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2017-10-24r-htmltable: Create new package. (#5882)lingnanyuan1-0/+47
2017-10-24r-htmlwidgets: Update verion to 0.9 (#5881)lingnanyuan1-3/+4
2017-10-24r-checkmate: Create new package. (#5880)lingnanyuan1-0/+39
2017-10-24r-geoquery: created new package (#5879)Yifan Zhu1-0/+44
* r-geoquery: created new package * r-geoquery: added versioned dependency on r
2017-10-24r-knitr: Update version to 1.17. (#5878)lingnanyuan1-1/+3
2017-10-24r-httr: added list_url and version 1.3.1 (#5877)Yifan Zhu1-0/+2
2017-10-24r-rcpparmadillo: Create new package. (#5875)lingnanyuan1-0/+38
2017-10-24r-curl: added list_url and version 3.0 (#5874)Yifan Zhu1-0/+2
2017-10-24r-yaml: Update version to 2.1.14 (#5856)lingnanyuan1-0/+2
2017-10-24r-formatr: Update version to 1.5 (#5855)lingnanyuan1-2/+4
2017-10-24r-crayon: Update version to 1.3.4 (#5854)lingnanyuan1-2/+4
2017-10-24r-sourcetools: Create new package. (#5853)lingnanyuan1-0/+38
2017-10-24r-testit: Update version to 0.7 (#5852)lingnanyuan1-1/+3
2017-10-24r-markdown: Update version to 0.8. (#5851)lingnanyuan1-1/+3
2017-10-24r-base64: created new package (#5850)Yifan Zhu1-0/+39
2017-10-24r-illuminaio: created new package (#5849)Yifan Zhu1-0/+39
2017-10-24r-evaluate: Update version to 0.10.1. (#5847)lingnanyuan1-2/+4
* r-evaluate: Update version to 0.10.1. * r-evaluate: update list_url.
2017-10-24bioconductor update (#5786)lingnanyuan22-47/+71
* 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.
2017-10-24r-siggenes: new package (#5831)Yifan Zhu1-0/+42
* r-siggenes: created new package * deleted extra indent
2017-10-24r-affyrnadegradation: Create new package. (#5830)lingnanyuan1-0/+42
2017-10-24r-affyqcreport: Create new package. (#5829)lingnanyuan1-0/+46
2017-10-24r-nor1mix: created new package (#5828)Yifan Zhu1-0/+39
2017-10-24r-affyplm: Create new package. (#5827)lingnanyuan1-0/+46
2017-10-24r-affypdnn: Create new package. (#5826)lingnanyuan1-0/+38
2017-10-24r-beanplot: created new package (#5825)Yifan Zhu1-0/+36
* r-beanplot: created new package * correct according to flake8
2017-10-24Updated external package versions. (#5833)Aaron Fisher1-3/+1
2017-10-24r-bumphunter: new package (#5824)Yifan Zhu1-0/+50
* r-bumphunter: created new package * r-bumphunter: added description
2017-10-24Update for 'hdf5'. (#5790)Sergey Kosukhin2-52/+55
* Refactoring for 'hdf5'. * Remove 'unsupported' variant.
2017-10-24go: Update to 1.9.1 (#5868)Michael Kuhn1-0/+1
2017-10-24do not use 'l' as a variable name, to appease new flake8 versionTodd Gamblin8-55/+53
- 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.
2017-10-24Fix bare 'except:' to placate errors in new flake8 version.Todd Gamblin17-27/+27
- fixes E722 errors from latest version of flake8 - requires us to not use 'bare except:' and catch BaseException instead
2017-10-24log tests use tmpdir properlyTodd Gamblin1-30/+35
2017-10-24fix bugs found with stricter flake8 rulesTodd Gamblin8-11/+19
- 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.
2017-10-24remove wildcards from make spack core and packagesTodd Gamblin85-161/+231
- This removes all wildcard imports EXCEPT `from spack import *` in packages
2017-10-24flake8: no wildcards in core; only `import *` from spack in packagesTodd Gamblin4-29/+78
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.
2017-10-24add newlines at end of some package filesTodd Gamblin6-6/+6
2017-10-24add --all option to `spack flake8`Todd Gamblin1-14/+41
- `-a`/`--all` causes flake8 to run on all files rather than just different ones.
2017-10-23package: remove bare except statements (#5896)scheibelp1-2/+2
2017-10-23jansson: enable shared library (#5857)Mark Grondona1-0/+9
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.
2017-10-20getting_started.rst: removed tip suggesting the use of 2 Spack instances (#4061)Massimiliano Culpo1-13/+0
2017-10-20module-type argument defaults to 'tcl' instead of every known type (#5751)Massimiliano Culpo3-3/+6
fixes #5721 This is to solve the fact that lmod needs to be configured by the user (to specify a core compiler).
2017-10-20buildcache command updates (#5860)Patrick Gartung3-37/+159
* Add better spec matching to spack buildcache * skip download of spec.yaml and keys if they exist * autopep8
2017-10-20new package: hpgmg (#4888)jiseung1-0/+87
* 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
2017-10-20Update Getting Started docs to clarify that full Xcode suite is required for ↵Adam J. Stewart2-6/+79
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
2017-10-20perl: add old version (#5844)George Hartzell2-0/+42
2017-10-20xsbench: add v14 (#5835)Christoph Junghans1-0/+1
2017-10-19spack blame can take a path to a file in the Spack repo (#5793)Todd Gamblin2-7/+28
- Previously `spack blame` only worked for package names; now it works for paths as well, so developers can use it on core spack files.
2017-10-19perl: ignore perllocal.pod files during package activation (#5271)Milton Woods1-0/+39
2017-10-19Allow documentation to build in Python 3 (#5736)Adam J. Stewart1-7/+2
2017-10-19bcl2fastq needs `with working_dir:` after changes in #5776 (#5803)George Hartzell1-10/+14
#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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