Add a tip re building software externally

Add a tip about using `autoload: all` when building packages outside
of the tree that use artifacts (e.g. libraries, includes) within the
tree.
2019-02-12 22:02:13 +01:00
Chris Green
05f565356f Allow secondary generators when building with CMake. (#9324)
CMake supports the notion of secondary generators which provide extra
information to (e.g.) IDEs over and above that normally provided by
the primary generator. Spack only supports the 'Unix Makefiles' and
'Ninja' primary generators but was not parsing out the primary
generator when a secondary generator was also included (e.g. for
a generator attribute like 'Codeblocks - Ninja'). This adds a regex
for extracting the primary generator for validation.

Since the secondary generator is irrelevant to a Spack build, it is
passed on to CMake without further validation.
2019-02-12 12:39:19 -06:00
健美猞猁
f9c27f52bd casacore: new package (#7471) 2019-02-12 17:22:48 +01:00
Ben Morgan
8fd4e9a9fa xerces-c: Add cxxstd variant (#10561)
Add variant to support compiling against main C++ standards if needed
for ABI compatibility. Use 'default' value as Xerces-C autoconf system
does not enforce a minimum, or set a default, C++ standard.
2019-02-12 09:40:59 +01:00
Brian Van Essen
dc12ca5c76 lbann: updated versions (#10568) 2019-02-12 09:05:32 +01:00
Matthias Diener
068eefb4f5 remove remaining lzma dependencies (#10553) 2019-02-12 09:03:50 +01:00
Matthias Diener
6e38423d1c openssl: add version 1.1.1a (#10562) 2019-02-12 08:58:50 +01:00
Omar Padron
0ef139ac4d work around an issue with docker/dockerhub (#10547)
* try to workaround an issue with docker/dockerhub
* apply workaround only when running in travis
2019-02-08 16:39:40 -08:00
Javier Cervantes
36ebd7462c root package major update (#8428)
* Extend current recipe for root package
* Add removed old version
* Add dependency type for Python and R packages
* Add compiler variants
* Adding new root version: 6.14.00
* Add back the minimum cmake version required
* LZ4 and xxhash support for old (using builtin options) and new versions (external packages)
* Set PYTHONPATH in setup_environment
* Address typos and issues pointed by HadrienG2
* Add newer ROOT versions
* Solve support for asimage
* Define incompatible variants
* Organize old dependencies
* Add support for minuit
* Add support for pythia6
* Remove unneeded list_url
* Update license header
* Remove block of commented old dependencies
* Contrain Qt version
* Comment pythia8 variant/dependency, not supported by spack
* Force not to build pythia8
2019-02-08 09:17:07 -08:00
Matthias Diener
ff67009161 libarchive: remove lzma dependency (#10517)
lzma was last updated in 2008 and has compilation
issues on some platforms. The format has been superceded
by xz (see e.g. https://tukaani.org/xz/).
2019-02-08 16:33:13 +01:00
Denis Davydov
5623ac3d6b CudaPackage: fix wrong version range (#10551) 2019-02-08 16:32:43 +01:00
Robert Blake
a55fc5b963 Adding a package for cardioid. (#10448)
* Adding a package for cardioid.

* Changing package to pass flake8

* Removing template leftovers per @ax3l 's advice

* Adding a homepage so tests pass.

* Removing whitespace for flake8

* Changing the name of master branch to match spack standards.
2019-02-08 11:17:26 +01:00
Michael Kuhn
84bc2a4215 meson: add 0.49.1 and disable rpath stripping (#10463)
rpath stripping breaks (at least) the gtkplus build because at-spi2-atk's
dependencies can not be found.
2019-02-08 11:15:49 +01:00
Peter Scheibel
d8746d596e
bug report template: suggest --stacktrace instead of -s (#10548)
1137b18 removed the -s option from spack such that to see a stack
trace you must pass the --stacktrace option. The bug report templates
were not updated accordingly.
2019-02-07 21:06:57 -06:00
Piotr Luszczek
f093515002 netlib-scalapack package: add CMake test patch (#10452)
Add patch to fix Fortran mangling in CMake test

This is a fix for builds with GCC 6/7/8 and CMake 2/3. It includes
a link to the issue where this is reported. For now, the Spack
package applies the patch to all releases >= 2.0.2
2019-02-07 20:58:27 -06:00
Justin Stanley
ec6de8326e repeatmasker package: add variant for cross_match engine (#10534) 2019-02-07 16:53:30 -06:00
wspear
76feb0205d New package: py-jupyterhub (#10461)
This package depends on both python 3.5+ and node-js which depends on
python 2.7/2.8 to build. Currently it can only be installed if the
node-js package's python dependency is manually removed, so node-js
will build with python found on the system rather than provided by
spack. Upcoming commits may allow spack to reconcile this
automatically.
2019-02-07 16:47:46 -06:00
Justin Stanley
ef89ae03bc mirdeep2 package: make sure bins are executable (#10515) 2019-02-07 13:05:19 -06:00
mathsen
570af0c313 Trilinos package: update superlu-dist dependency (#10511)
Trilinos master branch gets the latest superlu-dist (currently 6.1.0)
2019-02-07 12:58:45 -06:00
Massimiliano Culpo
58f1dc037a log-parse: fix error message when no error lines are found (#10543) 2019-02-07 12:19:19 -06:00
Satish Balay
b8684b318c
petsc: petscvariables is used from user makefiles - so it should not have spack compilers listed (#10365) 2019-02-07 09:09:23 -06:00
Satish Balay
1d71a5ea57
petsc4py and libensemble: add @develop dependencies (#10539)
* py-petsc4py: add @develop

* py-libensemble: add @develop dependency on py-petsc4py@develop
2019-02-07 09:06:31 -06:00
Satish Balay
0ad1b2a2c8
petsc@xsdk-0.2.0: fix sowing dependency (#10535) 2019-02-07 09:05:43 -06:00
Satish Balay
753fec39ae
xsdk@develop fixes (#10521)
* xsdk@develop: switch trilinos from @master to @develop

* xsdk@develop: dtk - fix trilinos dependency on dtk.
 - dkt-3.0 should be used with trilinos-12.4*
 - dtk/master should be used with trilinos@develop
2019-02-07 09:05:14 -06:00
Justin Stanley
09a884322f orthofiller: new package at 1.1.4 (#10373) 2019-02-07 10:22:36 +01:00
Gregory Lee
f0cb4580d1 fixed checksum (#10393) 2019-02-07 10:20:45 +01:00
Levi Baber
af7f1bb3ca new package: perl logger simple (#10509) 2019-02-07 10:19:07 +01:00
Levi Baber
07b5a6a512 perl-file-homedir: new package (#10533) 2019-02-07 10:09:20 +01:00
Levi Baber
4679c11098 py-biopython: new version (#10532) 2019-02-07 10:08:45 +01:00