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2017-10-24'spack install' can overwrite an existing installation (#5384)Massimiliano Culpo4-52/+274
'spack install' can now reinstall a spec even if it has dependents, via the --overwrite option. This option moves the current installation in a temporary directory. If the reinstallation is successful the temporary is removed, otherwise a rollback is performed.
2017-10-24slepc and petsc version updates (#5863)Denis Davydov2-3/+2
slepc: add 3.8.0 petsc: no longer prefer 3.7.7
2017-10-24r-minfi: created new package (#5887)Yifan Zhu1-0/+63
2017-10-24Add a package: thrust. (#3729)健美猫1-0/+40
2017-10-24r-nlme: added list_url and version 3.1-131 (#5890)Yifan Zhu1-0/+2
2017-10-24r-genomicalignments: created new package (#5785)Yifan Zhu1-0/+49
* r-genomicalignments: created new package * r-genomicalignments: using git repo source instead
2017-10-24r-reshape: created new package (#5889)Yifan Zhu1-0/+38
2017-10-24r-data-table: added list_url and version 1.10.4-2 (#5888)Yifan Zhu1-0/+2
2017-10-24Fix bug in spack flake8 when no files differ from develop (#5898)Todd Gamblin1-1/+4
2017-10-24r-mass: Update version to 7.3-47 (#5885)lingnanyuan1-2/+4
2017-10-24r-acepack: Create new package. (#5884)lingnanyuan1-0/+35
2017-10-24r-latticeextra: Create new package. (#5883)lingnanyuan1-0/+41
* r-latticeextra: Create new package. * r-latticeextra: Update list_url.
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