Commit graph

7700 commits

Author SHA1 Message Date
David Hows
c629a6f780 Fix mysqldb1 (#9978)
* Update package.py

* Add MYSQL Package file

* Fixes for linter
2019-03-12 20:57:29 -05:00
Elizabeth Fischer
82e9c01b5c New package: py-mysql-connector (#10327)
* New package: py-mysql-connector

* Fixed docstring

* 1. Determined that py-setuptools was not needed at all, so removed.
2. Added py-protobuf.  Docs seem to imply that only C protobuf library is required; however, the Python setup.py says differently, and some Python code seems to reference protobuf too.  I don't know why this worked for me, but it looks like including py-protobuf is the right thing to do.

* Applied solution detailed in:

https://github.com/mysql/mysql-connector-python/pull/9

Uncommenting this patch will make `error: option --single-version-externally-managed not recognized`  reappear.

* Clean up / reorder lines

* flake8
2019-03-12 20:52:43 -05:00
Eric Martin
3d7164c13f varscan: set VARSCAN_HOME variable to jar file location (#10744) 2019-03-12 20:29:48 -05:00
Eric Martin
0ebd81bd15 py-pytables: Add hdf5 1.10.x support for versions above 3.4.0 (#10746) 2019-03-12 20:29:24 -05:00
David Poliakoff
d5c3ce790f Update caliper package (#10750)
* Updating Caliper package with a shared lib option

* Tightened version bounds on Caliper package

* Removed testing. Loosened version constraints

* Add Caliper 2.0.1, cleanup dependency specs
2019-03-12 20:28:13 -05:00
Rob Latham
da28b592fc "Werror" too strict for recent compilers (#10802)
rapidjson gives warnings with gcc-7.3 and branch fall through
2019-03-12 20:10:51 -05:00
Michael Kuhn
65f37746af qt: Use more system dependencies and fix build with new gcc versions (#10817)
qt currently falls back to bundled versions of sqlite, harfbuzz, pcre,
double-conversion and xcb. This adds the appropriate dependencies and
configure arguments. A new variant adds multibyte support to pcre and
pcre2, which is required by qt.

Additionally, newer versions of gcc (starting with @8.3.0) cause build
failures. This adds a patch to fix the problem.

The changes have been tested with all versions of qt currently available
in Spack. 5.2 and 5.3 do not build for reasons that seem to be unrelated
to these changes, though.
2019-03-12 20:04:11 -05:00
健美猞猁
a79230c832 casacore does not support fftw+mpi . (#10839) 2019-03-12 19:59:48 -05:00
健美猞猁
d32a342fc6 Aoflagger: a new package. (#10840)
* A new package: aoflagger.

* aoflagger does not support boost>1.66.0 .

* Add fftw~mpi dependency.

* flake8.

* Flake8.

* Update package heder.

* md5 -> sha256.
2019-03-12 19:59:24 -05:00
Axel Huebl
fd6d3f6b8c openPMD-api: shared variant (#10847)
Add a variant to control shared/static builds (one at a time) and
make shared the default.
2019-03-12 19:58:44 -05:00
Alberto Chiusole
46fb6ed5b6 Revert to manual flag enabling, due to RegCM bug in configure. (#10863)
The configure of RegCM treats --disable-FEATURE as --enable-FEATURE,
so we cannot use enable_or_disable.
2019-03-12 19:48:45 -05:00
Owen Solberg
dc5b16a8e9 added checksum for 20190222 release of gnu parallel (#10865) 2019-03-12 19:40:29 -05:00
Eric Martin
50193229ea py-llvmlite: Add versions 0.26.0 and 0.27.1 (#10866) 2019-03-12 19:40:01 -05:00
Mark W. Krentel
3ed6e78338 New package: ibm-java (#10777)
* Add binary package of the IBM Java SDK for big and little-endian
  powerpc (power7, 8 and 9).  The jdk and openjdk packages only install
  on x86_64.
* Add ibm-java as a java provider
* The jdk and openjdk packages only install on x86_64. Add conflicts
  for ppc64 and ppc64le to jdk and openjdk.
2019-03-12 18:05:47 -05:00
wspear
e1e5eb29d2 Elfutils package: add m4 dependency and version 0.176 (#10834)
* Elfutils requires m4 to build
* Add version 0.176
2019-03-12 17:35:59 -05:00
Robert Pavel
1450fe72fa New package: Draco (#10844) 2019-03-11 20:57:00 -05:00
Matthias Diener
5e68af5a78 scons package: add missing dependency to py-setuptools (#10856) 2019-03-11 20:30:12 -05:00
Jiawei Zhuang
74b33e9f82 OpenMPI: v4.0.0 + Slurm installation error (#10853)
shmemrun and oshrun do not exist in OpenMPI v4.0.0
(ref: https://www.open-mpi.org/doc/v4.0/)

The Spack OpenMPI package was failing the install by trying to
remove them. This guards the removal of several scripts when
using the Slurm scheduler to handle the case where they don't exist.
2019-03-11 20:18:50 -05:00
Michael Kuhn
1e6b13d335 Fix URLs for VI-HPS projects (#10821)
URLs for the opari2, otf2, and scorep packages have changed (although
the checksums are the same)
2019-03-11 20:12:44 -05:00
Stas Sergienko
9ffd508d7c mpich: add psm2 fabric support (#10814)
psm2 is only supported for versions 2.2 and up, so a conflict is
added for earlier versions
2019-03-11 20:10:02 -05:00
健美猞猁
888bb76758 New package: cotter (#10838) 2019-03-11 19:46:40 -05:00
Eric Martin
1d51cdf824 STAR: Add versions 2.7.0d and 2.7.0e (#10831) 2019-03-11 19:44:54 -05:00
Eric Martin
23b73ca982 py-chardet: Add version 3.0.2 (#10827) 2019-03-11 19:44:30 -05:00
Eric Martin
2e47b45d9f py-urllib3: Add version 1.21.1 (#10826) 2019-03-11 19:44:07 -05:00
Greg Sjaardema
204063e21a cgns package: add version 3.4.0 and update hdf5 dependency (#10803)
* Add version 3.4.0
* Update checksums for older versions to sha256
* Require hdf5~mpi when building with ~mpi
2019-03-11 19:43:16 -05:00
Eric Martin
dc0b6a0613 samtools package: Add version 1.5 and htslib 1.5 dependency (#10825) 2019-03-11 19:29:29 -05:00
Alberto Chiusole
2b591653fa hdf5 package: add version 1.10.5 (#10794) 2019-03-11 15:15:03 -05:00
Justin Stanley
46466381b8 py-crossmap: new package at 0.3.3 (#10854) 2019-03-11 15:13:02 -05:00
Michael Kuhn
9425075a23 flex: Apply 2.6.4 patch regardless of gcc version (#10841)
It seems that this is actually a glibc problem and while 2.6.4 builds
without the patch on newer versions of gcc (@8:), it still sometimes
segfaults (as observed during the doxygen build).
2019-03-11 15:12:28 -05:00
Ce Qin
43525d3445 mpich: remove libpciaccess dependency for MacOS (#10795) 2019-03-11 15:06:49 -05:00
Gregory Lee
1fd01af773
added intel 19.0.3 packages (#10835)
* added intel 19.0.3 packages

* added intel 19.0.3 packages
2019-03-11 07:03:24 -07:00
Chris Green
1931bc8b40
Add 2019.{3,4} and patches for pedantic warnings. (#10836) 2019-03-11 09:03:19 -05:00
Chris Green
7e22fdfa21
boost: patch for problem with warnings for 1.69.0. (#10820) 2019-03-11 09:02:50 -05:00
Eric Martin
43b45f4140 breseq package: Add version 0.33.2 and zlib dependency (#10747)
For zlib, also update the `CFLAGS`/`LDFLAGS`
2019-03-08 20:57:00 -06:00
Denis Davydov
c81e68030a intel: add 2019.3 (#10843) 2019-03-08 14:50:58 -08:00
Christoph Junghans
0d07dea2eb
snap: overwrite flags (#10832) 2019-03-07 14:53:04 -07:00
Christoph Junghans
c11e745421
cloverleaf3d: overwrite flags (#10830) 2019-03-07 14:08:52 -07:00
Christoph Junghans
2f7589adc4
cloverleaf: overwrite flags (#10829) 2019-03-07 14:08:36 -07:00
Levi Baber
016945f67a
autofact: fix dependency (#10818) 2019-03-07 13:51:40 -06:00
Eric Martin
e750c5af66 trimmomatic package: restrict java dependency to version 8 (#10741) 2019-03-07 13:49:57 -06:00
Tristan Carel
dd6e91fcb6 Nix package: update dependencies (#10646)
* Add 'fiber' as a default library for boost
* Add autoconf/automake etc. dependencies to libseccomp package
* New package: brotli
* New package: editline
* Add brotli, editline, boost dependencies to Nix
2019-03-07 13:32:55 -06:00
Matthias Maiterth
23822e9717 GEOPM package: add version 1.0.0-rc2 (#10737) 2019-03-07 13:18:05 -06:00
Eric Martin
d072a1e0e3 py-sip package: Add version 4.19.3 (#10742) 2019-03-07 13:16:54 -06:00
Eric Martin
435db9d1a5 seqtk package: Add version 1.3 (#10743) 2019-03-07 13:16:20 -06:00
Michael Kuhn
3fb75e1206 flex package: patch for building 2.6.4 with gcc 7 (#10754)
Remove 2.6.3 as preferred version (but keep it available for
building). The latest version (currently 2.6.4) is now preferred
(according to Spack's defaults).
2019-03-07 13:15:47 -06:00
Eric Martin
49e307398b py-certifi: Add version 2017.4.17 (#10828) 2019-03-07 13:09:26 -06:00
Michael Kuhn
2fed84058d py-flake8: Add missing dependencies for @3.7.7 (#10796)
* Update dependencies for py-flake8 when building version 3.7.7
* Add FIXME comment for an example dependency constraint which causes
  concretization to hang
* Add py-entrypoints version 0.3
* Add py-pycodestyle version 2.5.0
2019-03-07 12:50:30 -06:00
健美猞猁
42633e34ab CMake package: update libuv dependency constraints (#10824)
* Add libuv version 1.10.0
* CMake versions before 3.12.0 do not build with libuv version
  1.25.0, so a constraint is added to build earlier versions of
  CMake with libuv version 1.10.x
2019-03-07 12:42:24 -06:00
prs513rosewood
32bbffc869 thrust: add versions 1.9.0-1.9.4 (#10823) 2019-03-07 14:36:59 +01:00
Eric Martin
efdeb860d1 transdecoder package: Add version 5.5.0 and fix up url and installation paths (#10745)
* Add version 5.5.0 and fix installation locations
* URL format has changed as of version 5.5.0
* Update paths created for installation
2019-03-06 20:58:50 -06:00
Eric Martin
45856c3660 bsseeker2 package: Add versions 2.1.8 and 2.1.5 (#10748)
As of version 2.1.8, the url format changed, so also update that
2019-03-06 20:55:06 -06:00
Jeongseok Lee
0e22a94f81 Eigen package: support Spack-external builds using Eigen (#10751)
Update CPATH in setup_environment for Eigen, so that the
Spack-generated module for Eigen will help builds outside of Spack
use the appropriate include prefix for Eigen headers 
(<install_prefix>/include/eigen3/ rather than <install_prefix>/include/)
Note that this only updates the run-time environment, rather than the
build-time environment, so Spack builds depending on Eigen that use
pkgconfig will not be confused by the presence of the Eigen include
directory in CPATH.
2019-03-06 20:48:38 -06:00
Matthias Diener
836f40e30f scons: add version 3.0.4, cleanup URLs (#10806) 2019-03-06 20:39:39 -06:00
HAOCHENG LIU
a3a8ed7234 vtk-m package: turn off mpi support by default (#10755) 2019-03-06 20:34:49 -06:00
健美猞猁
9d880b8838 New package: dysco (#10767) 2019-03-06 20:25:06 -06:00
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
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
Jiawei Zhuang
433cc4a972 Fix sha256 sum for IOR (#10765) 2019-03-01 09:59:36 +01:00
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
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
Justin Stanley
2f4f828b45 wtdbg2: new package (#10639)
* wtdbg2: new package at 2.3

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