The problem was that the configure script was not using spack's compiler
wrappers. We now pass the proper compiler wrapper using the CC argument
explicitly.
Fixes#5892.
* r-a4: Add r dependency and update url.
* r-a4base: Add r dependency and update url.
* r-a4classif: update url and add r dependency.
* r-a4core: Update url and add r dependency.
* r-a4preproc: Update url and add r dependency.
* r-a4reporting: Update url and add r dependency.
* r-abaenrichment: Update url and add r dependency.
* r-absseq: Update url and add r dependency.
* r-acgh: Update url and add r dependency.
* r-acme: Update url and add r dependency.
* r-adsplit: Update url and add r dependency.
* r-affxparser: Update url and add r dependency.
* r-affycomp: Update url and add r dependency.
* r-affycompatible: Update url and add r dependency.
* r-affycontam: Update url and add r dependency.
* r-annaffy: Update url and add r dependency.
* r-annotate: Update url and add r dependency.
* r-annotate: Update url and add r dependency.
* r-annotationdbi: Update url and add r dependency.
* r-genefilter: Update url and add r dependency.
* r-mlinterfaces: Update url and add r dependency.
* r-limma: Update url and add r dependency.
* r-multtest: Update url and add r dependency.
* r-a4classif: Correct format.
* r-affycomp: Correct error.
- When you don't use wildcards, flake8 will find places where you used an
undefined name.
- This commit has all the bugfixes resulting from this static check.
Jansson builds only a static library by default, which is probably
not what most users want. Add Cmake args required to build a shared
library and enable those via a default 'shared' variant of the
package.
* new package: hpgmg
* removed build and changed extend() to append()
* changes based on comments
* pep8 compliant
* addressed rest of comments
* trigger checks
* changed from fe_fv to two boolean variants
* fixed compilation issues
* cleared up ambiguities in solver variants
* removed +mpi condition
* changes based on review
#5776 cleaned up the way the the current working directory is
managed (less magic state).
bcl2fastq is packaged like a russian doll, rather than an archive file
that contains the source, there's a zip file that contains a tar.gz
file that contains the source. The package definition has a bit of
extra code that unpacks the inner tarball.
That extra bit of code now needs to explicitly arrange to be in the
correct directory before it does its work.
* py-mpi4py: Add develop version and dependencies
- Add cython dependency for develop version
- Add explicit python dependency
* py-mpi4py: Specify 2.0.1 instead of develop for conditional dep
Perl installs a couple of config files that need to be munged so that
they don't refer to the spack compiler. These files are installed
read-only. Behind the scenes 'filter_file' moves its file to a safe
place, and tries to create a working file that is both O_WRONLY and
has the perms of the original file. On an NFSv4 filesystem, the
combination of 'r--r--r--' and O_WRONLY throws a permissions error.
This commit adds a simple context manager that temporarily makes the
files writable.
* Add a new +clanglibcpp option for Boost
Currently, the compile of boost with clang will use the stdlibc++. This patch adds an optional flag to use clangs included libc++ instead.
* Linting
Fix long lines and white space errors
- Tests use a session-scoped mock stage directory so as not to interfere
with the real install.
- Every test is forced to clean up after itself with an additional check.
We now automatically assert that no new files have been added to
`spack.stage_path` during each test.
- This means that tests that fail installs now need to clean up their
stages, but in all other cases the check is useful.
1.64 had issues serialization (make_array and others) when built with
+mpi+python. It appears that those issues are fixed in 1.65.1
so we can remove preferred tag from 1.63.
* initial update of sundials package
* fix bugs in initial sundials update
* add xsdk cmake setup, fix generic math option, add cuda/raja Makefiles to install fixes
* Fix lapack install bug, add new conflicts, clean up formatting
* Address pull requeset comments and make fomatting style consistent
Remove blas variant as blas is only needed when used by an external
linear solver. Set related CMake blas variables as needed depending
enabled external linear solvers.
Add minimum required CMake version.
Additional conflicts and dependencies for external libraries based
on mpi, indextype, and precision.
Fix SuperLU_MT logic to check which threading type SuperLU_MT was
configured with.
Add maintaiers.
Change Sundials solver options to use an array of values.
Consistently use % for formatting.
* change triple-single quotes to single quotes
* Change indextype option to a single int64 option
* Add dmlc/mxnet packags.
* Build mxnet+cuda+opencv with GCC-4.8.5 and GCC-5.4.0.
* Build mxnet version 0.10.0, 0.10.0.post1 and 0.10.0.post2.
* Add component version constrain for mxnet 0.10.0.x .
* Go through flake8.
* Replace commit hash with commit date as package version.
* Go throught Travis-CI.
* Update submodule version for 0.10.0.post2.
* Add openmp variant for dmlc-core and mxnet.
* Refine variant handling.
* Fix filter_file for dmlc-core.
* Cut long strings into multiple lies due to PEP8 requirements.
* Fix for PEP8.
* Add CUB_INCLUDE.
* Add py-mxnet: Python binding for MXNet.
* Remove distutils.dir_util.
* Add the profiler variant for mxnet.
* Add a shared variant for nnvm.
* Set USE_OPENMP to OFF by default.
* Fix flake8 errors.
* Fix flake8 issues.
* flake8 issues again.
closes#5506
The application of patches to upstream executables has been reworked
according to the suggestions of the main developer in #5506. In
particular we are not maintaining a dictionary that maps plumed
versions to the versions of patchable executables, and we are using a
non-interactive command to patch applications.
All the comments on substituting plumed at run-time do not apply here,
since we use RPATH and we want to maintain a 1:1 relationship between
the DAG hash and the plumed library used.
* Add package for aspell and ass't dictionaries
Add a package definition for aspell.
Add a handful of dictionaries to convince myself that the support for
a bunch of dictionaries works.
* Flake8 cleanup
* Use six's version of urlparse
`urlparse` is not python3 friendly. This works around it (stolen from
`.../cmd/md5.py`).
* Fix incorrect trimming regexp
* Clean up dictionary build
- more parsimonious use of `which` (`make()` has already been made)
- use `sh` instead of `bash`
* Use a helper method to generate info for variants
I figured out my issues with static methods. I *think* that it this
is pythonic.
* Convert aspell to an extendable package
Convert aspell to be extendable and rework the dictionaries to be
extensions.
As it stands, there's a great deal of cut and paste in the
dictionaries, I'll abstract that out next.
The {de,}activate methods copy a great deal of code out of
package.py. Perhaps there's a better way....
* Create AspellDictPackage and use it for the dictionaries
Reduce the repeated code, pull it into a base class.
I'm confused about why 'from spack import *' wasn't more useful in the
base class.
* Oops, -de & -es should be AspellDictPackages too
* Typo: pakcage -> package
* Address some commentary
* Update copyright dates, 2016->2017
This is a simple package that drops their shell wrapper into
prefix.bin and their jar files into prefix.lib.
The approach comes from the picard package.
* Updating ag to the latest version
* Pretty by request
* Restore url to previous value
There *is* an https version available, but I've also been told
to not just update the url when adding new version. I'm following
the latter advice and trusting security to the digest.
* Adding maven v3.5.0
Updating package file to include later version of maven but still signifying a preference for the older
* removing specific preference flag
* ncl: Fix temp directory
Currently, ncl is configured using a transient temp directory. This
leads to warnings such as this when executing ncl later on:
warning:"/tmp/ncl_ncar_xxxxxx" tmp dir does not exist or is not writable:
NCL functionality may be limited -- check TMPDIR environment variable
As this also breaks some functionality, use the system temp directory
instead (typically /tmp).
* ncl: Depend on esmf
esmf is required for some ncl scripts (such as ESMF_regridding.ncl).
* Add link dependency on xproto to xau
The libxcb build was failing like so:
```
1 error found in build log:
[ ... ]
131 checking whether to build developer documentation... yes
132 checking for doxygen... /usr/bin/doxygen
133 checking for dot... /usr/bin/dot
134 checking for CHECK... no
135 checking for XCBPROTO... yes
136 checking for NEEDED... no
>> 137 configure: error: Package requirements (pthread-stubs xau >= 0.99.2) were not met:
138
139 Package 'xproto', required by 'xau', not found
140
141 Consider adjusting the PKG_CONFIG_PATH environment variable if you
142 installed software in a non-standard prefix.
143
```
This adds a link dependency on libxproto that allows the libxcb build to
succeed.
* Change more build deps to build, link
These were also necessary for emacs+X to build.
* Fix flake8 complaint
* edits to address issues where spack concretization attempts to set properties on already-installed specs
* most added checks only need to check if the spec is concrete; they dont also need to check if the package is installed
* add test to ensure that patches are not applied to an installed spec
* add test to ensure that an error is detected when a dependent requests a dependency constraint which conflicts with a requested installed dependency
