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* r-evaluate: Update version to 0.10.1.
* r-evaluate: update list_url.
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* 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.
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* r-siggenes: created new package
* deleted extra indent
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* r-beanplot: created new package
* correct according to flake8
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* r-bumphunter: created new package
* r-bumphunter: added description
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* Refactoring for 'hdf5'.
* Remove 'unsupported' variant.
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- fixes E722 errors from latest version of flake8
- requires us to not use 'bare except:' and catch BaseException instead
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- 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.
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- This removes all wildcard imports EXCEPT `from spack import *` in packages
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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.
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* 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
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#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.
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* r-genomicfeatures: created new package
* modified version number and added versioned dependency on r
* fixed typo
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* dealii: blacklist boost 1.64 and 1.65
* flake8
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* 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
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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.
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* 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
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- 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.
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number (#5783)
* Forcing Paraview to avoid using git describe to determine its own version number.
* Shortening references to spec in paraview.
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depend on SLEPc (#5755)
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* Add krims to spack
* Add lazyten to spack
* Add description for lazyten
* Changes suggested by @davydden and @junghans
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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.
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