Commit graph

8935 commits

Author SHA1 Message Date
Toyohisa Kameyama
d238b9d394 breseq: fix dependency and limit compiler version. (#13013) 2019-10-02 11:56:37 -05:00
Andreas Baumbach
64ff27626e update py-jupyter-notebook to use the real releases (#13020)
* github releases are not released versions, but from-source
  releases
* they lack the mimification of the JS/CSS components and as
  such require node-js and npm, this conflicts with python@3:
* this commit
  * drops the from-source dependencies on node-js and npm and
  * updates the checksums to the correct sha256 hashes of the
    pypi releases. The pypi-tarballs are different
2019-10-02 11:39:55 -05:00
Axel Huebl
bec2830802
ZFP: CMake Package (#12999)
* ZFP: CMake Package

ZFP is primarily build via CMake, which will have all install logic
and configuration files generated.
The 0.5.0 release did not support this yet, so we toss it.

* Patch ADIOS1: ZFP 0.5.1+ support

* ZFP: Expose all CMake variants
2019-10-01 23:28:36 -07:00
George Hartzell
22e75b77e3 direnv: add info for version 2.20.0 (#13007) 2019-10-01 22:34:14 -05:00
Sinan
d20e3517c2 new package: py-python-ldap (#12599)
* new package: py-python-ldap

* fix dependency types

* improvements

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

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

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

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

* add openldap dependency
2019-10-01 20:59:53 -05:00
Sinan
91488ed8f5 New package: py-python-mapnik (#12786) 2019-10-01 18:37:34 -07:00
codeandkey
5c2b01ebcf picard: add 2.20.8 2019-10-01 18:19:37 -07:00
Daryl W. Grunau
248bc17bb0 go-md2man: disable module-mode (#12985)
* go-md2man: disable module-mode

* Update var/spack/repos/builtin/packages/go-md2man/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01 19:17:10 -05:00
Eduardo Arango
c1ecd037d7 add singularity 3.4.1 (#12995)
* add singularity 3.4.1

Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>

* revert some changes

Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>

* add maintainers list to pkg singularity

Add @alalazo and me to the Singularity maintainers list

* Update var/spack/repos/builtin/packages/singularity/package.py

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

* Update var/spack/repos/builtin/packages/singularity/package.py

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

* Update var/spack/repos/builtin/packages/singularity/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01 19:16:20 -05:00
Axel Huebl
436afdd2a8
Dataspaces: Fix Fetch URL, Savanna Spec (#13001) 2019-10-01 14:52:44 -07:00
Peter Scheibel
3575f9b382
GCC package: don't set CC etc. based on bin dir if it doesn't exist (#13000)
7bcb306 updated setup_environment in the GCC package to examine the
bin/ directory to find alternatively-named instances of CC, but this
failed to account for when GCC was being installed and failed when
it attempted to list the not-yet-existing installation prefix. This
commit updates the logic to skip this search if the bin/ directory
doesn't exist.
2019-10-01 14:29:01 -07:00
Massimiliano Culpo
245c1bb208 libaio: fixed a condition that checks whether we are running on OS X (#12976)
* libaio: fixed a condition that checks whether we are running on OS X

* libaio: simplified package by adding an explicit conflict for darwin

* libaio: added information to the docstring

* fio: added version 3.16, added conflict when using libaio, docstring

* lvm2: conflict due to libaio dep, improved docstring, simpler install

* mariadb: conflict due to libaio dep, improved docstring, version 10.4.7

* mariadb: the dependency on libaio is now conditional, removed conflict

* mariadb: fixed a typo in previous commit

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

* libaio: turned into a MakefilePackage
2019-10-01 15:35:50 -05:00
Jimmy Tang
a7e64e5396 Kaldi package: add version 7637de7 and egs (#12911) 2019-10-01 10:24:03 -07:00
Jeffrey Salmond
5868e0f5f2 add new mercurial versions (#12997) 2019-10-01 12:08:28 -05:00
Christopher Edsall
82a3ee0868 Update chapel to current (1.19 -> 1.20) (#12991) 2019-10-01 11:47:57 -05:00
Axel Huebl
10e4d611a5 ADIOS2: 2.5.0 (#12987)
Add the latest ADIOS2 release, v2.5.0 .
2019-10-01 10:49:52 -05:00
Satish Balay
b9a860820a hypre: add version 2.18.0 (#12992) 2019-10-01 10:48:40 -05:00
Mark Olesen
f939697863 add adios2 dependency and configuration for newest OpenFOAM (#12993) 2019-10-01 10:48:14 -05:00
noguchi-k
5b4040ea36 libcerf:add CFLAGS for fujitsu compiler (#12990)
* libcerf:add CFLAGS for fujitsu compiler

* fix for flake8
2019-10-01 08:54:01 -05:00
egreen77
cfc17e9506 Update nano (#12980) 2019-09-30 16:27:29 -05:00
Adam J. Stewart
5b2b0ee9a3
Revert "update neovim (#12965)" (#12978)
This reverts commit 86a85b7eb2.
2019-09-30 13:18:27 -05:00
Satish Balay
c70f9bffe2 petsc, slepc: add new versions - 3.12.0 (#12979) 2019-09-30 13:18:11 -05:00
Seth R. Johnson
7bcb306d4a Fix GCC environment variables for external installations (#12454)
Unlike the compiler binary name search logic, the `setup_environment` in
GCC's package assumes the compiler names are *exactly* `gcc`, `g++`,
etc. In many external installations (Homebrew, Macports) the
installation includes only *suffixed* versions such as `gcc-9`.

This patch uses the GCC compiler search suffixes to actually locate the
correct filenames for the installed compilers, allowing the
Spack-generated module file to have useful definitions of CC, CXX, etc.

It also allows for the possibility that the user's external installation
of GCC is compiled without Fortran support, in which case the `FC`
environment variables are not defined.
2019-09-30 11:02:32 -07:00
t-karatsu
139eaa1306 otf2: add configure args to specify compiler commands. (#12711)
* otf2: add configure args to specify compiler commands.

* Modify the reference of the compile commands.
2019-09-30 08:18:09 -05:00
Glenn Johnson
c56f03a3ba The perl-uri-escape package duplicates perl-uri (#12971)
* The perl-uri-escape package duplicates perl-uri

The Perl URI::Escape module is in the Perl URI package so the Spack
perl-uri-escape package is a duplicate of the perl-uri package. This PR
does the following:

- replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')`
  in packages that dependend on perl-uri-escape
- add the version from perl-uri-escape to perl-uri
- remove the unneeded dependency from perl-uri
- remove the perl-uri-escape package

* Reinstated perl-test-needs dependency

Put the perl-test-needs dependency for perl-uri back in but set it to
type='test'.

* For tests to succeed the type must be ('build', 'test')
2019-09-29 09:27:42 -05:00
Massimiliano Culpo
467261803f raxml: simplified recipe by removing SIMD variants (#12952)
Now the support for SSE3 or AVX is tested on the selected target
2019-09-28 13:45:01 -05:00
t-karatsu
c065c25a4c bowtie: fix for aarch64, and bugfix about c++11-narrowing. (#12953) 2019-09-28 13:44:02 -05:00
Massimiliano Culpo
4cebc68f06 vdt: simplified recipe by removing SIMD variants (#12954)
Now the support for SSE3 or AVX is tested on the selected target
2019-09-28 13:41:57 -05:00
Jaroslav Hron
7e9365036f correct with-xxx-lib= options (#12964) 2019-09-28 13:39:45 -05:00
Patrick Schratz
86a85b7eb2 update neovim (#12965) 2019-09-28 13:28:27 -05:00
Shintaro Iwasaki
3776eccc4b bolt: add a new version, 1.0rc2 (#12966) 2019-09-28 13:27:33 -05:00
Daryl W. Grunau
8db94bcc86 eospac: laws.lanl.gov -> laws-green.lanl.gov (#12970) 2019-09-27 17:28:38 -07:00
Ross Miller
c49c37af9b py-adios package: restrict python dependency to <=3.6.x (#12932)
The adios code (currently) won't compile against the Python 3.7 C API.
This change adds a dependency on 3.6 or less.
2019-09-27 17:19:36 -07:00
Kevin Huck
b4c28182dc Tau package: turn off unsupported variants by default on OSX (#12890) 2019-09-27 17:16:44 -07:00
G-Ragghianti
61d41eea7f New package: libibumad (#12886) 2019-09-27 17:02:34 -07:00
Glenn Johnson
fc99eddb12 New package: maker and dependencies (#12904) 2019-09-27 14:59:58 -07:00
Seth R. Johnson
5201d2615e qt4: fix 'arch' string due to microarchitecture change (#12957)
qt4 fails to build because it's expecting something like 'x86_64' rather 
than 'broadwell'.
2019-09-26 21:15:17 +02:00
Massimiliano Culpo
90236bc9f5
Update target comparison semantic for a few packages (#12947)
Use spec.target.family instead of spec.architecture.target
2019-09-26 10:25:12 +02:00
Massimiliano Culpo
31e5318c24
Removed references to '(-march|-mtune|-mcpu)=native' (#12948)
Now that Spack injects microarchitecture specific optimizations for
the selected target, packages should avoid adding flags that could
step over those.
2019-09-26 10:02:08 +02:00
Massimiliano Culpo
78d051b534
parsimonator: simplified recipe by removing SIMD variants (#12949)
Now the support for SSE3 or AVX is tested on the selected target
2019-09-26 09:33:18 +02:00
Seth R. Johnson
f2967b6c16 New package: flibcpp (Fortran bindings to C++ standard library) (#12926) 2019-09-25 19:25:24 -07:00
liuyangzhuan
b384504218 butterflypack package: add version 1.0.3 (#12927) 2019-09-25 19:16:47 -07:00
Glenn Johnson
dd626a0f07 interproscan package: add version 4.8, patch for version 5 (#12897)
This PR adds interproscan-4.8, which has a completely different build
system than version 5. Note that this builds for running on a host as
opposed to a queue system. I am fairly certain that a queue system can
be configured later.

This PR also adds a patch for intrproscan-5 to build when the user
building the packages has a large GID by setting posix mode for tar.
2019-09-25 19:04:57 -07:00
Sinan
c5860d89b7 libspatialite package: add version 3.0.1 and missing dependencies (#12843) 2019-09-25 18:48:48 -07:00
Sinan
507b28de18 py-imageio package: add versions 2.4.1 and 2.5.0 (#12884) 2019-09-25 18:44:57 -07:00
Matthieu Dorier
e6cae978b8 llvm, mesa: update target comparison semantics (#12914)
* llvm: fixed issues with syntax and formatting
  * use spec.architecture.target.family
  * use spec.target instead of spec.architecture.target
* mesa: use == instead of __contains__
2019-09-25 16:41:02 -07:00
Adam J. Stewart
4e858e24b0
libflame: fix macOS build (#12950) 2019-09-25 18:37:33 -05:00
Matthieu Dorier
71cc29691b openblas: fixed a query to target family (#12910) 2019-09-25 22:15:23 +02:00
Christoph Junghans
ccfe8aaf76
portage: fix RelWithDebInfo build (#12944) 2019-09-25 11:29:43 -06:00
Christoph Junghans
e123058721
kokkos-kernels: initial commit (#12934) 2019-09-25 09:00:01 -06:00