Commit graph

8825 commits

Author SHA1 Message Date
Glenn P Johnson
b046ee20f5 Fixes for augustus package
- add missing perl dependency
- only filter Makefile if referred to dependency is in the spec
- rewrite the shebang line of scripts to use spack perl
- remove tabix dependency as tabix and bgzip are part of htslib
2019-09-13 19:07:35 -07:00
Glenn P Johnson
2256890d4e Update genemark-et package
- add version 4.46
- add missing perl dependencies
- new version has different source layout
- filter shebang to use spack perl
2019-09-13 19:05:02 -07:00
Sinan
6df57bb2d0 New package: py-pykwalify (#12540) 2019-09-13 12:22:08 -07:00
Frédéric Simonis
3f06d5c12a preCICE: added versions 1.6.0 and 1.6.1 (#12809) 2019-09-13 16:04:50 +02:00
Glenn Johnson
3cc95c6427 diamond: added version 0.9.25 (#12805) 2019-09-13 07:37:52 +02:00
Sinan
48e9090252 New package: py-ruamel-yaml (#12543) 2019-09-12 15:46:39 -07:00
Owen Solberg
78f3f4c309 Singularity package: add version 3.4.0 (#12785)
This version in combination with the included patch can install
without root.
2019-09-12 13:45:00 -07:00
Owen Solberg
6608876747 New package: cryptsetup (#12762)
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-12 13:41:53 -07:00
Sinan
b95b4bb9e0 add compilation option to sqlite (#12794)
* add compilation option to sqlite

* rename variant

* fix bug

* re-rename variant
2019-09-12 15:31:03 -05:00
ktsai7
96ba5a1265 Update legion gasnet config (#12523) 2019-09-12 13:46:37 -06:00
Simo Tuomisto
5a6d060b52 py-gpaw: Fixed broken fftw linking in newer versions of py-gpaw (#12795) 2019-09-12 09:36:45 -05:00
brietzke
3269f712f0 fgsl: new version + fix for recent spack commit (#12790) 2019-09-11 20:15:50 -05:00
Chris Green
e727e79b73 jsoncpp: new versions, support cxxstd variant. (#12780) 2019-09-11 12:32:49 +02:00
Owen Solberg
e3d06dc0d7 create package popt (#12783) 2019-09-10 21:33:33 -05:00
Jonas Lippuner
97641aab63 fix bug in p4est (don't use MPI spec if not compiling with MPI) (#12784) 2019-09-10 19:39:42 -05:00
Hironori-Yamaji
9962696128 openmx: new package (#12768)
* openmx: new package

* openmx: use copy method
2019-09-10 12:59:13 -05:00
Janne Blomqvist
3f1762bcc2 cuda: New version 10.1.243 (#12777)
* cuda: New version 10.1.243

Adds CUDA 10.1.243. The installer command-line arguments have slightly
changed, hence in the install method the version needs to be inspected
in order to give the correct arguments for the new installer.

* cuda: Combine common command-line arguments

The CUDA 10.1+ installer has slightly different command-line arguments
than previous versions.  Keep the common parts together and only split
where they are different.

* Make flake8 happy
2019-09-10 10:52:55 -07:00
Owen Solberg
c23bea80bd py-atropos: new package (#12745)
* create new package py-atropos

* remove whitespace

* make tqdm and pysam dependencies optional, exposed as variants
2019-09-10 12:18:31 -05:00
Hironori-Yamaji
fefd998509 ccs-qcd: disable parallel builds (#12775) 2019-09-10 14:19:09 +02:00
xfzhao
c30f9c6833 update bbmap (#12721)
* update bbmap

* remove one extra comment line
2019-09-09 12:55:06 -05:00
Michael Kuhn
62f0286f5e Fix pkgconfig dependencies (#12714)
pkgconfig is the virtual dependency, pkg-config is an implementation.
2019-09-09 12:54:46 -05:00
brietzke
4de32033b1 Update py-bokeh: new version & dependencies" (#12724)
* update py-bokeh: new version & dependencies

* Revert "update py-bokeh: new version & dependencies"

This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.

* update py-bokeh: new version & dependencies

* trigger travis-ci

* adjust python dependency-type to br
2019-09-09 11:59:27 -05:00
brietzke
155a667b7a New package: py-fsspec (#12725)
* update py-bokeh: new version & dependencies

* Revert "update py-bokeh: new version & dependencies"

This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.

* new package: py-fsspec: add package.py

* trigger travis-ci

* adjust python dependency-type to br
2019-09-09 11:58:49 -05:00
Dan Lipsa
1a8c572316 Paraview version (#12766)
* Update paraview

* Paraview 5.6.2 provides only .xz (no .gz)

* Add list_url and list_depth
2019-09-09 11:57:53 -05:00
viniciusvgp
7849dbb529 binutils: fix undefined symbol libintl_dgettext (#12770) 2019-09-09 11:05:04 -05:00
Greg Sjaardema
db1fb16840 CGNS: Add setting of RPATH on Darwin (#9984)
* CGNS: Add setting of RPATH on Darwin

This should go in the CGNS CMakeLists.txt, but it isn't there yet and won't be in previous versions, so best to handle it here.  
If building on darwin/MacOSX, need to set the RPATH so applications can find shared library correctly.

* Restrict MACOSX_RPATH setting

This has now been added to the CGNS distribution, so the setting of `CMAKE_MACOSX_RPATH` should be restricted to current and previous releases and not upcoming releases.
2019-09-08 17:14:56 -05:00
Geoffrey Oxberry
983e6b4a4a fribidi@1.0.5: new package (#12386) 2019-09-08 17:10:39 -05:00
Sinan
4a18d40a66 new package: py-iniparse (#12638)
* new package: py-iniparse

* add git version supporting python3

* redo python dependency
2019-09-08 17:09:24 -05:00
Sinan
d66caf7a66 Package/py configobj (#12639)
* new package: py-configojb

* add version 4.7.2

* improve dependencies

* fix url for versions > 5.0.0

* Update var/spack/repos/builtin/packages/py-configobj/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-configobj/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* use format to create url strings

* fix typo

* improve style

* Update var/spack/repos/builtin/packages/py-configobj/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08 17:08:59 -05:00
Owen Solberg
2ad6bed77c for fakeroot support, add "shadow" dependency (#12754)
* adding checksum for singularity 3.4, adding dep for shadow

* make v3.4 a TODO for now -- needs cryptsetup package first
2019-09-08 13:55:15 -05:00
Adam J. Stewart
bff667051b
Fix PyQt installation (#12479)
* Fix PyQt installation

* Switch dependency type

* Replace SIP dependency with resource

* Relax py-pyqt4 Qt dependency
2019-09-08 10:48:50 -05:00
Simo Tuomisto
5a21c781f3 py-gpaw: Fixing missing numpy include path, adding newer version of p… (#12737)
* py-gpaw: Fixing missing numpy include path, adding newer version of py-gpaw and fixing a bug with libxc.c in older py-gpaw

* py-gpaw: Fix Python and ASE version dependencies

- GPAW 19.8.1 requires Python 3.x, add dependency on python@3.5:

- GPAW releases are associated with a corresponding ASE release, add
  matching ASE version dependencies.

* py-gpaw: Enable the scalapack variant by default

GPAW installation instructions say scalapack is optional but "highly
recommended". Thus enable it by default.
2019-09-08 10:46:47 -05:00
Owen Solberg
8fd8b54e97 py-cutadapt: Updated version checksum (#12741)
* add new cutadapt release 2.5, and adjust dependencies conditional on version

* use https, not ssh, for git url

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08 10:46:08 -05:00
Owen Solberg
fe26678299 new package: py-bz2file (#12761)
* update py-xopen (add 0.8.2 checksum)

* refine version specific dependencies

add py-bz2file, which needs to be created

* create py-bz2file

* Revert "refine version specific dependencies"

This reverts commit 70649da98851fefb2f936ca99a012fe6bef07b70.

* Revert "update py-xopen (add 0.8.2 checksum)"

This reverts commit 7400f44caa6e98419eb4bc3107704b91e8a2018b.
2019-09-08 10:38:37 -05:00
Owen Solberg
b83fa3909e py-xopen: update release 0.8.2 checksum (#12742)
* update py-xopen (add 0.8.2 checksum)

* refine version specific dependencies

add py-bz2file, which needs to be created

* py-bz2file needed when built with python 2.7

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* space after comma
2019-09-08 10:38:19 -05:00
Owen Solberg
4468ee2437 py-dnaio: new package need by py-cutadapt (#12743)
* add new package py-dnaio

* provide git url with https, not ssh, protocol

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08 10:37:49 -05:00
Todd Gamblin
a2220f3150 flake8: make entire repository pass spack flake8 -a
- Fix trailing whitespace missed by the bug described in #12755.

- Fix other style issues that have crept in over time (this can happen
  when flake8 adds new checks with new versions)
2019-09-07 23:59:10 -07:00
Owen Solberg
48c3c833e8 patch boost version 1.54-1.55 when being built with ANY gcc version after 5.0 (#12718) 2019-09-07 22:45:53 -05:00
Kevin Huck
35221c127e Updating TAU package. Fixing compiler specification for OSX (#12720)
and making Fortran an option that can be disabled.  Also added
support for the POSIX I/O wrapper and OMPT for OpenMP.
2019-09-07 22:44:40 -05:00
Howard Pritchard
1a38285be9 mesa: disable use of libunwind for arm arch (#12735)
There are problems with libunwind for arm and trying to use it with mesa.
See for example:

https://github.com/grate-driver/mesa/issues/6

disabling use of libunwind for arm, allows the package to be built

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2019-09-07 22:33:30 -05:00
Jonas Lippuner
c3a2528022 add mpi variant to p4est package to allow turning off MPI (#12739) 2019-09-07 22:29:53 -05:00
Axel Huebl
331e4e32be ncurses: improve build time (#12621)
Apply configure options to skip manpage generation
and test builds for both wide and non-wide builts.
2019-09-07 22:27:07 -05:00
Ruben Di Battista
ac7a17754f luarocks: Use make command instead of install (#12703)
This way luarocks does not attempt to pull stuff from the internet.

Fix #3909
2019-09-07 21:06:52 -05:00
Adam J. Stewart
faa3d6a2a5
Add py-numpy 1.17.2 (#12753) 2019-09-07 20:44:46 -05:00
Piotr Luszczek
bbdb033e5f Add patches to work around CMake versions (#12744)
- Use of symbol testing macro requires explicit include()
- CMake policies are not version-portable and the support has to queried
  based on CMake version
2019-09-07 19:04:20 -05:00
Owen Solberg
c4da66be4c font-util 1.3.2 (#12728) 2019-09-07 18:57:22 -05:00
Sinan
754ce972a3 new package: py-pygdal (#12747) 2019-09-07 18:23:38 -05:00
Vanessasaurus
25bbc27716 adding shadow-uidmap (#12750)
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
2019-09-07 17:36:45 -05:00
Mathias Jacquelin
696e12da98 upcxx: new package
Adding a UPC++ spack package pointing to the default 2019.3.2 UPC++
version, and allowing to build UPC++ with the experimental CUDA variant.
2019-09-06 16:04:33 -07:00
Toyohisa Kameyama
5def1dd39d openspeedshop: fixed build on arm. (#11861)
* openspeedshop: fixed build on arm.

* remove patch comment.
2019-09-06 13:26:24 -07:00