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Author SHA1 Message Date
Greg Becker
bd1a0a9ad4
view remove: directly check whether specs own files before removing from view (#16955) 
Bugfix for hardlinks and copies
 2020-06-08 06:43:52 +02:00
Mark W. Krentel
763760cfe0
hpcviewer, ibm-java: updates versions (#16987) 
hpcviewer: added v2020.05.
ibm-java:  added v8.0.6.10.
 2020-06-08 06:15:37 +02:00
iarspider
664c32efb4
py-ipykernel: added v5.1.1 (#16988) 2020-06-08 06:11:24 +02:00
Toyohisa Kameyama
b00f97f7cc
boost: Don't use pre-compiled headers for Fujitsu compiler (#16914) 
* boost: Dopn't use pre compile header.

* move %fj.
 2020-06-07 09:39:53 -05:00
John Jolly
33923320a8
rose: Add build dependencies for flex and bison (#16981) 2020-06-07 09:36:14 -05:00
Sinan
a2c6f6a703
py-gast: add version 0.3.3 (#16945) 
* py-gast: add version 0.3.3

* add python version constraints

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-07 09:33:03 -05:00
iarspider
6498b752d1
Add rpy2@3.0.4 (#16924) 
* Add rpy2@3.0.4

* Style fixes

* Update package.py

* Proper Python version requirement
 2020-06-06 16:33:34 -05:00
Toyohisa Kameyama
7bc44fa165
ffr: fix mpi programs to use mpi compiler wrapper. (#16948) 2020-06-06 16:30:43 -05:00
vvolkl
8f291c7e95
[prmon] add package (#16949) 2020-06-06 16:29:42 -05:00
Michael Kuhn
ad2dd4be01
mongo-c-driver: Add 1.16.2 (#16956) 
This also updates libbson to the corresponding version and adds a few
missing older versions.
 2020-06-06 16:18:48 -05:00
Matthieu Dorier
543f9f91d4
added CTRE package (#16964) 2020-06-06 16:14:40 -05:00
John Jolly
46a751081d
gcc: Fix error 'size of array is negative' (#16969) 
gcc 9.3.0 and glibc 2.31 (found in the base install of Ubuntu 20.04)
cause the gcc package to error during build with the error:

    "size of array 'assertion_failed__####' is negative"

Previous to this fix, the error was resolved for v8.1.0 <= gcc <= v9.2.0
via two patches.

This fix backports those patches for v5.3.0 <= gcc <= v7.4.0

Potentially these patches need to be backported to versions of gcc
before v5.3.0, but other compile issues need to be resolved for earlier
versions of gcc first.

Fixes #16968
 2020-06-06 16:14:11 -05:00
Tom Payerle
885808cc13
intel-tbb: Fix for #16938 add custom libs method (#16972) 
* intel-tbb: Fix for #16938 add custom libs method

Override the libs method to look for libraries of form libtbb*
(instead of inherited which looks for libintel-tbb*)

* Fixing pre-existing flake8 issues
 2020-06-06 16:12:46 -05:00
darmac
c835b93109
Add new package: py-louie (#16983) 2020-06-06 16:02:15 -05:00
darmac
77fbdff8a2
Add new package: lxc (#16984) 2020-06-06 16:00:59 -05:00
Sinan
36f9550178
py-mysqlclient: relax dependency constraint, add new versions (#16985) 
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-06 16:00:29 -05:00
Sinan
73d13461b1
ensure xla is turned off (#16974) 
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-06 15:51:19 -05:00
Sinan
7b6e1ae9d3
py-astunparse: add version 1.6.3 (#16946) 
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-06 15:50:16 -05:00
darmac
c5ac168f31
protobuf: support aarch64 @2.5.0 (#16862) 
* protobuf: support aarch64 @2.5.0

* refine cmake args

* fix patch name
 2020-06-06 15:47:30 -05:00
Nithin Senthil Kumar
944f0abb36
Update package for MVAPICH2 2.3.4 release (#16960) 
Co-authored-by: senthilkumar.16 <senthilkumar.16@nowlab.cse.ohio-state.edu>
 2020-06-06 12:51:27 +02:00
John Jolly
d755cc8ce9
iegenlib: add build dependencies for automake and libtool (#16980) 2020-06-06 09:55:14 +02:00
Andrew Gaspar
374f1a62e2
py-flake8: add version 2.8.2 (#16959) 
* py-flake8: add version 3.8.2
  * This version depends on different versions of py-pycodestyle
    and py-pyflakes
  * When built for python@:3.7, this depends on the
    py-importlib-metadata backport library
* py-pycodestyle: add version 2.6.0
* py-pyflakes: add version 2.2.0
 2020-06-05 18:25:42 -07:00
Amjad Kotobi
27eb7d9f5f
xrootd: add version 4.12.1 (#16966) 2020-06-05 18:18:00 -07:00
Sinan
a08f3dd505
New package: py-asteval (#16976) 2020-06-05 18:16:13 -07:00
Michael Kuhn
bfa05628cb pkgconf: Add 1.7.3 2020-06-05 18:14:20 -07:00
Christoph Junghans
76abf35813
cajita: got merged in cabana (#16971) 2020-06-05 12:38:07 -06:00
Tomoki, Karatsu
89cc507cf6
cmake: add linker option for VerifyFortranC when using Fujitsu compiler. (#16963) 2020-06-05 13:29:36 +02:00
Tomoki, Karatsu
c3be6d903a
cmake: modify FindMPI.cmake to treat Fujitsu MPI correctly (#16864) 2020-06-05 13:25:02 +02:00
Tomoki, Karatsu
8be7823cc5
suite-sparse: change the condition to add C11 flag. (#16859) 2020-06-05 13:17:41 +02:00
eugeneswalker
92e24950e5
add erlang version 23.0 (#16961) 2020-06-04 22:49:46 -07:00
Andrew Gaspar
0d43e41da0
Rust v1.44.0 (#16957) 
* libgit2 v1.0.1

* Rust 1.44.0

* Fix flake8
 2020-06-04 16:59:14 -05:00
Andrew Gaspar
0a3601a3f1
libgit2 v1.0.1 (#16952) 2020-06-04 16:34:19 -05:00
eugeneswalker
44ec8cc4e4
sz: patch in ctag optionality from robertu94/sz 3637a87f986c (#16953) 2020-06-04 09:16:11 -07:00
eugeneswalker
b64ec7fba4
pass hwloc to configure via useropt; use lib/ or lib64/ as appropriate for libunwind (#16941) 2020-06-04 06:58:33 -07:00
Adam J. Stewart
7617054a5d
Fix obsolete references to wx package (#16944) 2020-06-04 08:05:48 -05:00
Adam J. Stewart
0dd1d1f21a
NumPy: add 1.18.5 (#16943) 2020-06-04 08:05:22 -05:00
iarspider
ad50a02188
Add matplotlib 3.1.0 (#16921) 2020-06-03 22:26:13 -05:00
iarspider
6f4631ee48
Add py-jupyter-core@4.6.1 (#16922) 2020-06-03 22:25:38 -05:00
Seth R. Johnson
104a0c4259
Trilinos: add Stratimikos package (#16925) 
Stratimikos is an optional dependency for our project. It depends on
Thyra, and thyra has subpackages that should be enabled based on
tpetra/epetra/epetraext.
 2020-06-03 22:25:09 -05:00
Mathew Cleveland
02548c56fa
+ Add opppy-0_1_3 (#16926) 
+ Update maintainers for OPPPY package
+ remove "run" requirement for setuptools and sphynx

Co-authored-by: Cleveland <cleveland@lanl.gov>
 2020-06-03 22:16:46 -05:00
iarspider
16e8e434c2
Add pytest@5.3.4 (#16927) 
Dropping atomicwrites dependency: https://github.com/pytest-dev/pytest/issues/6147
 2020-06-03 22:15:01 -05:00
Seth R. Johnson
6f6c243699
mpfr: update hash for 4.0.2 patch (#16937) 2020-06-03 22:11:44 -05:00
Adam J. Stewart
61f61f3cde
py-openpyxl: add 3.0.3 (#16940) 2020-06-03 22:09:58 -05:00
Adam J. Stewart
5a7b555314
IPython: fix setuptools dependency (#16915) 
* IPython: fix setuptools dependency

* Remove extra colon
 2020-06-03 22:09:40 -05:00
Tom Payerle
0fb671a19e
Gnuplot fix 16928 (#16929) 
* gnuplot: Fix for #16928

Dependency for --with-wx flag mistyped (should be wxwidgets)

* Revert "gnuplot: Fix for #16928"

This reverts commit 2b85814e5ccf5c9b2c70c7959994e89c18fdc3d8.

* gnuplot: Fix for #16928

Dependency spec for --with-wx flag mistyped (should be wxwidgets, not
wx)
 2020-06-03 22:08:07 -05:00
shanedsnyder
748be57790
update darshan-runtime & darshan-util versions (#16934) 
* update darshan-runtime & darshan-util versions

includes up through the current release, 3.2.1

* remove pre-releases, not needed in spack
 2020-06-03 18:05:46 -07:00
eugeneswalker
0086c47546
patch lambda capture issue for @1.1906.1, fixed in upstream faodel@master (#16935) 2020-06-03 11:38:27 -07:00
Greg Becker
3347ef2de4
Feature: add option to create view by copying/relocating files (#16480) 
* add subcommand `spack view copy/relocate`

* update bash completions

* add copy/relocate commands to view tests

* allow copied views to be removed
 2020-06-03 09:45:13 -07:00
dmorone
600e2cfc4f
amber: updated dependency constraint on cuda (#16919) 
Fix message 'amber requires cuda version :10.1.243, but spec asked for 10.2.89'
 2020-06-03 13:17:36 +02:00
Amjad Kotobi
eed82a19be
openssh: added v8.3p1 and v8.1p1 (#16917) 2020-06-03 11:28:42 +02:00
Amjad Kotobi
417eb3c5b1
git: added v2.27.0 (#16918) 2020-06-03 11:24:08 +02:00
Justin S
5604c8d91a
mummer4: new package at 4.0.0-beta2 (#16907) 2020-06-02 22:09:39 -05:00
Robert Blake
0e71e8716a
Add new package: sbml (#16898) 
* Adding a module for sbml.

* Adding support for all the languages.

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

Co-authored-by: Greg Becker <becker33@llnl.gov>

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

Co-authored-by: Greg Becker <becker33@llnl.gov>

Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
 2020-06-02 17:54:50 -07:00
Adam J. Stewart
7f086af05e
Ruby: add warning about Avira antivirus (#16882) 2020-06-02 15:05:50 -07:00
Toyohisa Kameyama
76142124d2
alsa-lib: Add new version and python dependency. (#16905) 
Add version 1.2.2.
Add conditional python dependency.
Add patch for 1.1.4.1 and python.
 2020-06-02 14:23:14 -07:00
Justin S
5d37439a7b
gmap-gsnap: add 2020-06-01 (#16906) 2020-06-02 14:21:00 -07:00
Chuck Atkins
5ace804dc2
Bump ADIOS to 2.6.0 (#16908) 2020-06-02 14:15:23 -07:00
iarspider
9a17d48455
Add ipython 7.5.0 (#16801) 
* Add ipython 7.5.0

* Update dependencies

* Update package.py
 2020-06-02 15:09:35 -05:00
takanori-ihara
b60ab6eefd
ruby: fixed build with Fujitsu compilers (#16889) 2020-06-02 11:07:48 +02:00
Xavier Delaruelle
c7851f896c
environment-modules: added v4.5.1 (#16896) 2020-06-02 11:06:02 +02:00
Greg Becker
2795414a80
Fix satisfaction checks for excluding variants from matrices (#16893) 
Because of the way abstract variants are implemented, the following 
spec matrix does not work as intended:
```
matrix:
- [foo]
- [bar=a, bar=b]
exclude:
- bar=a
```
because abstract variants always satisfy any variant of the same
name, regardless of values.

This PR converts abstract variants to whatever their appropriate 
type is before running satisfaction checks for the excludes clause 
in a matrix.

fixes #16841
 2020-06-02 11:02:28 +02:00
takanori-ihara
0875c6a5d0
py-grpcio: fixed build with Fujitsu compilers (#16900) 2020-06-02 10:55:55 +02:00
Axel Huebl
6aa0e9944e
ccache: added v3.7.9 (#16902) 
Add the latest CCache release. Fixes issues with `-x cu` that are
not present in the last checksummed release. This fixes workflows
with CMake.
 2020-06-02 10:53:12 +02:00
Sinan
7f2db5c5b0
qt: add conflict for old gcc (#16904) 
Co-authored-by: Sinan81 <Sinan81@github>
 2020-06-02 10:51:35 +02:00
Michael Kuhn
6035b32748
go: added v1.14.4 and v1.13.12 (#16903) 2020-06-02 10:48:35 +02:00
Jonathon Anderson
feda2a3073
openmpi: add opa-psm2 dependency (#16873) 
Also document with_or_without and enable_or_disable, (which are used
to configure the opa-psm2 dependency).
 2020-06-01 15:33:24 -07:00
Amjad Kotobi
ab6905d5fa
r-exactextractr: package type fixed (#16881) 
* r-exactextractr: should inherit from RPackage
* r-exactextractr: fixed URL
 2020-06-01 14:01:41 -07:00
t-karatsu
9741de504f netcdf-cxx4: Add 'doxygen' dependency. 2020-06-01 13:56:07 -07:00
Jianwen WEI
4387975556 miniforge3: add version 4.8.3-4. 2020-06-01 13:54:53 -07:00
mic84
fe74c22184
amrex: add version 20.06 (#16895) 2020-06-01 13:53:49 -07:00
Christoph Junghans
daea1fcef6
exampm: fix build (#16894) 
* cabana: add mpi variant

* cajita: initial import

* exampm: update deps

* flake8
 2020-06-01 13:58:09 -06:00
健美猞猁
de63e1c2ac
healpix-cxx: added new package at v3.50.0 (#16846) 2020-06-01 06:13:35 +02:00
Greg Becker
b1bd777403
petsc: fix conditional activation of parmetis (#16533) 2020-05-31 14:13:10 -05:00
Hector Martinez-Seara
23a5f3f200
Updated unison to v2.51.2 (#16772) 
The current package does not work. Also several ocaml versions do
not compile such as 4.09.0. Updated to the new ocaml version to
4.10.0, which is now a prerequisite.
 2020-05-31 13:58:37 -05:00
iarspider
6282e337f3
Add new version of py-astroid (#16805) 
* Add new version of py-astroid

* Add new version of py-lazy-object-proxy

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-05-31 13:54:33 -05:00
健美猞猁
3896a401db
Install libsharp header files to include/libsharp. (#16847) 
* Install libsharp header files to include/libsharp.

* Fix flake8 issues.

* Simplify specification of install path.
 2020-05-30 23:09:27 -05:00
Jordan Ogas
66b8b5ab37
add charliecloud 0.16 (#16810) 
* add charliecloud/0.16

* tidy comments
 2020-05-30 22:10:50 -05:00
darmac
2fdb6b5e44
Add new package: canal (#16790) 2020-05-30 21:45:59 -05:00
takanori-ihara
e2fa74c533
Add new package:linsys-v (#16823) 2020-05-30 21:20:08 -05:00
Satish Balay
1ec8d928fa
petsc@3.13: update superlu-dist dependency - as superlu-dist@6.3.1 has API change (#16849) 2020-05-30 21:10:34 -05:00
Erik Schnetter
b00080d2da
ssht: Install include files into "include/ssht" (#16879) 2020-05-30 21:08:18 -05:00
Adam J. Stewart
9eebc6b4c1
horovod: added v0.19.4 (#16878) 2020-05-30 20:22:00 +02:00
Adam J. Stewart
d76eb1fa51
Pandas: add 1.0.4 (#16877) 2020-05-30 11:09:10 -05:00
noguchi-k
816f780be8
revocap-refiner: add space and remove unused function. (#16861) 2020-05-30 10:57:12 -05:00
darmac
7a363e2a3f
Add new package: netkit-ftp (#16876) 
* Add new package: netkit-ftp

* remove parallel constraint
 2020-05-30 10:47:47 -05:00
Jen Herting
3a66d0773c
perl-bioperl: fixed version 1.007002 (#16826) 
* [perl-bioperl] fixed url for version 1.007002
* [perl-bioperl] fixed conditional method directives
 2020-05-30 00:17:01 -07:00
Amjad Kotobi
857d2c9150 r-lfe: New package 2020-05-30 00:15:50 -07:00
Michael Kuhn
3cc0e1a333
cpio: add patch to fix build with gcc@10: (#16844) 2020-05-30 00:14:57 -07:00
Amjad Kotobi
58cc75ac29
git-lfs: add versions 2.10.0, 2.11.0 (#16850) 2020-05-30 00:14:24 -07:00
Ben Morgan
c35ced1465
geant4: New version 10.6.2 (#16868) 
Update both main and data packages. Data versions have not changed
in new version.

Provide new python variant to build Python bindings for 10.6.2 and
newer. Add dependencies on python and Boost+python required by variant.
 2020-05-30 00:13:24 -07:00
Nicholas Sly
ec5959694c
Add netcdf-c~parallel-netcdf variant specification to netcdf-fortran~mpi. (#16671) 
Co-authored-by: sly <sly@lanl.gov>
 2020-05-29 09:48:03 -07:00
Christoph Junghans
11fc6c5791
examinimd/miniaero: fix build with kokkos-legacy (#16867) 
* examinimd/miniaero: fix build with kokkos-legacy

* flake8
 2020-05-29 10:17:55 -06:00
0t1s1
2aca0cf565
gridlab-d: added new package. (#16816) 2020-05-29 09:37:12 +02:00
Christoph Junghans
623cc7427e
legion: add v20.03.0 (#16848) 2020-05-28 14:58:55 -06:00
Marc Allen
712fc696ba
npm: use mkdirp instead of mkdir (#16835) 
fixes #16833

Co-authored-by: Marc Allen <mrcall@amazon.com>
 2020-05-28 12:33:09 +02:00
Luca Heltai
a6779061d7
dealii: deal with nanoflann after 9.2.0 (#16839) 2020-05-28 12:02:34 +02:00
Adam J. Stewart
4351c2eb32
Update checksum for PyTorch patch (#16837) 2020-05-28 11:27:59 +02:00
Toyohisa Kameyama
ab65a8ee27
opencv: fix to build version 3.2.0 with Fujitsu compiler (#16840) 2020-05-28 11:23:15 +02:00
Joseph Ciurej
87cd375559
ffmpeg: add a maintainer to the package (#16830) 2020-05-27 22:51:19 +02:00
Toyohisa Kameyama
4d5a68731a
ffmpeg: set compilers command. (#16799) 2020-05-27 21:04:37 +02:00