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2018-03-17hwloc: constrain dependency on numactl (#7509)Massimiliano Culpo1-1/+1
fixes #7505
2018-03-15hwloc: updated package (#7483)Massimiliano Culpo2-25/+51
This includes: * Added latest available versions (1.11.9, 2.0.0) * Added variants to enable graphical output from lstopo * Enabled build of the bundled netloc package if @2.0.0: * Added dependency from numactl if @:1.11.9 * Added a constraint to avoid using hwloc@2.0.0 with openmpi
2018-03-14Added Tagged Release of ExaMiniMD (#7485)Robert Pavel1-2/+2
2018-03-14cube: Fix qt detection (#7242)Michael Kuhn2-0/+26
cube's configure only recognizes qt versions with single digit version components and breaks with qt 5.10. Patch the configure files directly to avoid having to regenerate them.
2018-03-14phylip: new version (#7467)Levi Baber1-0/+1
2018-03-14postgresql: add newest version 10.3 (#7455)Sinan1-0/+1
2018-03-14Fix extends('tcl') environment (#7473)Federico Ficarelli1-5/+19
2018-03-14Xterm: Fix URL (#7476)Matthias Diener1-1/+1
2018-03-14Provide new package: mscgen. (#7477)Kelly (KT) Thompson1-0/+42
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/
2018-03-13r-tfbstools: new package (#7243)Yifan Zhu1-0/+68
2018-03-13llvm 6.0.0 released as stable (#7459)Stephen McDowell1-0/+16
Relase notes: http://releases.llvm.org/6.0.0/docs/ReleaseNotes.html
2018-03-13add an option to build tbb statically (#7407)Cyrus Harrison1-1/+13
2018-03-13Fix dependency conflict in FEniCS. (#7404)f-sim1-1/+1
2018-03-13Treat tcl as extendable (#7410)Federico Ficarelli2-3/+45
* Make tcl package extendable * Let tk extend tcl * Fix environment for Tcl extensions
2018-03-12Fix bugs in `spack dependencies` command (#7435)Todd Gamblin3-20/+35
- 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
2018-03-12Constructing a SpecBuildInterface from another gives no inconsistent MRO (#7457)Massimiliano Culpo2-1/+34
fixes #7239
2018-03-12arpack-ng: add develop (#7458)Denis Davydov1-0/+1
2018-03-10astral: needs zip (#7443)Levi Baber1-0/+1
2018-03-09Fix bug in lua package instroduced by PR #7434 (#7450)Patrick Gartung1-1/+1
Fixes issue #7449
2018-03-09Augustus hash (#7447)Levi Baber1-6/+16
* augustus: 3.3 package hash changed * augustus: bamtools libraries now seem to be in lib64 * augustus: fix lib problem with older bamtools
2018-03-09spack buildcache: allow unsigned tarballs (#7440)Patrick Gartung4-67/+49
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).
2018-03-09resource: convert symlink to real path (#7417)Levi Baber1-1/+1
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.
2018-03-09new package: tcptrace (#6993)sknigh3-0/+99
Also added missing deps for libpcap: bison and flex
2018-03-09new package: cistem (#7438)Levi Baber1-0/+40
2018-03-09new package: py-bcbio-gff (#7129)Eric1-0/+39
2018-03-09new package: deconseq-standalone (#7290)Eric1-0/+60
2018-03-09replace dash with underscore in os name/version (#7381)scheibelp1-2/+2
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 '_'.
2018-03-09Boost: More Bintray (#7389)Axel Huebl1-2/+4
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.
2018-03-09cmake: new version (#7429)Federico Ficarelli1-0/+1
2018-03-09r-cner: new package (#7228)Yifan Zhu2-0/+59
2018-03-08lua package: add lib64 to LUA_PATH and LUA_CPATH (#7434)Patrick Gartung1-0/+6
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)
2018-03-08json-c: Update to 0.13.1 (#7419)Michael Kuhn1-0/+7
* 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
2018-03-08Added new package: ghost (#7362)jthies1-0/+87
2018-03-08hoomd-blue version bump and compiler updated (#7021)Brock Palen1-3/+7
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.
2018-03-08Added compiler conflict to prank (#7168)zenln1-0/+1
2018-03-08Help newer versions of trilinos/zoltan2 successfully configure. (#7059)Kelly (KT) Thompson1-2/+3
+ 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.
2018-03-08New package r-phangorn and its dependencies (#7034)Yifan Zhu4-1/+90
2018-03-08star: needs zlib (#7418)Levi Baber1-0/+2
2018-03-08dislin: new package (#7305)Yifan Zhu1-0/+53
2018-03-07Generalized ExaSP2 Install (#7422)Robert Pavel1-4/+3
Generalized ExaSP2 Install to use glob due to changes in naming convention between previous release and current development branch
2018-03-07cdbfasta: needs zlib (#7413)Levi Baber1-0/+2
2018-03-07gcta: new package (#7425)snehring1-0/+48
2018-03-07OpenSpeedShop package: add support for building on cray (#7338)Jim Galarowicz10-82/+233
2018-03-07orthofinder: Create new package. (#7364)lingnanyuan1-0/+53
2018-03-07fmt: add version (#7415)Federico Ficarelli1-0/+1
2018-03-07Changed CudaPackage base class to PackageBase (#7416)Massimiliano Culpo1-2/+2
CudaPackage is always used as a mixin. As such it should inherit from PackageBase, and not Package.
2018-03-07py-gpaw package with variants for MPI, FFTW and ScaLAPACK (#7373)simo-tuomisto2-0/+108
2018-03-07Relion 2.1 - Using CudaPackage class (#6707)Douglas Duckworth1-11/+7
2018-03-07lammps: add version 20180222 (#7408)Christoph Junghans1-0/+1
2018-03-06Improved binary relocation: error checking and reporting (#7314)Patrick Gartung5-149/+352
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
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