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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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- new E741 flake8 checks disallow 'l', 'O', and 'I' as variable names
- rework parts of the code that use this, to be compliant
- we could add exceptions for this, but we're trying to mostly keep up
with PEP8 and we already have more than a few exceptions.
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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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There are now separate flake8 configs for core vs. packages:
- core has a smaller set of flake8 exceptions
- packages allow `from spack import *` and module globals
- Allows core to take advantage of static checking for undefined names
- Allows packages to keep using Spack tricks like `from spack import *`
and dependencies setting globals for dependents.
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- `-a`/`--all` causes flake8 to run on all files rather than just
different ones.
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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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fixes #5721
This is to solve the fact that lmod needs to be configured
by the user (to specify a core compiler).
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* Add better spec matching to spack buildcache
* skip download of spec.yaml and keys if they exist
* autopep8
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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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qt (#4958)
* Update Getting Started docs to clarify that full Xcode suite is required for qt
* Better error message when only the command-line tools are installed
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- Previously `spack blame` only worked for package names; now it works
for paths as well, so developers can use it on core spack files.
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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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