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Author SHA1 Message Date
Justin Stanley
9dfea8ee17 circos: new package starting at 0.69-6 (#9761) 
* circos: new package starting at 0.69-6

* circos: add homepage, simplify paths

* circos: simplified more paths
 2018-11-19 20:44:01 -06:00
Sinan
0a0e5642df gdk-pixbuf: explicitly disable building of gtk-docs (#9882) 2018-11-19 20:42:56 -06:00
Levi Baber
535035b223 r-rrpp: new package (#9887) 2018-11-19 20:42:45 -06:00
Jon Rood
1972376865 Adding openmpi version 4.0.0 (#9888) 2018-11-19 20:42:34 -06:00
Eric
177c5f3c6d breseq: Add version 0.33.1 (#9889) 2018-11-19 20:42:21 -06:00
Sinan
47a641f13b package/harfbuzz: disable building of gtk-docs, add new version (#9891) 2018-11-19 20:42:08 -06:00
Levi Baber
561a561d23 r-crosstalk: remove unnecessary constraint (#9892) 2018-11-19 20:41:41 -06:00
Levi Baber
71943703f2 r-geomorph: new version (#9890) 
* r-geomorph: new version

* r-geomorph: min r version
 2018-11-19 20:41:19 -06:00
Levi Baber
43a26d0850 r-diversitree: new package (#9893) 
* r-diversitree: new package

* r-diversitree: system reqs
 2018-11-19 20:41:01 -06:00
Levi Baber
7e1f96c0aa r-paleotree: new package (#9895) 2018-11-19 20:39:42 -06:00
Sinan
000bb8ca39 package/pango: disable gtk-docs (#9896) 2018-11-19 20:38:52 -06:00
Sinan
71464a8b0a package/gtkplus: disable gtk-docs (#9897) 2018-11-19 20:38:34 -06:00
Mark C. Miller
a6efd22e60 Explicitly set FC= empty for non-fortran builds (#9898) 2018-11-19 20:38:06 -06:00
Eric
0c1988ffdf Trimmomatic: Add version 0.38 (#9883) 2018-11-19 15:56:49 -06:00
Jon Rood
c8a1a81a87 Adding intel-parallel-studio cluster 2019.1 version (#9884) 2018-11-19 15:56:31 -06:00
Daniel Topa
7402112b1f Add UCX v1.4.0 (#9881) 
Verification build
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5
==> Installing libsigsegv
==> Installing m4
==> Installing pkgconf
==> Installing ncurses
==> Installing readline
==> Installing gdbm
==> Installing perl
==> Installing autoconf
==> Installing automake
==> Installing libtool
==> Installing numactl
==> Installing zlib
==> Installing openssl
==> Installing diffutils
==> Installing bzip2
==> Installing xz
==> Installing libxml2
==> Installing tar
==> Installing gettext
==> Installing help2man
==> Installing bison
==> Installing flex
==> Installing libnl
==> Installing rdma-core
==> Installing ucx
==> Successfully installed ucx
  Fetch: 1.17s.  Build: 40.59s.  Total: 41.76s.
[+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack spec ucx
Input spec
--------------------------------
ucx

Concretized
--------------------------------
ucx@1.4.0%gcc@4.8.5 arch=linux-centos7-x86_64
    ^numactl@2.0.11%gcc@4.8.5 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64
        ^autoconf@2.69%gcc@4.8.5 arch=linux-centos7-x86_64
            ^m4@1.4.18%gcc@4.8.5 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64
                ^libsigsegv@2.11%gcc@4.8.5 arch=linux-centos7-x86_64
            ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64
                ^gdbm@1.18.1%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^readline@7.0%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-centos7-x86_64
                            ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-centos7-x86_64
        ^automake@1.16.1%gcc@4.8.5 arch=linux-centos7-x86_64
        ^libtool@2.4.6%gcc@4.8.5 arch=linux-centos7-x86_64
    ^rdma-core@20%gcc@4.8.5 build_type=RelWithDebInfo arch=linux-centos7-x86_64
        ^cmake@3.12.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64
            ^openssl@1.0.2o%gcc@4.8.5+systemcerts arch=linux-centos7-x86_64
                ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64
        ^libnl@3.3.0%gcc@4.8.5 arch=linux-centos7-x86_64
            ^bison@3.0.5%gcc@4.8.5 arch=linux-centos7-x86_64
                ^diffutils@3.6%gcc@4.8.5 arch=linux-centos7-x86_64
                ^help2man@1.47.4%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^gettext@0.19.8.1%gcc@4.8.5+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64
                        ^bzip2@1.0.6%gcc@4.8.5+shared arch=linux-centos7-x86_64
                        ^libxml2@2.9.8%gcc@4.8.5~python arch=linux-centos7-x86_64
                            ^xz@5.2.4%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^tar@1.30%gcc@4.8.5 arch=linux-centos7-x86_64
            ^flex@2.6.3%gcc@4.8.5+lex arch=linux-centos7-x86_64

Environment:
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ echo $HOSTNAME
darwin-fe2.lanl.gov

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq
model name      : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ lsb_release -d
-bash: lsb_release: command not found

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ uname -a
Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ date
Mon Nov 19 10:47:47 MST 2018

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ pwd
/scratch/users/dantopa/new-spack/pr.ucx.spack

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2018-11-19 13:20:22 -06:00
Andrea Negri
494d48f012 new package: mongo-cxx-driver (#9880) 
* new package: mongo-cxx-driver

* fixed url
 2018-11-19 13:19:19 -06:00
Eric
36b4758a97 samtools: make zlib/bzip2 dependencies unconditional (#9866) 2018-11-19 10:36:48 -08:00
Andrea Negri
9aa9359604 libmongoc: updated versions (#9877) 2018-11-18 20:35:24 -06:00
Alberto Chiusole
c61250e2ef New package: ecFlow, a work flow manager. (#9867) 
* New package: ecFlow, a work flow manager.

* Fix pep8 style issues.
 2018-11-18 10:13:31 -06:00
Sajid Ali
c45080398c Add +x variant to petsc. (#9830) 
* 	modified:   var/spack/repos/builtin/packages/petsc/package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-11-17 21:35:37 -06:00
simo-tuomisto
93879e575d mixcr: Added a new package for MiXCR. (#9864) 
* mixcr: Added a new package for MiXCR.

* mixcr: Fixed spack license string.
 2018-11-17 21:19:04 -06:00
Christoph Junghans
26e51ff170 lammps package: added new versions (#9868) 2018-11-16 14:52:26 -08:00
Sinan
22cd6494be py-cython: add new versions (#9846) 2018-11-16 13:20:34 -08:00
Justin Stanley
9dff444570 new package: r-gensa (starting at 1.1.7) (#9858) 2018-11-16 13:13:48 -08:00
Eric
dc2911208f py-ply: fix download url (#9862) 2018-11-16 13:12:05 -08:00
Eric
61adf39fe1 vt package: add zlib dependency (#9870) 2018-11-16 12:52:15 -08:00
Levi Baber
0a57f90d75 r-rgl: update url, add new version (#9796) 2018-11-16 15:26:09 +01:00
Michael Kuhn
c645c8e2a6 py-cffi: add missing pkgconfig dependency (#9784) 2018-11-15 19:38:52 +01:00
Michael Kuhn
d4f8bd5b8d py-cryptography: add 2.3.1 (#9785) 
Required for openssl@1.1 compatibility.
 2018-11-15 18:27:29 +01:00
Michael Kuhn
480951c231 krb5: add missing bison dependency for yacc (#9778) 2018-11-15 17:54:51 +01:00
Michael Kuhn
4d426e63f0 globus-toolkit: add missing pkgconfig dependency (#9775) 2018-11-15 17:54:22 +01:00
Hadrien G
d7983e2aa4 Fix and update verrou (#9847) 
* Fix verrou-python integration

* Add verrou 2.1.0

* Patch level changed in v2.1.0
 2018-11-15 10:22:13 -06:00
Denis Davydov
32884dbc03 dbcsr: minor fixes due to upstream changes (#9799) 2018-11-15 17:10:50 +01:00
Leonhard Reichenbach
2b64047e07 Updated protobuf and py-protobuf to version 3.6.1 (#9536) 
* Updated protobuf and py-protobuf to version 3.6.1

also updated the download link as the repository has moved

* protobuf: modified conflict
 2018-11-15 16:59:04 +01:00
Adam J. Stewart
2723db9f73
Add GMT, CitcomS, and fstrack packages (#9768) 
* Add initial packages for citcoms and dependencies

* Ignore Pythia imports

* Add py-merlin package

* Add GMT package

* Fixes to get GMT working

* Get hc package building

* Get CitcomS 3.2.0 working

* Add fstrack package

* Fix hash
 2018-11-14 23:30:44 -06:00
Levi Baber
b9c50249cf r-cairo: new package (#9794) 
* r-cairo: new package

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

Co-Authored-By: baberlevi <baberlevi@gmail.com>
 2018-11-14 21:44:55 -06:00
dorier
8a41cbf813 Argobots: added @develop version and +valgrind variant (#9664) 
* added develop version in argobots package and added valgrind variant

* made autotools required only for develop version

* corrected style

* Added --disable-valgrind

Added --disable-valgrind to explicitly disable it when +valgrind isn't provided.
 2018-11-14 21:39:35 -06:00
Justin Stanley
12177e41f0 r-phytools: new package at 0.6-60 (#9766) 
* r-phytools: new package at 0.6-60

* r-phytools: add list_url

* r-phytools: add deps, dep versions
 2018-11-14 21:39:05 -06:00
Geoffrey Oxberry
605dc8bf85 openblas: add headers property (#9831) 
This commit adds only the public headers from the full list of headers
installed by OpenBLAS; this list of headers is the same as in
netlib-lapack.
 2018-11-14 21:35:42 -06:00
Mark W. Krentel
b53eb2026a elfutils: add version 0.174. (#9812) 
Pass cflags to configure so that configure gets the values from the
spack install line.

Disable -Werror so that we don't fail the build over a stray warning.
 2018-11-14 19:05:08 -06:00
Mark W. Krentel
2554e24d09 libunwind: add version for current snapshot (#9770) 
Libunwind releases are few and far between, so we need access to
recent snapshots from the git repository.

Pass cflags to configure so that make will respect the value from the
spack install line.
 2018-11-14 18:56:52 -06:00
Sergey Kosukhin
75e86a61fe netcdf-fortran: add LDFLAGS to fix contents of libnetcdff.la. (#9647) 2018-11-14 09:40:16 -06:00
Levi Baber
6a08eb88b1 new package: time (#9842) 2018-11-14 09:38:37 -06:00
Michael Kuhn
9a7a532084 node-js: add 10.13.0 and 11.1.0 (#9781) 
Required for openssl@1.1 compatibility.
 2018-11-13 11:39:52 -06:00
Michael Kuhn
e20efb3f8f cmake: add 3.12.4 (#9758) 2018-11-13 11:34:09 -06:00
Michael Kuhn
eddba22e1c perl-net-ssleay: fix build (#9783) 
- Add 1.85
- OPENSSL_PREFIX has to be set in the environment, otherwise Spack's
  openssl will not be found
 2018-11-13 11:30:04 -06:00
Justin Stanley
e1f9ddd574 erne: new package starting at 2.1.1 (#9676) 
* erne: new package starting at 2.1.1

* erne: remove unused configure args

* erne: remove unused prefix arg

* erne: add explicit mpi disable
 2018-11-13 11:02:39 -06:00
Luigi Calori
4f27bb4f4e Fix #9673 : build fonts on powerpc architecture (#9683) 
* use AutotoolsPackage so config.guess get updated by autoreconf step, fix build problem on ppc #9673

* same error, same fix under ppc arch
 2018-11-13 11:01:46 -06:00
Douglas Duckworth
ab48a96149 added r-bindr v 0.1.1 (#9717) 2018-11-13 10:58:31 -06:00
Levi Baber
b668e66b81 r-genomeinfodbdata: url fix (#9732) 2018-11-13 10:57:04 -06:00
Matthias Diener
8b1a5a8e6c intel-parallel-studio: add missing updates (#9742) 
* intel-parallel-studio: add missing updates

* add 2018.4
 2018-11-13 10:56:31 -06:00
Levi Baber
25d71e68f2 Packages/trinotate fix (#9745) 
* trinotate: fix perl location

* trinotate: not where that is

* trinotate: glob

* trinotate: needs perl-dbd-sqlite
 2018-11-13 10:55:59 -06:00
Alberto Chiusole
7938ff9653 Add pic variant to cflags in boost. (#9750) 
* Add pic variant to cflags in boost.

* Improve description in pic variant of boost, see #9750.
 2018-11-13 10:55:01 -06:00
Miles Perry
63535542a1 new version (#9752) 2018-11-13 10:53:47 -06:00
Michael Kuhn
05a4d5a0c6 glib: add 2.56.3 (#9754) 2018-11-13 10:52:56 -06:00
Michael Kuhn
55f8dbbba0 sqlite: add 3.25.3 (#9756) 2018-11-13 10:50:54 -06:00
Michael Kuhn
c7f2c819a1 gdbm: add 1.18.1 (#9757) 2018-11-13 10:50:30 -06:00
Michael Kuhn
52e990dfa1 lmdb: add 0.9.22 (#9759) 2018-11-13 10:49:24 -06:00
Daryl W. Grunau
ff30ab462b eospac version bump (#9763) 2018-11-13 10:47:11 -06:00
Justin Stanley
c26a965c3b r-combinat: new package at 0.0-8 (#9764) 
* r-combinat: new package at 0.0-8

* r-combinat: add list_url
 2018-11-13 10:41:54 -06:00
Michael Kuhn
a852028b02 glib: explicitly disable gtk-doc (#9771) 
glib should not use the globally installed gtk-doc. Otherwise, gtk-doc
can fail with Python errors such as `ImportError: No module named site`.

This is due to the fact that Spack sets `PYTHONHOME`, which can confuse
the global Python installation that is used by gtk-doc.
 2018-11-13 10:37:19 -06:00
Michael Kuhn
fe8c287036 nginx: add 1.15.6 (#9780) 
Needed to compile with gcc@8 and recent versions of glibc.
 2018-11-13 10:25:00 -06:00
Eric
3cd3631fb6 DIAMOND: add version 0.9.22 (#9790) 2018-11-13 10:20:53 -06:00
Eric
4b63b93485 stringtie: add version 1.3.4d (#9791) 2018-11-13 10:20:30 -06:00
Hans Pabst
23c2d5af38 LIBXSMM 1.10 (#9813) 
* LIBXSMM 1.10

* Accurately replaced MD5 with SHA256 sums (libxsmm).
 2018-11-13 10:09:47 -06:00
Eric
fea0722daa aragorn: add version 1.2.36 (#9817) 2018-11-13 10:09:14 -06:00
Eric
5ba76cf908 minimap2: Add versions 2.10 and 2.14 (#9818) 
* Also add missing zlib dependency
 2018-11-13 10:08:42 -06:00
Quinn
2f454c5317 New Package: Nyancat (#9819) 
* nyancat: adding the most important piece of software ever written

* nyancat: some formatting updates

* nyancat: flake8 error fix
 2018-11-13 10:07:54 -06:00
Matthias Diener
6743aef554 charm++: add version 6.9.0 (#9827) 2018-11-13 10:03:22 -06:00
Christoph Junghans
78c7a8218c gromacs: added 2018.[34] (#9828) 2018-11-13 10:02:59 -06:00
Geoffrey Oxberry
f1e5f8e37b hypre: patch only @2.13.0 and @2.14.0 on darwin (#9832) 2018-11-13 09:54:09 -06:00
Michael Kuhn
3f0fc98062 wt: add missing pkgconfig dependency and fix boost version range (#9835) 
wt does not build with newer versions of boost.
 2018-11-13 09:53:44 -06:00
Michael Kuhn
59a6eada53 libssh: fix fetching and add 0.8.5 (#9779) 
Required for openssl@1.1 compatibility.
 2018-11-13 09:51:57 -06:00
Michael Kuhn
68222f2639 libevent: add 2.1.8 and 2.0.22 (#9777) 
- 2.1.8 is required for openssl@1.1 compatibility
- Introduce url_for_version since the URL has changed starting with
  version 2.0.22
 2018-11-13 09:51:26 -06:00
Valentin Clement (バレンタイン クレメン)
1388f6e907 Add new version 1.2.0 to the package (#9837) 2018-11-13 09:49:08 -06:00
Matthias Diener
86b7e6abc3 man-db: add missing gdbm dependency (#9751) 2018-11-13 09:41:43 -06:00
Michael Kuhn
cc928481f8 openssh: add 7.9p1 (#9782) 
- Required for openssl@1.1 compatibility
- Fix openssh's privilege separation path to be below the prefix
 2018-11-13 09:41:17 -06:00
Jon Rood
b4c7ffd424 Adding Paraview version 5.6. (#9788) 2018-11-13 09:36:18 -06:00
Michael Kuhn
86e00e7294 ruby: add 2.5.3 (#9793) 
Required for openssl@1.1 compatibility.
 2018-11-13 09:35:47 -06:00
Michael Kuhn
66ef3c2b18 thrift: add missing pkgconfig dependency (#9834) 
Without pkgconfig, Spack's openssl cannot be found.
 2018-11-13 09:34:51 -06:00
Eric
f48820a71e barrnap package: Add versions 0.6 and 0.7 (#9820) 2018-11-13 09:33:56 -06:00
Phil Tooley
16aa37bdfe New package: openimageio (#9715) 2018-11-13 00:14:29 -06:00
Phil Tooley
ff09fd5a85 New package: dcmtk (#9716) 2018-11-13 00:08:29 -06:00
Michael Kuhn
f56f6d4e38 Fix pkg-config dependencies (#9738) 
Replace dependencies on specific pkgconfig implementation (e.g. pkgconf)
with dependency on pkgconfig virtual package
 2018-11-13 00:01:41 -06:00
Michael Kuhn
077e509dda gplates package: improvements (#9735) 
- Add version 2.1.0
- Now that #9264 has been merged, gplates seems to build fine with newer
  versions of gcc (tested with gcc@8)
- When using the ninja generator, gplates can be built in parallel
 2018-11-12 23:56:59 -06:00
Alberto Chiusole
c7c3fab744 Add 'pic' variant to netcdf packages (#9605) 2018-11-12 23:54:11 -06:00
Peer-Timo Bremer
91302f89e4 TALASS package: replace old version with new version (#9703) 
New version has bug fixes
 2018-11-12 23:38:03 -06:00
Manav Bhatia
0b86675879 libMesh: new version and dependency updates (#9709) 
* added v1.3.1 checksum
* added vtk and petsc variants
* bugfix: enable petsc when slepc variant is specified
 2018-11-12 23:29:58 -06:00
Daniel Topa
79ad078f78 Open MPI: add versions 3.1.3, 3.0.3, update checksums (#9734) 
All checksums are now sha256
 2018-11-12 23:26:39 -06:00
Michael Kuhn
47d74f3bca pkgconf: Add 1.5.4 (#9737) 2018-11-12 23:22:34 -06:00
Matthias Diener
dbdee8e542 chrpath: add new package (#9708) 2018-11-12 23:21:56 -06:00
Phil Tooley
02cdfd654e version/dependency updates for ilmbase and openexr (#9714) 
* include zlib dependency for openexr, fixes #7274
* version bump to openexr/ilmbase 2.3.0
 2018-11-12 23:18:54 -06:00
Cameron Stanavige
230bdce34e new package: flatcc (#9695) 2018-11-12 23:11:52 -06:00
Axel Huebl
152346f275 nlohmann-json: add new version 3.4.0 (#9692) 2018-11-12 23:08:40 -06:00
Ross Miller
7c267e8534 py-numba: update dependencies and versions (#9706) 
The latest version of py-numba (0.40.1) wants a newer version of
py-llvmlite.  Had to add that version to py-llvmlite/package.py.
 2018-11-12 23:07:40 -06:00
Justin Stanley
87df41e0ca migrate: new package starting at 3.6.11 (#9707) 2018-11-12 23:05:54 -06:00
Sinan
9e67216593 new package: PyH5glance (#9700) 2018-11-12 18:55:49 -06:00
Sinan
ec7e5d3b8b new package: python htmlgen (#9699) 2018-11-12 18:47:04 -06:00
Denis Davydov
e04adbca66 gnuplot: add X11 dependency and QT terminal (#9722) 2018-11-12 18:45:27 -06:00
Justin Stanley
553cecaade r-manipulatewidget: new package at 0.10.0 (#9826) 2018-11-12 18:41:03 -06:00
Justin Stanley
2ee0d98be1 r-webshot: new package at 0.5.1 (#9824) 2018-11-12 18:38:48 -06:00
Levi Baber
dcb696bd3f r-callr: adding new dependencies (#9730) 2018-11-12 18:38:03 -06:00
Justin Stanley
5ed3873f2f r-convevol: new package at 1.3 (#9767) 2018-11-12 18:36:31 -06:00
Justin Stanley
8357c1e0bc r-miniui: new package at 0.1.1.1 (#9823) 2018-11-12 18:34:56 -06:00
Justin Stanley
407bfbc2cb r-clustergeneration: new package at 1.3.4 (#9765) 2018-11-12 18:34:03 -06:00
Jim Galarowicz
5dc0b65719 Update Dyninst package file for TBB dependency (#9728) 
* Update Dyninst package file for TBB dependency

Dyninst master and 10.0 release
versions require the tbb package.  This mod
updates the tbb versions adding the one that
dyninst uses and adds the required spack package
changes to dyninst/package.py.

* Put new version of tbb in proper location, per reviewer comment.

* Only depend on tbb if building the development version.

* Changes for the release of Dyninst 10.0.0
 2018-11-09 13:35:11 -08:00
Nichols A. Romero
236b34f3df Introduce fftw-api virtual package for Intel-MKL and FFTW (#9618) 
* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages.

* make fftw default package for fftw-api virtual package

* virtual package test assertion now provides location of default virtual packages.

* Change name of virtual package to fftw-api and used versioned interface.
 2018-11-09 08:16:11 -08:00
Todd Gamblin
0e60fcccfb utils: merge spack.environment into spack.util.environment 
- `spack.util.environment` is the new home for routines that modify
  environment variables.

- This is to make room for `spack.environment` to contain new routines
  for dealing with spack environments
 2018-11-09 00:31:24 -08:00
Justin Stanley
d1b17e8207 canu: use built-in makefile install (#9726) 2018-11-08 10:28:10 +01:00
Denis Davydov
8f4d6caf32 muparser: minor fixes to 2.2.5 and add 2.2.6 with CMake (#9724) 
* muparser: minor fixes to 2.2.5 and add 2.2.6 with CMake
* dealii: make muparser optional
 2018-11-08 10:05:52 +01:00
Michael Kuhn
da193a07a3 ncl: Add 6.5.0 (#9736) 2018-11-08 10:03:29 +01:00
Levi Baber
55b6105af7
r-delayedarray: new dep in latest vers (#9731) 2018-11-07 10:27:08 -06:00
Valentin Clement (バレンタイン クレメン)
768111c365 Use the raw compiler path for the preprocessing pass in CLAW driver (#9748) 2018-11-07 15:24:24 +01:00
Peter Scheibel
7d97e8b067 New repo for advanced packaging tutorial (#9711) 
* modified tutorial packages

* update hint in hdf5 tutorial file (typo for suggested argument)

* add repo.yaml to tutorial repository

* update tutorial docs to refer user to tutorial package repository

* flake edits

* recommend site scope vs. defaults

* you don't specify the repo's name when adding a repo, just the path
 2018-11-06 19:57:32 -08:00
Levi Baber
4ba3c81bc8
snpeff: add wrapper for SnpSift.jar (#9674) 2018-11-06 08:36:47 -06:00
sknigh
d5327d8d4b Add OpenMPI 3.1.3 and a bug patch (#9680) 2018-11-06 09:12:48 +01:00
Gregory Lee
e6eb2b960e py-backports-functools-lru-cache: add to 'backports' namespace (#9720) 2018-11-05 16:01:03 -08:00
Justin Stanley
d7c9128875 new package: homer (starting at 4.9.1) (#9669) 2018-11-02 18:18:05 -07:00
Eric
b471a3626e freetype: enable-freetype-config build option for 2.9.1 (#9653) 
This builds the 'freetype-config' binary which can be used to get
configuration information about the freetype install, used by some
dependents.
 2018-11-02 18:06:40 -07:00
Tim Law
a33d123e2e Add version 2.0.2 of BookLeaf_Cpp and version 3.0.2 of Typhon. (#9662) 2018-11-02 13:30:52 -07:00
Dmitriy
36ddcc2e97 henson: new package (#9657) 
* henson: new package

* henson: change github path to henson-insitu

* henson: make mpi-wrappers=off by default

* henson: remove unsued variable and spaces to make linter happy

* henson: rename version master to develop
 2018-11-01 18:15:12 +01:00
Thomas Stitt
6a3552274f xeus: new package (#9682) 
* xeus: new package
cppzmq: add version 4.3.0
zeromq: make libsodium optional, on by default

* xeus: add patch so it builds, add new version
nlohmann-json: add more versions
cryptopp: add more versions

* xeus: flake8

* xeus: fix license
 2018-10-31 20:23:44 -07:00
Abhinav Bhatele
939ce40032 ecp-proxy-apps: disable building CANDLE Benchmarks by default (#9691) 
add as a variant
 2018-10-31 12:50:37 -06:00
Federico Ficarelli
383cda2c90 lbzip2: add new package (#9688) 2018-10-31 18:08:00 +01:00
Kelly (KT) Thompson
a3ff21eb2b Provide a newer doxygen version. (#9681) 
* Provide a newer doxygen version.

+ Also provide a patch that allows collaboration diagrams to work properly with
  C++ std::shared_ptr<T>. Ref:
  6c380ba91a
 2018-10-31 18:03:13 +01:00
健美猞猁
79e70afed4 Packmol: a new package. (#9687) 2018-10-31 17:32:09 +01:00
Justin Stanley
abad2c9743 r-dismo: new package starting at 1.1-4 (#9675) 2018-10-31 11:28:09 +01:00
Jim Galarowicz
c10d432a2e Update openspeedshop and cbtf-krell module creation code (#9234) 
* Add the setting of CBTF_MPI_IMPLEMENTATION to the cbtf-krell
  and openspeeedshop package files, so that the mpi implementation
  can be found by the tool.  This allows users to not have to
  set this manually if only one mpi implementation is specified
  in the build.
* Update version ranges for dependencies of cbtf packages
 2018-10-30 18:41:08 -07:00
Ross Miller
718be8a645 Update dependencies for py-llvmlite (#9668) 
Change dependency on llvm from >=6.0 to 6.0:6.99.

Refs #9667
 2018-10-30 21:33:43 +01:00
Alberto Chiusole
f602fd8ea4 New package: RegCM, regional climate model. (#9655) 2018-10-30 13:32:59 -07:00
Axel Huebl
33b65ecca0 GCC: ISL and mpfr upper bounds (#9513) 
* GCC: constrain version 6, 7, and 8 to build with ISL version at
  most 0.18
* GCC version 9 (not yet released) will be compatible with
  ISL version 0.20 so future GCC releases are constrained to build
  with ISL version at most 0.20
* ISL: Add v0.15, replace all md5 sums with sha256 sums for ISL
  versions
* GCC versions before 6 were constrained to build with ISL 0.14
  but have been confirmed to work with ISL 0.15
* GCC: Place an upper bound on GCC's mpfr dependency
 2018-10-30 13:26:41 -07:00
Ruben Di Battista
3c387bfa39 vtk: remove redundant option setting (#9597) 
This eliminates duplicates for a couple options which are set
multiple times.
 2018-10-30 12:47:48 -07:00
Abhinav Bhatele
26bacbcb8c caliper: specify path to libunwind (#9670) 2018-10-30 18:37:44 +01:00
Dave
be48d41ab1 warpx: Fixes for building on NERSC (#9671) 2018-10-30 18:25:32 +01:00
jthies
38a1732c5a Jthies/xsdk add phist (#8980) 
* packages/phist: add variant 'fortran' to enable/disable building the Fortran bindings

* xsdk: add phist

* packages/xsdk: add a comment reg. updating phist dependency

* packages/phist: +fortran variant is only for versions 1.7:

* packages/phist: update comments

* xsdk: forgot to specify kernel library for phist (picked tpetra, assuming trilinos+tpetra will be installed)

* packages/phist: add variant 'openmp' to allow disabling OpenMP

* phist: fix compile error due to missing -lm

* flake8: fix warnings

* packages/phist: fix cmake flag: XSDK_ENABLE_Fortran (rather than XSDK_BUILD_Fortran)

* packages/phist: allow disabling building the scamac matrix generator (which causes trouble on some systems)

* packages/xsdk: disable scamac within phist because it caused problems for @balay and is not essential for now

* packages/phist: actually disable scamac via cmake if ~scamac

* phist: disable openmp from xsdk
 2018-10-30 08:12:15 -05:00
jthies
930d6af815 packages/phist: new version 1.7.3 (#9672) 2018-10-30 11:13:11 +01:00
Dan Han
2209d571ea R rjags - new version (#9568) 
* REMOVED: -callr: updated to newest version, added sha256, added listurl

* r-rjags: updated

* r-rjags: fix new version
 2018-10-29 16:12:20 -05:00
snehring
1e54a42cc9 hoomd-blue: fixing issue during build with newer cmakes (#9543) 
* Constrain to build with CMake <= 3.9.6
* Specify installation prefix to match install prefix format of
  other Spack python libraries
 2018-10-29 13:46:35 -07:00
Satish Balay
8d4c15e0bd
strumpack: update to version 3.1.1 (#9666) 2018-10-29 15:34:14 -05:00
Satish Balay
6eef6a1d77
slepc: update to version 3.10.1 (#9665) 2018-10-29 15:33:50 -05:00
Miles Perry
2bd453c4a7 add package Feature/sentieon (#9557) 
* added package sentieon

* change file location

* updated spack header license and added license_vars

* fixed flake8 error

* fixed license header

* fix license header

* license

* added import os.path

* edits

* flake8 edits
 2018-10-29 15:02:27 -05:00
Justin Stanley
c46a39179b orca: new package starting at 4.0.1.2 (#9297) 
* orca: new package starting at 4.0.1.2

* orca: fix typo

* orca: fix boilerplate

* orca: reorder deps, add openmpi runtime dependency

* orca: license update
 2018-10-29 14:49:58 -05:00
David Wells
c96c38a08f Expand the libMesh dependency list (#9642) 
This commit overhauls the libMesh package script in a number of ways:

* We now inherit from AutotoolsPackage.
* libMesh contains about a dozen third-party dependencies that can
  only be provided by the copy bundled with libMesh. This  patch
  enumerates all such bundled dependencies and disables all of them
  by default.
* libMesh supports compilation with external installations of boost,
  eigen, hdf5, slepc, and tbb; this patch adds all of them to
  package.py.
* libMesh will look for a few system executables (xz, bzip, gdb) by
  default. This is now disabled.
* libMesh will now used a copy of perl installed by spack instead of
  trying to find the system copy.
* Compilation with non-system MPI installations requires an additional
  flag (--with-mpi=); this has been added.
 2018-10-29 11:50:43 -07:00
Dmitriy
be5c92f7cd diy: new package (#9628) 2018-10-29 10:20:46 +01:00
Denis Davydov
23726617ba Updated octave and gnuplot versions (#9660) 
* octave: add 4.2.2, 4.4.0 and 4.4.1
* gnuplot: add 5.2.5
 2018-10-29 09:32:30 +01:00
Denis Davydov
d191cb0102 pyfypp: add setuptools build dependency (#9650) 2018-10-26 19:41:10 -07:00
dorier
c8092b3ab7 damaris: add support for VisIt and Catalyst (#9651) 2018-10-26 19:40:25 -07:00
Justin Stanley
91aed716f9 new package: phyluce (starting at 1.6.7) (#9633) 2018-10-26 19:33:32 -07:00
dorier
13e5c3fbe2 VisIt: build vtk without mpi support (#9649) 
VisIt cannot use VTK built with mpi support (which was enabled by
default starting in #9494)
 2018-10-26 19:01:39 -07:00