Commit graph

8005 commits

Author SHA1 Message Date
nshtg
45e8e4b4fb libsodium: Update to 1.0.15 (#6643) 2017-12-11 17:27:09 -07:00
nshtg
25aa21a7a7 git: Update to 2.15.1 (#6642) 2017-12-11 17:26:53 -07:00
nshtg
74938f58d2 openssl: Update to 1.0.2n (#6641)
From 07.12.2017, fixes CVE-2017-3737
2017-12-11 17:26:37 -07:00
Brian Van Essen
6fec473e9e Py h5py update (#6635) 2017-12-11 17:26:13 -07:00
becker33
9d8ea00966
add -d option for edit command (#6416)
* add -d option for edit command and improve suffix extrapolation from '.py' to use glob
2017-12-11 16:17:53 -08:00
健美猫
e19aa80734 intel-parallel-studio: restrict patch to versions > 2016 (#6523)
Fixes #6522

Patch psxevars.sh and psxevars.csh only when year > 2016.
pxevars.csh does not exist for versions before 2017. psxevars.sh
does not appear to require this patch for versions before 2017.
2017-12-11 13:14:24 -08:00
Massimiliano Culpo
bd5d6b2bfa Simplified "Environment-Modules" section in getting started guide. (#6410)
Fixes #2440

The "Getting started" guide should be short and sweet. This commit
simplifies the "Environment-Modules" section pruning:

 - outdated / wrong suggestions as noted in #2440
 - uncommon setups that are better treated in a reference guide
2017-12-11 11:34:39 -08:00
Johann Klähn
e83c3d1b6a bazel: include SPACK_DEBUG_LOG_ID in environment (#6562)
Fixes #6521.

Bazel's build system filters environment variables, including those
set by Spack for use by its compiler wrapper. This updates the patch
to include the SPACK_DEBUG_LOG_ID variable added in #5837.
2017-12-11 10:34:06 -08:00
Satish Balay
53b2ec356b disable plasma in xsdk 0.3.0 (#6621) 2017-12-10 17:51:54 -08:00
Adam J. Stewart
f41a263a28 Fix reference to self.versions in neovim package (#6639) 2017-12-10 21:43:49 +01:00
Cyrus Harrison
95a384f051 updates to conduit and ascent packages (new PR) (#6584)
* optional path to use spacks py-site-pkgs, install host-cfg for provenance

* add more comments and address review requests

* only use st-pkgs-dir when +python

* ascent does not need doxygen

* capture mpiexec if it exists

* added missing import

* flake8 fix

* default adios variant to False

* ascent develop now reqs conduit master

* optional path to use spacks py-site-pkgs, install host-cfg for provenance

* add more comments and address review requests

* only use st-pkgs-dir when +python

* ascent does not need doxygen

* capture mpiexec if it exists

* added missing import

* flake8 fix

* default adios variant to False

* ascent develop now reqs conduit master

* conduit: use hdf5 1.8 for wider output compat
2017-12-08 13:43:12 -08:00
Chris Green
e279299b9b Relax restriction on lua version. (#5886) 2017-12-08 20:52:00 +01:00
Thilina Rathnayake
c1bc1be2a7 Add NekCEM package to spack (#6509) 2017-12-08 10:30:42 -07:00
Thilina Rathnayake
d6db532095 Update the Nekbone package (#6508) 2017-12-08 10:29:58 -07:00
healther
4c02e7e9f4 add restriction to py-setuptools dependency on py-flake8 (#6589) 2017-12-08 10:22:52 -07:00
Eric
bb8e7ee023 Perl-statistics-descriptive: Create new package (#6588) 2017-12-08 10:22:16 -07:00
Axel Huebl
5bf19a9d84 Fix AstroPy: Missing Markupsafe (#6630)
`py-markupsafe` was missing during `spack install` as a build error.
2017-12-08 10:21:46 -07:00
Axel Huebl
353ea07040 Add: Py-Plotly (#6628)
* Add: Py-Plotly

The requirements of py-plotlit are rather strict fixed to specific
versions, so I did not add an "upper versions" `:` to the constrains.
See
  https://github.com/plotly/plotly.py/blob/master/requirements.txt

* Py-Requests, Py-Six, Py-Pytz: Older Versions

Add two older versions of requests, pytz and six for plotly.
2017-12-08 10:21:28 -07:00
Paschalis Korosoglou
5e8139cbd1 Fix in download url for package libaio (#6616) 2017-12-08 10:20:14 -07:00
nshtg
e283a79da6 Update zsh to 5.4.2 (#6609) 2017-12-08 10:19:40 -07:00
lingnanyuan
3474dd5d40 r-tidycensus: Create new package. (#6595) 2017-12-08 10:18:45 -07:00
lingnanyuan
cc20ad0eec r-rgdal: Create new package. (#6593) 2017-12-08 10:18:29 -07:00
lingnanyuan
85c4224474 r-tigris: Create new package. (#6591) 2017-12-08 10:18:11 -07:00
nshtg
173236dacf Update openSSL to 1.0.2m/1.1.0g (#6596) 2017-12-08 10:13:58 -07:00
nshtg
fd764b9946 Update openSSH to 7.6p1 (#6598) 2017-12-08 10:13:41 -07:00
nshtg
1954075091 Update tmux to 2.6 (#6597) 2017-12-08 10:13:22 -07:00
Tzanio Kolev
2343e5185d Updated hash for v1.0 tag of Laghos (#6626) 2017-12-08 10:12:33 -07:00
Sergey Kosukhin
bd92cc0a1a Package 'openjpeg': set INSTALL_NAME_DIR on MacOS for old versions. (#6603) 2017-12-08 13:36:20 +01:00
Paschalis Korosoglou
1bdea98978 r-rhtslib: added build dependency on autoconf (#6627) 2017-12-08 11:18:25 +01:00
Eric
1c72a5da3a py-cogent: Create new package (#6624) 2017-12-08 10:38:37 +01:00
Denis Davydov
23d56a75ab dealii: update boost dependency (#6586)
(i) blacklst 1.65.0 due to issues on Ubuntu with gcc 5.4.0
(ii) add a patch for 1.65.1 to fix serialization
(iii) simplify boost's depends_on()
2017-12-08 10:37:54 +01:00
lingnanyuan
96476a32e5 py-htseq: Create new package. (#6623) 2017-12-08 10:36:57 +01:00
Brian Van Essen
20fc7d56d7 Candle benchmarks update (#6619)
Added a dependency on HDF5 support for the CANDLE benchmarks.
2017-12-08 10:34:49 +01:00
Benedikt Riedel
df184c707a Adding openssl dependency to xrootd. Closes #6601 (#6618) 2017-12-08 10:33:08 +01:00
nshtg
17692d6c05 Update vim to 8.0.1376 (#6599) 2017-12-08 10:29:50 +01:00
Eric
6f34c68aff subread: Add version 1.6.0 (#6615) 2017-12-08 10:26:18 +01:00
Denis Davydov
26e109027b qrupdate: fix blas/lapack and compilation of macOS (#6614) 2017-12-08 10:24:44 +01:00
Eric
62d5bb41a8 py-reportlab: Create new package (#6612) 2017-12-08 10:22:46 +01:00
nshtg
636ed371d8 Update fish to 2.7.0 (#6608) 2017-12-08 10:15:40 +01:00
Eric
91eca9143e bedtools2: Add version 2.27.0 (#6606) 2017-12-08 10:13:13 +01:00
Kelly (KT) Thompson
147a12dd06 Provide a patch to allow hdf5@1.10.1 to build with intel/18.0.1. (#6583)
This is known issue.  See:

https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
2017-12-08 09:55:06 +01:00
Sergey Kosukhin
a593553d48 Update for 'eccodes'. (#6604) 2017-12-08 09:34:37 +01:00
Sergey Kosukhin
a110a86ad6 Update for 'grib-api'. (#6605) 2017-12-08 09:33:30 +01:00
Jon Rood
69e76a0a89 Update openfast package to explicity pass MPI implementation during cmake configure. (#6590) 2017-12-08 09:09:35 +01:00
Axel Huebl
f49c186f4f wxWidgets: Fix builds (#6560)
- depends on GTK+ with X enabled
  (btw, non-X backends are deprecated/removed in GTK+)
- patch for 3.0.1-3.0.2: missing include caused multiple
  `error: call of overloaded ‘abs(XYPOSITION)’ is ambiguous`
  (seen in GCC 6.3.0); fixed in 3.0.3+
2017-12-07 08:33:08 +01:00
Massimiliano Culpo
05b10ce967
config.py: fixed comments that refer to variables following them (#6585)
According to the documentation here:

  http://www.sphinx-doc.org/en/stable/ext/autodoc.html

"For module data members and class attributes, documentation can either
be put into a comment with special formatting (using a #: to start the
comment instead of just #), or in a docstring after the definition."
2017-12-07 08:09:53 +01:00
lingnanyuan
3a4329c77d r-pathview: Create new package. (#6582) 2017-12-06 18:29:45 -07:00
lingnanyuan
c2ea795b08 r-kegggraph: Create new package. (#6580) 2017-12-06 18:29:22 -07:00
lingnanyuan
96c95db793 r-org-hs-eg-db: Create new package. (#6581) 2017-12-06 18:29:04 -07:00
Sergey Kosukhin
9a4dd413bb Package 'libszip': update checksum and list_depth. (#6587) 2017-12-06 18:28:11 -07:00