Commit graph

8744 commits

Author SHA1 Message Date
Levi Baber
1cde74656b phylip: new version (#7467) 2018-03-14 08:56:15 +01:00
Sinan
e378044f16 postgresql: add newest version 10.3 (#7455) 2018-03-14 08:54:02 +01:00
Federico Ficarelli
b5879d7d07 Fix extends('tcl') environment (#7473) 2018-03-14 07:02:50 +01:00
Matthias Diener
73dd58b68a Xterm: Fix URL (#7476) 2018-03-14 06:58:42 +01:00
Kelly (KT) Thompson
86f9c9fc73 Provide new package: mscgen. (#7477)
Mscgen is a small program that parses Message Sequence Chart descriptions and
produces PNG, SVG, EPS or server side image maps (ismaps) as the output.

See http://www.mcternan.me.uk/mscgen/
2018-03-14 06:56:11 +01:00
Yifan Zhu
5bd8ec8160 r-tfbstools: new package (#7243) 2018-03-13 12:40:41 +01:00
Stephen McDowell
6f76c2124a llvm 6.0.0 released as stable (#7459)
Relase notes: http://releases.llvm.org/6.0.0/docs/ReleaseNotes.html
2018-03-13 11:34:19 +01:00
Cyrus Harrison
f8d3a0225f add an option to build tbb statically (#7407) 2018-03-13 08:08:02 +01:00
f-sim
1329f3baca Fix dependency conflict in FEniCS. (#7404) 2018-03-13 08:04:09 +01:00
Federico Ficarelli
b594f89d5e Treat tcl as extendable (#7410)
* Make tcl package extendable

* Let tk extend tcl

* Fix environment for Tcl extensions
2018-03-13 10:31:03 +09:00
Todd Gamblin
b4a9e37a98
Fix bugs in spack dependencies command (#7435)
- transitive dependencies were not being handled correctly

- restructure code to do recursion and mark visited packages properly

- add `-V` option to *not* expand virtuals in spack dependencies
2018-03-12 17:26:58 +09:00
Massimiliano Culpo
a1c8ce82f2 Constructing a SpecBuildInterface from another gives no inconsistent MRO (#7457)
fixes #7239
2018-03-12 17:07:08 +09:00
Denis Davydov
a4ed76c207 arpack-ng: add develop (#7458) 2018-03-12 09:06:37 +01:00
Levi Baber
39bfa12f22 astral: needs zip (#7443) 2018-03-10 10:56:59 +09:00
Patrick Gartung
82aa54151a Fix bug in lua package instroduced by PR #7434 (#7450)
Fixes issue #7449
2018-03-09 16:57:46 -08:00
Levi Baber
3945b2adb4 Augustus hash (#7447)
* augustus: 3.3 package hash changed

* augustus: bamtools libraries now seem to be in lib64

* augustus: fix lib problem with older bamtools
2018-03-09 16:05:39 -08:00
Patrick Gartung
a4e75c7f0e spack buildcache: allow unsigned tarballs (#7440)
This re-adds the option to create and install unsigned tarballs, now
with the -u option (--unsigned) rather than the -y option.

This also changes the "keys" command, replacing the -y/--yes-to-all
option with the -t/--trust option (which has the same effect but is
more-clearly named).
2018-03-09 15:29:10 -08:00
Levi Baber
38bb0e3e7d resource: convert symlink to real path (#7417)
Fixes #7130

shutil.move expects a source path like "/x/y/" to be a directory and
fails if "/x/y" is a symlink. This invokes realpath on the source
path to avoid the issue.
2018-03-09 12:40:57 -08:00
sknigh
9d3d7d3216 new package: tcptrace (#6993)
Also added missing deps for libpcap: bison and flex
2018-03-09 10:46:57 -08:00
Levi Baber
1eeb918f0d new package: cistem (#7438) 2018-03-09 10:19:10 -08:00
Eric
d2f0e57771 new package: py-bcbio-gff (#7129) 2018-03-09 10:14:53 -08:00
Eric
2f97aea4e4 new package: deconseq-standalone (#7290) 2018-03-09 10:13:41 -08:00
scheibelp
f27f20e5b3
replace dash with underscore in os name/version (#7381)
Fixes #7356

In some cases OperatingSystem (e.g. LinuxDistro) was getting
instantiated with a version that contains dashes. This breaks because
the concretizer later converts this value to a string and re-parses
it, and the '-' character is used to separate architecture components.
This adds a guard in the initializer to convert '-' to '_'.
2018-03-09 10:03:58 -08:00
Axel Huebl
869c654c37 Boost: More Bintray (#7389)
There are two additional releases moved to bintray.
Change to bintray for 1.64 and 1.65 as well since SF downloads are
too instable.
2018-03-09 09:57:41 -08:00
Federico Ficarelli
8ad40babd6 cmake: new version (#7429) 2018-03-09 09:18:58 +01:00
Yifan Zhu
b6440fd10e r-cner: new package (#7228) 2018-03-09 08:36:26 +01:00
Patrick Gartung
331f5f27eb lua package: add lib64 to LUA_PATH and LUA_CPATH (#7434)
This is needed when using system lua on RHEL and clones where lua
is installed in /usr/lib64. Note that the path entry for lua in
packages.yaml should specify the major/minor version of lua (since
this is used to calculate the lua lib directory)
2018-03-08 20:18:55 -08:00
Michael Kuhn
74bb15285b json-c: Update to 0.13.1 (#7419)
* json-c: Update to 0.13.1

0.12.1 does not compile with GCC 7.

* json-c: Add patch to make 0.12.1 build with gcc 7
2018-03-08 14:25:29 -08:00
jthies
bcde37633d Added new package: ghost (#7362) 2018-03-08 11:16:51 +01:00
Brock Palen
732432df50 hoomd-blue version bump and compiler updated (#7021)
updated hoomd-blue to latest tagged release in repo.  This version also supports newer gcc6 compilers, so added constraint for older version to avoid breaking existing installs.
2018-03-08 09:35:59 +01:00
zenln
ad183f652f Added compiler conflict to prank (#7168) 2018-03-08 08:47:46 +01:00
Kelly (KT) Thompson
ac7fef3253 Help newer versions of trilinos/zoltan2 successfully configure. (#7059)
+ Newer versions of zoltan2 are doing test compiles that link to parmetis.  If
  these checks don't find `metis.h`, the check fails.
+ This small tweak ensures that the zoltan2 configure step can find `metis.h`
  that is provided by spack.
2018-03-08 08:39:35 +01:00
Yifan Zhu
66c46ae655 New package r-phangorn and its dependencies (#7034) 2018-03-08 08:30:02 +01:00
Levi Baber
98808196cb star: needs zlib (#7418) 2018-03-08 08:27:41 +01:00
Yifan Zhu
64f1fbb2e2 dislin: new package (#7305) 2018-03-08 06:38:17 +01:00
Robert Pavel
1cf451b62c Generalized ExaSP2 Install (#7422)
Generalized ExaSP2 Install to use glob due to changes in naming
convention between previous release and current development branch
2018-03-07 15:46:53 -08:00
Levi Baber
13e6fc730d cdbfasta: needs zlib (#7413) 2018-03-07 15:42:37 -08:00
snehring
cb64e32296 gcta: new package (#7425) 2018-03-07 15:40:51 -08:00
Jim Galarowicz
7f3a72fb33 OpenSpeedShop package: add support for building on cray (#7338) 2018-03-07 14:26:07 -08:00
lingnanyuan
f393a2c146 orthofinder: Create new package. (#7364) 2018-03-07 20:45:45 +01:00
Federico Ficarelli
ef310d9f66 fmt: add version (#7415) 2018-03-07 13:59:20 +01:00
Massimiliano Culpo
d77dd298eb
Changed CudaPackage base class to PackageBase (#7416)
CudaPackage is always used as a mixin. As such it should inherit from
PackageBase, and not Package.
2018-03-07 13:45:11 +01:00
simo-tuomisto
da48d3113c py-gpaw package with variants for MPI, FFTW and ScaLAPACK (#7373) 2018-03-07 09:30:47 +01:00
Douglas Duckworth
0f114d9718 Relion 2.1 - Using CudaPackage class (#6707) 2018-03-07 07:45:48 +01:00
Christoph Junghans
95b2738549 lammps: add version 20180222 (#7408) 2018-03-07 06:32:06 +01:00
Patrick Gartung
f5467957bc Improved binary relocation: error checking and reporting (#7314)
Fixes #7237
Fixes #6404
Fixes #6418
Fixes #6369

Identify when binary relocation fails to remove all instances of the
source prefix (and report an error to the user unless they specify
-a to allow the old root to appear). This check occurs at two stages:
during "bincache create" all instances of the root are replaced with
a special placeholder string ("@@@@..."), and a failure occurs if the
root is detected at this point; when the binary package is extracted
there is a second check. This addresses #7237 and #6418.

This is intended to be compatible with previously-created binary
packages.

This also adds:

* Better error messages for "spack install --use-cache" (#6404)
* Faster relocation on Mac OS (using a single call to
  install_name_tool for all files rather than a call for each file)
* Clean up when "buildcache create" fails (addresses #6369)
* Explicit error message when the spack instance extracting the binary
  package uses a different install layout than the spack instance that
  created the binary package (since this is currently not supported)
* Remove the option to create unsigned binary packages with -y
2018-03-06 18:02:53 -08:00
Christoph Junghans
360feb4193
minighost: rework link logic (#7402) 2018-03-06 15:51:12 -07:00
Mike Pozulp
b0795d84c7 adds patches required to build hdf5 1.8.10 (#7386)
For hdf5 `1.8.10` and some compilers, the hdf5 build system adds the
'-ansi' flag. hdf5 1.8.10 is not actually ansi compliant so this
adds a patch to modify the places where it violates ansi
compatibility (which ends up being a few comments).
2018-03-06 12:49:36 -08:00
Eric
ea7879bce5 bowtie2: Add version 2.3.4.1 (#7252) 2018-03-06 18:48:48 +01:00
Geoffrey Oxberry
5ed6e6f184 pnmpi@1.7: new package (#7051)
Add PnMPI, a dynamic MPI tool infrastructure that builds on top of the
PMPI interface.
2018-03-06 18:48:28 +01:00