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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
2017-10-24r-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
2017-10-24Fix bare 'except:' to placate errors in new flake8 version.Todd Gamblin5-6/+6
- fixes E722 errors from latest version of flake8 - requires us to not use 'bare except:' and catch BaseException instead
2017-10-24fix bugs found with stricter flake8 rulesTodd Gamblin1-2/+2
- 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 Gamblin9-32/+36
- This removes all wildcard imports EXCEPT `from spack import *` in packages
2017-10-24add newlines at end of some package filesTodd Gamblin6-6/+6
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.
2017-10-20new 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
2017-10-20perl: add old version (#5844)George Hartzell2-0/+42
2017-10-20xsbench: add v14 (#5835)Christoph Junghans1-0/+1
2017-10-19perl: ignore perllocal.pod files during package activation (#5271)Milton Woods1-0/+39
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.
2017-10-19libxml2: use spack's xz (#5816)Christoph Junghans1-4/+7