Commit graph

7734 commits

Author SHA1 Message Date
Denis Davydov
de3ff1a96b gettext: fix dependency type of xz (#10935) 2019-03-20 04:57:08 +01:00
sknigh
e717230bf8 added yara (#10901) 2019-03-20 04:55:02 +01:00
fcannini
9a8c4cf071 gromacs: make sure cuda support is disabled when cuda=False (#10936)
* abinit: Fix building with hdf5/netcdf.

* gromacs: Fix attempt to build with cuda support when 'cuda=False'

If for some reason there's a cuda toolkit installed by other means,
(i.e. not by spack) cmake will still try to build with cuda support,
even though 'cuda=False' is the default of the spec.

* Revert "abinit: Fix building with hdf5/netcdf."

This reverts commit e16f725e37b91193fe519b1821446c76ab551928.

This should not be here.
2019-03-20 04:54:03 +01:00
Michael Kuhn
1db5a3e0a3 libfabric: add 1.6.2 (#10918) 2019-03-20 04:52:50 +01:00
Matthias Diener
d935048982 git: add version 2.21.0 (#10937) 2019-03-20 04:49:47 +01:00
Michael Kuhn
b48a6f22be strace: add 5.0 (#10940) 2019-03-20 04:48:13 +01:00
Michael Kuhn
09d57d8cee libeatmydata: new package (#10941) 2019-03-20 04:47:45 +01:00
Kelly (KT) Thompson
a1eeeadfd8 Branson: provide new versions. (#10926)
* Branson: provide new versions.

+ Also update dependencies (newer version have fewer dependencies).

* fix style issue
2019-03-19 08:49:58 -06:00
Kelly (KT) Thompson
29ce8eb892 Draco: add variants (#10925)
* Draco: add variants

+ This package has many optional build dependencies that were not registered in
  older versions of this recipe.  I've added (and tested) this more complete
  list of optional dependencies: parmetis, superlu-dist, qt.

* fix style issues
2019-03-19 08:49:30 -06:00
Owen Solberg
3618d405b1 added checksum for new bowtie2 version (#10930) 2019-03-19 15:14:25 +01:00
Christoph Junghans
a6ccd99054
cabana: cuda backend (#10660) 2019-03-18 14:02:28 -06:00
Massimiliano Culpo
4aead5e35b
redis: new package (#10915)
Added versions from 4.0.11 to 5.0.3

closes #9180
2019-03-16 14:47:11 +01:00
Mark W. Krentel
e811e23f2e hpcviewer: new package (#10878)
* hpcviewer: new package

Add binary package for hpcviewer and hpctraceviewer for the Rice
hpctoolkit on Linux x86_64, ppc64 and ppc64le.

* ibm-java: add property 'home' so that spec['java'].home will work.

* Flake

* More flake.

* Test that the version, machine type pair exists before using it in the
sha dictionaries so that 'spack info' doesn't crash on unsupported
configurations.
2019-03-15 15:47:22 -05:00
Chris Green
6de6d5396c New package: mariadb-c-client (#7729)
* mariadb-c-client is a new package using the distinct, LGPL,
  MySQL-compatible client library from mariadb.com. It provides the
  virtual package mariadb-client
* mariadb is recorded as a provider of the mariadb-client virtual
* The mysql-client virtual package is also added, and mariadb-c-client
  is recorded as a provider for it
2019-03-15 14:12:30 -05:00
Adam J. Stewart
82e3380049
Add latest version and missing dependencies of MySQL (#10904)
* Add latest version and missing dependencies of MySQL

* m4 only needed on solaris
2019-03-15 14:01:54 -05:00
Christoph Junghans
4baf3d9d02 py-espressopp: add v2.0.2 (#10909) 2019-03-15 12:59:23 -05:00
Matthias Diener
dd09ab697b cmake: add version 3.14.0 (#10908) 2019-03-15 11:49:59 -05:00
Adam J. Stewart
cba5a8058e
Add ladot package (#10905) 2019-03-15 01:13:25 -05:00
Adam J. Stewart
4e6285a19b
Ensure that every package has a description (#10896) 2019-03-14 20:49:07 -05:00
Jordan Ogas
1d73868333 charliecloud: added version 0.9.8 (#10900) 2019-03-14 20:36:53 +01:00
Chris Green
6a9f02c96f cppunit: support cxxstd. (#10888) 2019-03-14 16:17:31 +01:00
Elizabeth Fischer
f15f3076db libxaw: added version 1.0.12 (#10591) 2019-03-14 12:55:56 +01:00
Levi Baber
a71664a42d py-pybigwig: needs curl at link time (#10892) 2019-03-14 11:07:50 +01:00
Cody Balos
4025ec9508 sundials: add new version (4.1.0) (#10890) 2019-03-14 11:00:22 +01:00
Nichols A. Romero
ec5bf38245 QMCPACK More CUDA Fixes (#10864)
* Throw InstallError if more than one GPU architecture is passed to cuda_arch. Previous cuda_arch test was not actually working because comparison with none string was on the cuda_arch list instead of the first entry of the list.

* Removing redundant cuda_arch statement.
2019-03-13 16:03:28 -05:00
Eric Martin
2bca687605 py-treehash: Create new package (#10872) 2019-03-13 16:03:09 -05:00
Levi Baber
39c40ee3fc revbayes: new version (#10873) 2019-03-13 21:36:13 +01:00
Michael Kuhn
d3365e4356 libplist, libusbmuxd: Fix pkgconfig dependency (#10876)
pkgconfig is the correct virtual provider.
2019-03-13 14:55:23 -05:00
Michael Kuhn
db79317eb9 cubelib, cubew: Add missing pkgconfig dependency (#10875) 2019-03-13 20:15:02 +01:00
Michael Kuhn
3019068e0c mpich: Add patch to fix node list parsing (#10870)
mpich@3.3 introduced a new regex-based function for node list parsing
that does not recognize hostnames without a dash properly.
2019-03-13 10:58:05 -07:00
Eric Martin
358226b946 py-biomine: new package (#10868) 2019-03-13 15:17:06 +01:00
Eric Martin
6a87b6215f help2man: Add version 1.47.8 and perl runtime dependency (#10862) 2019-03-13 15:11:45 +01:00
Eric Martin
7d50567423 py-advancedhtmlparser: new package (#10867) 2019-03-13 15:06:01 +01:00
Eric Martin
ffbc4f199e fqtrim: Create new package (#10861) 2019-03-12 21:30:30 -05:00
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