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Author SHA1 Message Date
Yifan Zhu
5742ec4fea r-openssl: changed homepage url to the CRAN package homepage, added list_url and added version 0.9.7 (#5848) 2017-10-25 11:12:31 +02:00
Praveen C
5b9de2eaba Glibc 2.26 does not provide xlocale.h (#5862) 2017-10-25 10:39:32 +02:00
Ondřej Čertík
882480fad6 gdbm: pass in proper CPPFLAGS (#5893) 
The problem was that the configure script was not using spack's compiler
wrappers. We now pass the proper compiler wrapper using the CC argument
explicitly.

Fixes #5892.
 2017-10-25 07:09:41 +02:00
Abhinav Bhatele
b47ff33f11 Add a new package for AMG and fix build issues in the amg2013 package (#5909) 
* amg2013: fix build issues

* amg: add new package

* Update package.py

* amg2013: standardize option name

* amg: standardize option names
 2017-10-24 21:06:33 -06:00
Ondřej Čertík
39616a2fe1 hypre: make mpi dependency optional (#5905) 2017-10-24 18:53:12 -07:00
Robert Pavel
68f7b7863a Added Spackage for SW4Lite proxy (#5917) 
Added Spackage for C version of SW4Lite proxy. Fortran will follow once
race conditions involving .mod files are resolved
 2017-10-24 15:31:05 -06:00
Massimiliano Culpo
8b7d2d0f24 'spack install' can overwrite an existing installation (#5384) 
'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.
 2017-10-24 12:32:30 -07:00
Denis Davydov
31813ef2c7 slepc and petsc version updates (#5863) 
slepc: add 3.8.0
petsc: no longer prefer 3.7.7
 2017-10-24 10:57:14 -07:00
Yifan Zhu
8c306b7b83 r-minfi: created new package (#5887) 2017-10-24 14:07:45 +02:00
健美猫
37ce53c48f Add a package: thrust. (#3729) 2017-10-24 11:39:38 +02:00
Yifan Zhu
1ee60e7c63 r-nlme: added list_url and version 3.1-131 (#5890) 2017-10-24 11:30:49 +02:00
Yifan Zhu
2a2203895a r-genomicalignments: created new package (#5785) 
* r-genomicalignments: created new package

* r-genomicalignments: using git repo source instead
 2017-10-24 11:30:33 +02:00
Yifan Zhu
a68f9dcc26 r-reshape: created new package (#5889) 2017-10-24 11:29:56 +02:00
Yifan Zhu
43d39a6b00 r-data-table: added list_url and version 1.10.4-2 (#5888) 2017-10-24 11:29:42 +02:00
Todd Gamblin
3f68cc2ba7 Fix bug in spack flake8 when no files differ from develop (#5898) 2017-10-24 11:29:18 +02:00
lingnanyuan
896d4c8d0c r-mass: Update version to 7.3-47 (#5885) 2017-10-24 11:27:04 +02:00
lingnanyuan
cc06112959 r-acepack: Create new package. (#5884) 2017-10-24 11:26:37 +02:00
lingnanyuan
b09f0cdbe1 r-latticeextra: Create new package. (#5883) 
* r-latticeextra: Create new package.

* r-latticeextra: Update list_url.
 2017-10-24 11:26:20 +02:00
lingnanyuan
01215d705f r-htmltable: Create new package. (#5882) 2017-10-24 11:25:58 +02:00
lingnanyuan
8c0b95c398 r-htmlwidgets: Update verion to 0.9 (#5881) 2017-10-24 11:25:42 +02:00
lingnanyuan
22e96a10ad r-checkmate: Create new package. (#5880) 2017-10-24 11:25:24 +02:00
Yifan Zhu
17d94a5b51 r-geoquery: created new package (#5879) 
* r-geoquery: created new package

* r-geoquery: added versioned dependency on r
 2017-10-24 11:25:02 +02:00
lingnanyuan
25d38fe077 r-knitr: Update version to 1.17. (#5878) 2017-10-24 11:24:45 +02:00
Yifan Zhu
bba655d6d7 r-httr: added list_url and version 1.3.1 (#5877) 2017-10-24 11:24:29 +02:00
lingnanyuan
d4d44f0c63 r-rcpparmadillo: Create new package. (#5875) 2017-10-24 11:24:16 +02:00
Yifan Zhu
eeb1edd8e5 r-curl: added list_url and version 3.0 (#5874) 2017-10-24 11:23:54 +02:00
lingnanyuan
859b9972d3 r-yaml: Update version to 2.1.14 (#5856) 2017-10-24 11:23:38 +02:00
lingnanyuan
ae578069bd r-formatr: Update version to 1.5 (#5855) 2017-10-24 11:23:17 +02:00
lingnanyuan
050b753bb7 r-crayon: Update version to 1.3.4 (#5854) 2017-10-24 11:23:00 +02:00
lingnanyuan
764b7a7ad1 r-sourcetools: Create new package. (#5853) 2017-10-24 11:22:42 +02:00
lingnanyuan
4b50598252 r-testit: Update version to 0.7 (#5852) 2017-10-24 11:22:23 +02:00
lingnanyuan
6b87875d81 r-markdown: Update version to 0.8. (#5851) 2017-10-24 11:22:05 +02:00
Yifan Zhu
ab96705f05 r-base64: created new package (#5850) 2017-10-24 11:21:48 +02:00
Yifan Zhu
f814e9bba1 r-illuminaio: created new package (#5849) 2017-10-24 11:21:31 +02:00
lingnanyuan
7a176ca89e r-evaluate: Update version to 0.10.1. (#5847) 
* r-evaluate: Update version to 0.10.1.

* r-evaluate: update list_url.
 2017-10-24 11:20:47 +02:00
lingnanyuan
420048350f bioconductor update (#5786) 
* 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.
 2017-10-24 11:19:19 +02:00
Yifan Zhu
f9f0c1472f r-siggenes: new package (#5831) 
* r-siggenes: created new package

* deleted extra indent
 2017-10-24 11:14:04 +02:00
lingnanyuan
cea33af464 r-affyrnadegradation: Create new package. (#5830) 2017-10-24 11:13:53 +02:00
lingnanyuan
2ede483149 r-affyqcreport: Create new package. (#5829) 2017-10-24 11:13:44 +02:00
Yifan Zhu
edac742f84 r-nor1mix: created new package (#5828) 2017-10-24 11:13:04 +02:00
lingnanyuan
46b385761d r-affyplm: Create new package. (#5827) 2017-10-24 11:12:56 +02:00
lingnanyuan
2c5b3a2268 r-affypdnn: Create new package. (#5826) 2017-10-24 11:12:47 +02:00
Yifan Zhu
6fd0030acb r-beanplot: created new package (#5825) 
* r-beanplot: created new package

* correct according to flake8
 2017-10-24 11:12:15 +02:00
Aaron Fisher
204217f7c1 Updated external package versions. (#5833) 2017-10-24 11:10:59 +02:00
Yifan Zhu
968144f1c5 r-bumphunter: new package (#5824) 
* r-bumphunter: created new package

* r-bumphunter: added description
 2017-10-24 11:09:38 +02:00
Sergey Kosukhin
161dca6d5d Update for 'hdf5'. (#5790) 
* Refactoring for 'hdf5'.

* Remove 'unsupported' variant.
 2017-10-24 11:09:08 +02:00
Michael Kuhn
c7ac4e3774 go: Update to 1.9.1 (#5868) 2017-10-24 11:02:33 +02:00
Todd Gamblin
6b5ca38723 do not use 'l' as a variable name, to appease new flake8 version 
- 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.
 2017-10-24 10:05:36 +02:00
Todd Gamblin
5449884b2e Fix bare 'except:' to placate errors in new flake8 version. 
- fixes E722 errors from latest version of flake8
- requires us to not use 'bare except:' and catch BaseException instead
 2017-10-24 10:05:36 +02:00
Todd Gamblin
b98fc48273 log tests use tmpdir properly 2017-10-24 10:05:36 +02:00