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7049 commits

Author SHA1 Message Date
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