Commit graph

8964 commits

Author SHA1 Message Date
Toyohisa Kameyama
cb89949018 migrate: add zlib dependency. (#13039)
* migrate: add zlib dependency.

* flake8.

* autotools related tools change to build.
2019-10-04 13:14:09 -05:00
Felix Thaler
437236781d LLVM 9.0.0 (#13050) 2019-10-04 09:56:12 -07:00
Massimiliano Culpo
2cd800306d fftw: simplify the recipe and make use of specific targets (#12889)
* fftw: grouped precisions in a single variant

* fftw: simd options are now based on target features and not on variants

* fftw: simplified computing the selected precisions
2019-10-03 22:32:42 -05:00
t-karatsu
46e319ecd4 boost: Use gcc toolset for bootstrap with Fujitsu compiler. (#12876) 2019-10-03 22:20:55 -05:00
Toyohisa Kameyama
938bae1ab6 graphmap: add zlib dependency. (#13031) 2019-10-03 22:20:13 -05:00
Toyohisa Kameyama
b89fa3e01a fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030) 2019-10-03 22:19:58 -05:00
Toyohisa Kameyama
4046e10b95 hapcut2: add zlib dependency. (#13032) 2019-10-03 22:19:43 -05:00
Toyohisa Kameyama
2233a7b493 liblbxutil: Add zlib dependency. (#13033) 2019-10-03 22:19:22 -05:00
Toyohisa Kameyama
bb1d0ff6fb metabat: Add zlib and ncurses dependency. (#13034) 2019-10-03 22:18:55 -05:00
Toyohisa Kameyama
58a64f69e7 muse: add zlib dependency. (#13040) 2019-10-03 22:18:27 -05:00
Toyohisa Kameyama
c97be22ff5 ngmlr: add zlib dependency. (#13041) 2019-10-03 22:18:12 -05:00
Andreas Baumbach
4e7ea627c8 fix ipykernel dependency, newer versions are python3-only (#13019)
* fix ipykernel dependency, newer versions are python3-only

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

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

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-03 22:17:16 -05:00
George Hartzell
882843974b Update cctools to v7.0.18 (#13037)
- add version/checksum info for v7.0.18
- update checksum for v6.1.1 to use sha256, while I have the editor
  open...
2019-10-03 18:57:20 -05:00
Owen Solberg
bef702d0f3 updated manta checksum (#13038) 2019-10-03 18:23:47 -05:00
Adam J. Stewart
69acb024a5
Add py-flye 2.6 (#13025) 2019-10-03 10:32:00 -05:00
Adam J. Stewart
dac34147c0 Add EasyBuild 4.0.0 (#13024)
* Add EasyBuild 4.0.0

* Update homepage, remove no longer required deps

* Replace version ranges with fixed versions
2019-10-03 16:48:42 +02:00
Chuck Atkins
b973f038fd
Update ECP Data & Vis SDK packages (#13027)
* ecp-io-sdk: Add faodel and sort variants

* ecp-viz-sdk: Re-enable catalyst, sort variants, turn on by default

* ecp-io-sdk and ecp-viz-sdk: Fix dependency variants
2019-10-03 10:05:02 -04:00
Massimiliano Culpo
76b9c56110 Remove support for generating dotkit files (#11986)
Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.

A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.

* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
2019-10-02 22:15:01 -07:00
Miroslav Stoyanov
b11984767b added tasmanian version 7.0 to spack (#13003) 2019-10-02 18:35:49 -05:00
Sinan
b084d095bc New package: mapnik (#12708) 2019-10-02 13:50:57 -07:00
Tiziano Müller
d99b92febd libint + cp2k: 2-stage build with 'tune' and 'fortran' variants (#12475)
* libint: switch to 2-stage build for 2.6.0+

* libint: add tune and fortran variants

* cp2k: add support for libint >= 2.0

* cp2k: use pkg-config for linking libxc
2019-10-02 21:31:19 +02:00
Toyohisa Kameyama
da18ac3a0f cdhit: add zlib dependency. (#13015)
* cdhit: add zlib dependency.

* Add zlib variant.
2019-10-02 12:55:05 -05:00
Toyohisa Kameyama
b85ff04681 denovogear: Add missing zlib depenbdency and fix open handling error. (#13017) 2019-10-02 12:54:50 -05:00
Toyohisa Kameyama
58c01792ef cnpy: add zlib dependency. (#13016) 2019-10-02 12:54:31 -05:00
Dan Lipsa
210dd594a1 Add cuda to paraview build. (#12996) 2019-10-02 12:00:03 -05:00
George Hartzell
21e95e4141 Singularity 3.4.1 still needs the makefile patch (#13008)
* Singularity 3.4.1 still needs the makefile patch

* Constrain build patch to 3.4.0:3.4.1
2019-10-02 11:59:11 -05:00
Sinan
afca223b3d new package: openldap (#12748)
* new package: openldap

* fix mistake

* remove template text

* fix build error involving perl

* flake8

* improvements

* introduce multi valued variant for tls support

* improve tls variant

* overwrite build phase as opposed install

* improve style
2019-10-02 11:58:46 -05:00
Toyohisa Kameyama
1550d5cae6 ants: missing zlib dependency and fix working directory in install. (#13010) 2019-10-02 11:58:25 -05:00
Toyohisa Kameyama
7d9514d3fa breakdancer: missing ncurses dependency. (#13011) 2019-10-02 11:57:05 -05:00
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