* Add patching for xlf when %clang. Changes are effective only when Fortran compiler is 'XL'.
* Use the right version for trilinos when patching for seacas.
setting to use, instead of the spack compiler.
%clang can use multiple Fortran compilers with different options, so
we need to know what compiler is used in order to provide the correct
options.
* Add new version (3.4.0) with new variant (pumi).
* Fix an issue: skip the tests in examples/pumi as they require
files that are not included in the mfem distribution/repository.
* Use patches to fix the testing issues with PUMI and PETSc v3.9.
* Use the new bit.ly short link for v3.4.
* Add the ability to build the dyninst master branch under the develop version name. Fix elfutils and libdwarf to work with the various dyninst versions and vice-versa.
* Add reviewer suggested change to dyninst package file. Remove colon in spec.satisfies clause.
* Add reviewer suggested change to dyninst package file. Remove duplicate lines.
* Add reviewer suggested change to dyninst package file. Encompass all versions under 10.0 with respect to using libdwarf in the build.
Fixes the following problem:
==> Installing trilinos
==> Warning: Suspicious requests to set or unset 'LD_LIBRARY_PATH' found
==> Warning: env.unset('LD_LIBRARY_PATH') at /home/balay/spack.new/lib/spack/spack/build_environment.py:269
==> Warning: ---> env.set('%s' % key, value) at /home/balay/spack.new/lib/spack/spack/build_environment.py:292
==> Trying to clone git repository: https://github.com/trilinos/Trilinos.git at tag develop
Fetching tags only, you probably meant:
git fetch --tags
error: pathspec 'develop' did not match any file(s) known to git.
==> Fetching from [git] https://github.com/trilinos/Trilinos.git failed.
==> Error: FetchError: All fetchers failed for trilinos-develop-tgkpnctp6nn4imoizxlw4ymqyztcie4n
The patch to select ELPA API needs to be applied to
version 6.2.0 too.
The link line of hdf5 is computed incorrectly from
the configuration part of the build-system. To fix
this the relevant file (make.inc) is patched.
* py-pybind11: Additionally install python extensions e.g. run python setup
* py-projectq: Added new package for quantum computing
* py-projectq: corrected typos
* edited flake8 incompatibilities
* additional flake8 faults
* changes according to suggestions
* flake8 errors fixed
* typo and missing environment variable set
* py-pybind11:added setup_environemt
* py-projectq:changed version according to request
* flake8 correction
* py-pybind11:changed to setup_py and removed noop
* py-projectq:removed dependency and changed type of py-pytest dependency
* py-pybind11: flake8 error corrected
* py-projectq: Small error correction
* Git's gitk needs TK's wish to be found in PATH
* Add a _runtime_ dependency on `tk`
* Add an environment rule to add the path to TK's `wish` program to $PATH for
the generated `git` modulefile.
* Make TclTk run environment an optional variant for git.
* Cleanup based on PR recommendations.
The following improvements are made to cxx standard support
(e.g. compiler.cxxNN_flag functions) in compilers:
* Add cxx98_flag property
* Add support for throwing an exception when a flag is not supported (previously
if a flag was not supported the application was terminated with tty.die)
* The name of the flag associated with e.g. c++14 standard support changes for
different compiler versions (e.g. c++1y vs c++14). This makes a few corrections
on what flag to return for which version.
* Added tests to confirm that versions report expected flags for various c++
standards (or raise an exception for versions that don't provide a given cxx
standard)
Note that if a given cxx standard is the default, the associated flag property will
return ""; cxx98 is assumed to be the default standard so this is the behavior for
the associated property in the base compiler class.
Package changes:
* Improvements to the boost spec to take advantage of the improved standard
flag facility.
* Update the clingo spec to catch the new exception rather than look for an
empty flag to indicate non-support (which is not part of the compiler flag API)
The tcl package references the original sources upon install, and the tk build
requires the tcl sources. This updates the tcl package to install its sources following
the example of #4102, and also updates the tclConfig.sh file to properly reference
the installed sources (rather than the staging directory created by Spack).
* Update to 2018.3 and improve version URLs, dependencies and patching.
Improve to version -> URL translation to be algorithmic rather than manual.
Make binutils build dependency explicit where appropriate because we're sensitive to the assembler used.
Build's use of '-mrtm' is only patched away if it needs to be because the assembler is too old.
Incorporate @adamjstewart request to convert GCC version check to a conflict.
* Allow specification of C++ standard.
* Improve TBB patch per PR comments.
* Restrict RTM patch application to older OS only.
* New version 2018_U4.
* Delete support for old versions of Elemental in Hydrogen
* Fix cmake_args versions in lbann
* Remove unused import (again)
* Revert elemental to pre-llnl fork
* Strip tailing whitespace from libgfortran.so
* Fix flake8
* Remove debug print
* * Add back elemental@develop
* Prohibit installation of hydrogen previous to 0.99
* Fix flake8
* Change cmake_args error to a conflicts for old versions of Hydrogen
* Use ~ not -
* fermisciencetools: new package
* fermisciencetools: new package
* added comments about the error in building the source distribution; fixed flake8 errors
* add sqlitebrowser
Change-Id: I20cac709509e82d348cebc11b0d584b53b2ad3d4
* add message and clean up unnecessary code
Change-Id: Ib9d2229ee25d751274680d06824891ee78fa5970
* and make flake8 happy
Change-Id: I814eb89eefe1767af4d8043b08b61991750516df
* make gcc-independence great again
Change-Id: I75f7271757782a6735eb7f03c0551d190722974d
* remove explicit import of dso_suffix
Change-Id: I626c6391b22524895199db5508606c4cf22bf9b5
* add a shared variant for all supported versions
* address comment from @citibeth about MacOS lib installs
* address additional comments from @citibeth about MacOS lib installs
* set +shared variant to be default behavior
* add package py-cartopy
Change-Id: Ifbe541e852921c384a381594a2c1110814556311
* fix comments and flake8
Change-Id: I8d5e994580e8252e00654e68ad79d74e06089939
* remove pip dependency... not sure why added in the first place
Change-Id: Ie2a788887dac30778cc43931a0732980a347514d
* move build, link, run to default dependencies
Change-Id: I1ec0cb7dc4a697c4ca9e68a0cc0d8694cc21c100
Provides a patch for the fix in
https://github.com/ornladios/ADIOS/pull/182
Installed ADIOS MPI-enabled libraries are with that able to also
perform serial I/O without the need to start the whole app via
`mpiexec`.
* trilinos: add more package conflicts
This was done by putting in required lib dependencies from each
package's `cmake/Dependencies.cmake`.
* trilinos: added few more trilinos packages
* trilinos: hiccup fix
* add 1.4.13.4 for SZ
* undo spack link (change llnl/spack to spack/spack) and change .zip to .tar.gz
* revise package.py for SZ 1.4.13.4 based on Adam's comments.
* adding partially completed recipe for phast. will need clapack as dependency
* try to install phast
* seems to still need CLAPCK
* using CLAPACK instead
* phast: updated
* fixed flake8 error
* phast cannot build with clapack built with external blas?
* phast: depend on clapack built without external blas
* fixed flake8 errors
* phast: updated build_directory
* pybind11: test support
Add a test functionality to pybind11.
* CMake: test also on "make check"
Some projects use non-CTest manual targets for tests.
* Fix digest for abyss@1.5.2
The digest value for v1.5.2 appears to have changed. This value works
for me, today.
The existing value v2.0.2 works as is.
* Use "download" URL for ABYSS
Following the suggestion of the project team, switch to using the
release tarballs from the "download" URL instead of the automagically
generated ones at the "archive" URL.
Converstation here: https://github.com/bcgsc/abyss/issues/232
The URL that we were using for pigz only provides the current
version. When the author released v2.4 the package became
uninstallable (unless you have the tarball cached).
It turns out that their are tarballs of the tagged source tree
available on GitHub and they're sufficient to build things (no
additional bits needed).
This commit switches the URL to the GitHub archive URL.
Sadly, this changes the v2.3.4 digest, but that version was no longer
available/install-able anyway, so "net-net we're still in positive
territory".
Installing the current version of Picard fails with:
```
==> Error: Unable to parse extension from https://github.com/broadinstitute/picard/releases/download/2.18.3/picard.jar.
If this URL is for a tarball but does not include the file extension
in the name, you can explicitly declare it with the following syntax:
version('1.2.3', 'hash', extension='tar.gz')
If this URL is for a download like a .jar or .whl that does not need
to be expanded, or an uncompressed installation script, you can tell
Spack not to expand it with the following syntax:
version('1.2.3', 'hash', expand=False)
```
Fix it, but adding `expand=False`, like the other versions.
* fix missing -lrt for Centos6, issue: #7552
* fix missing -lrt for Centos6, issue: #7552
* fix using make() as opposed to patching
* remove patch, as the fix is provided withing package.py instead
* make flake8 happy
