Commit graph

10943 commits

Author SHA1 Message Date
Greg Sjaardema
c19df8be5d NetCDF package: update constraints on hdf5 mpi support (#10788)
Update NetCDF to require building hdf5 without mpi when NetCDF itself
is built without mpi support.
2019-03-06 20:20:16 -06:00
Satish Balay
35daaa440f omega-h: add version 9.22.2 and update gcc 8 conflict (#10776)
* Versions before 9.22.2 compiler with gcc 8.3 or later
* Added version 9.22.2, which compiles with all gcc 8.x versions
  (including those before 8.3)
2019-03-06 20:10:47 -06:00
Adam J. Stewart
f7223e54ed Make is a required dependency of Spack (#10386)
Update documentation on getting started to mention that a "make"
executable is required to build packages with Spack.
2019-03-06 19:46:54 -06:00
Ryan S. Elliott
39467e4d67 Update kim-api package and add openkim-models-v2 (#10780)
* Replace kim-api package with kim-api-v2, which has different
  versions and removes the 'cmake_args' method
* Add openkim-models-v2 as an extension package
2019-03-06 19:23:05 -06:00
Mark W. Krentel
edecdc3ace libelf: move url to fossies.org (#10815)
* libelf: move url to fossies.org

Libelf is no longer maintained and the original mr511.de web site no
longer exists.  The final release, 0.8.13 from Nov 2009 is still
archived at fossies.org.

Fixes #10757.

* Change the homepage to the FSF entry.
2019-03-06 11:42:44 -08:00
Gregory Lee
10b0251af0 added python 2.7.16 (#10805) 2019-03-06 11:05:32 -08:00
Gregory Lee
86a1230a60 build fixes for util-linux (#10811) 2019-03-06 11:04:53 -08:00
Cameron Stanavige
9f734e0cfd unifycr: dependency changes and new version (#10722)
New release of UnifyCR. Remove unsupported pre-1.0 versions

UnifyCR has had a few dependency changes to make the backend more
efficient. A new pre-release version has been released as well to
mark these changes. Prior versions are no longer supported.
2019-03-06 10:56:20 -08:00
Owen Solberg
ff7cd40ca1 update package rsem (#10813) 2019-03-06 14:57:54 +01:00
Isaac Whitfield
1605368148 libusbmuxd: new package (#10726) 2019-03-06 10:10:02 +01:00
健美猞猁
c5573e660c intel-parallel-studio package: add version cluster.2019.2 (#10782) 2019-03-05 18:08:00 -06:00
健美猞猁
40d66e34d3 New package: pal (#10766) 2019-03-05 17:41:54 -06:00
健美猞猁
063f5b63da New package: erfa (#10763) 2019-03-05 17:40:39 -06:00
Greg Sjaardema
4c493b065c NetCDF package: add version 4.6.3 and update naming (#10786)
* Add NetCDF version 4.6.3
* Naming scheme for artifacts >= 4.6.2 has changed. Add a
  url_for_version function to generate the appropriate URLs
2019-03-05 17:33:47 -06:00
clellsolomon
b72715ed7c Add fzf utility package (#10778)
* Add fzf utility package

* Fix "style checks" errors

- var/spack/repos/builtin/packages/fzf/package.py:32:
  [E226] missing whitespace around arithmetic operator
2019-03-05 17:17:48 -06:00
Michael Kuhn
5758e49c80 gcc package: Add 8.3.0 (#10772) 2019-03-05 17:15:57 -06:00
Gregory Lee
7bd8689f06 openss package: allow all 2.7.x versions (#10807)
Originally the version constraint range had an upper bound of 2.7.15
This allows all 2.7.x versions
2019-03-05 17:14:32 -06:00
Alberto Chiusole
63e172d2ac RegCM: intel FC 'hint', 4.7.0 intel warning, fcflags, fix extensions. (#10797)
This should fix and improve #9934, which was messed up by a fetch from develop
2019-03-05 21:30:53 +01:00
Gregory Lee
bad485a221 various package version updates and build fixes (#10775)
* various package version updates and build fixes
2019-03-05 11:59:47 -08:00
Matthias Diener
c939e36ed9 cantera: make sundials dependency optional (#10764) 2019-03-05 19:58:00 +01:00
Michael Kuhn
c717f56359 ncl: Add 6.6.2 (#10800) 2019-03-05 17:13:51 +01:00
Michael Kuhn
21fb7dadb3 openssl: Add 1.1.1b, 1.1.0j and 1.0.2r (#10779) 2019-03-05 16:26:18 +01:00
Matthias Diener
9ba4d4e2af git-lfs: add version 2.7.1 (#10770) 2019-03-05 16:25:20 +01:00
Greg Sjaardema
d580d2a033 seacas: Update NetCDF version requirement (#10787)
Modified NetCDF requirement to allow NetCDF-4.6.2 and subsequent versions.
2019-03-05 14:05:52 +01:00
Justin Stanley
f19a214a19 libbeagle: add 3.1.2 (#10789) 2019-03-05 14:02:52 +01:00
Peter Scheibel
af4a36c4d9
Header subdirectories for Python and Eigen (#10773)
Fixes #10769 

This updates the .headers property to include header subdirectories
for Python and Eigen (as is recommended by these packages).

#10623 updated the default behavior of .headers.directories to
exclude subdirectories (since this can cause clashes with system
headers). This broke some packages which depended on the old behavior
of .headers.directories: for example if you had
<package-prefix>/include/subdir/ex1.h, .headers.directories would
include <package-prefix>/include/subdir.
2019-03-04 12:36:51 -06:00
Brian Van Essen
0ce1500376 Package Updates for ECP CANDLE Supervisor (#10760)
* Add EQ-R package
* Add Fansi, Pillar, UTF8 (R) packages
* Add new versions for py-mdanalysis, r-cli, r-dplyr, r-pkgconfig,
  r-rlang, r-tibble, stc, and turbine packages
* Add hdf5 support for turbine
* Specify configure directory for stc package
2019-03-01 14:46:13 -06:00
Justin Stanley
c8557ba7d8 blast2go: new package at 5.2.5 (#10725)
* blast2go: new package at 5.2.5

* blast2go: remove redundant url
2019-03-01 12:36:00 -06:00
Matthias Diener
ee5e5ce3c6 new package: intel-pin (#10546) 2019-03-01 12:29:01 -06:00
Justin Stanley
1a8161a982 r-bfastspatial: new package at 0.6.2 (#10734) 2019-03-01 10:18:14 -06:00
Justin Stanley
cbc6a2070a r-bfast: new package at 1.5.7 (#10733) 2019-03-01 10:17:37 -06:00
Justin Stanley
94357a274c bedops: avoid static linking with glibc (#10456) 2019-03-01 10:17:01 -06:00
Justin Stanley
165d8da0c2 blast-legacy: new package at 2.2.26 (#10610)
* blast-legacy: new package at 2.2.26

* blast-legacy: compile from source

* blast-legacy: add missing os.symlink import

* blast-legacy: fix build script interpreter
2019-03-01 10:14:37 -06:00
Justin Stanley
f9947333ca bridger: new package at 2014-12-01 (#10611) 2019-03-01 10:09:23 -06:00
Justin Stanley
c4aba6a204 r-spatial: new package at 7.3-11 (#10728) 2019-03-01 09:57:59 -06:00
Justin Stanley
16af5f31d9 r-nortest: new package at 1.0-4 (#10729) 2019-03-01 09:55:30 -06:00
Justin Stanley
4f1044a072 r-xts: add 0.11-2 (#10730) 2019-03-01 09:54:26 -06:00
Justin Stanley
104a8a1422 r-gdalutils: new package at 2.0.1.14 (#10731) 2019-03-01 09:53:30 -06:00
Justin Stanley
0766e7fbbb r-rgdal: add 1.3-9 (#10732) 2019-03-01 09:52:07 -06:00
Justin Stanley
89f59f7ab0 hyphy: new package at 2.3.14 (#10759) 2019-03-01 09:31:46 -06:00
Patrick Gartung
1d4289afdd
This fixes a problem where the placeholder path was not in the first rpath entry.
* Rework of buildcache creation and install prefix checking using the functions introduced in
https://github.com/spack/spack/pull/9199

Instead of replacing rpaths with placeholder and then checking strings, make use of the functions
relocate.is_recocatable and relocate.is_file_relocatable to decide if a package needs the allow-root option.

This fixes a problem where the placeholder path was not in the first rpath entry. This was seen in c++ libraries and binaries because the compiler was outside the spack install base path and always appears first in the rpath.

Instead of checking the first rpath entry, all rpaths have the placeholder path and the old install path (if it exists) replaced with the new install path.

* flake8
2019-03-01 07:47:26 -06:00
Jiawei Zhuang
433cc4a972 Fix sha256 sum for IOR (#10765) 2019-03-01 09:59:36 +01:00
Massimiliano Culpo
e3af8ed454 Added a sub-command to show if packages are relocatable (#9199)
* Added the `spack buildcache preview` sub-command

This is similar to `spack spec -I` but highlights which nodes in a DAG
are relocatable and which are not.

spec.tree has been generalized a little to accept a status function,
instead of always showing the install status

The current implementation works only for ELF, and needs to be
generalized to other platforms.

* Added a test to check if an executable is relocatable or not

This test requires a few commands to be present in the environment.
Currently it will run only under python 3.7 (which uses Xenial instead
of Trusty).

* Added tests for the 'buildcache preview' command.

* Fixed codebase after rebase

* Fixed the list of apt addons for Python 3.7 in travis.yaml

* Only check ELF executables and shared libraries. Skip checking virtual or external packages. (#229)

* Fixed flake8 issues

* Add handling for macOS mach binaries (#231)
2019-02-28 15:36:47 -06:00
Sajid Ali
6d20e938da petsc: add +knl variant 2019-02-28 11:07:04 -06:00
Satish Balay
f8da8dbd0e
Trilinos: add release 12.14.1 (#10740)
xsdk: switch from 12.14.0-rc1 to 12.14.1
2019-02-28 11:05:05 -06:00
Michael Kuhn
617c1a3706 Fix shell integration with environment-modules@4 (#10736) 2019-02-28 13:22:44 +01:00
Eric Martin
4e80977506 py-tetoolkit: Add version 2.0.3 (#10749) 2019-02-28 12:59:30 +01:00
Owen Solberg
fac2dbda07 git-lfs: patch Makefile for v2.7.0 (#10720)
Fixes #10702

Same fix merged upstream in git-lfs/git-lfs#3545 -- it may appear
in future release v2.7.2 according to package maintainer.
2019-02-27 16:02:25 -06:00
Adam J. Stewart
a25edb51a9 Fix 'make test' detection when LANG is not in English (#10499) 2019-02-27 14:01:50 -06:00
Justin Stanley
2f4f828b45 wtdbg2: new package (#10639)
* wtdbg2: new package at 2.3

* wtdbg2: flake8 fix
2019-02-27 13:27:45 -06:00