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2019-01-30 modified: var/spack/repos/builtin/packages/libx11/package.py (#10473)Sajid Ali1-1/+2
2019-01-30py-pyfftw package: add version 0.11.1 (#10474)Sajid Ali1-0/+1
2019-01-29Add configparser v3.5.1, fixes backports namespace (#10433)George Hartzell1-0/+1
Fixes #8343 #4154 #7370 Closes #4155 All but one of the backports packages were using "pkgutil-style" namespacing, but configparser was using "pkg_resource-style". A namespace needs to be one style or another. This adds a new configparser version which switches to using the pkgutil-style namespace approach. With this update, one can now install flake8 with Spack and use it by loading modules.
2019-01-29debug output includes modulecmd output (#9476)Peter Scheibel1-7/+28
Debug output now includes the output of modulecmd executions. Only output module content when a failure occurs; always report when a module is loaded/unloaded.
2019-01-29rhash: Fix broken RPATH info on darwinChuck Atkins1-3/+3
The PREFIX variable in the makefiles is directly used to construct the install name on the library metadata on darwin. If not passed, the default /usr/local is used and the resulting librhash.dylib contains usage informaiton of /usr/local/lib/librhash.0.dylib. This adds the PREFIX= variable directly to the make command so the resulting usage metadata contains the correct valid library path.
2019-01-28add flux-core@0.11.0 and flux-sched@0.7.0 (#10447)Stephen Herbein2-5/+11
* flux-core: add v0.11.0 and updated dependencies libuuid hasn't been a direct dependency of flux-core since 2015 (well before any of the versions listed in the package). The yaml-cpp dependency moved to flux-sched when we moved the jobpsec library from core to sched. Some python3 incompatibilities were found in 0.11.0, so bump the python3 support back a version. * flux-sched: add v0.7.0 and make boost dependency more precise
2019-01-29llvm: various updates (#10427)Chuck Atkins1-0/+21
* llvm: Bump version to 7.0.1 * llvm: Added perl-data-dumper build dependency for openmp * llvm: Enable exception handling and RTTI Useful to have turned on in general with RTTI but also necessary to workaround some lldb stability issues with some versions of libstdc++.
2019-01-26Update the PMIx package (#10442)Ralph Castain1-27/+32
* Update the PMIx package - Add latest releases to the list. - Add dependency on hwloc for versions >= 3.0 - Flag preferred versions for libevent and hwloc - Improve the description - Point the project URL to the correct site Signed-off-by: Ralph Castain <rhc@pmix.org> * Only install the hwloc dependency for versions >= 3.0.0 Thanks to @ax3l for the suggestion Signed-off-by: Ralph Castain <rhc@pmix.org> * Add myself as a listed maintainer Signed-off-by: Ralph Castain <rhc@pmix.org>
2019-01-26add variant for a debug build (#10409)Cameron Smith1-0/+4
2019-01-26QMCPACK Update - Jan 2019 (#10252)Nichols A. Romero1-28/+98
* Add warnings for existing conflicts. New versions of QMCPACK require a compiler with C++14 support. * QMCPACK now requires a newer release of CMake. * Switch QMCPACK to using FFTW-api provider. * Relax dependencies on QMCPACK +da variant. * Add QMCPACK 3.6.0 release. * QMCPACK compiler-CUDA conflicts. * QMCPACK fix typo in expressing conflict. * Conditional needed since these variables are only used when FFTW is a dependency to QMCPACK. * QMCPACK QE variant dependency was underspecified. Must include MPI as a hard dependency on QE. * Update QMCPACK dependencies for HDF5, CMake and Boost. * QMCPACK clean-up, more consistent use of spec vs. self.spec. * Add support for collective I/O variant of QMCPACK. * Update QMCPACK conflicts for QE and PHDF5 variants. * Use built-in install method for QMCPACK starting with 3.6.0 * QMCPACK compiler C++14 conflicts were off by one version. * QMCPACK package needs to setup_environment method. * In support of PR#10252, get rid of slashes in string. * Migrate these to the CUDA package and make a seperate PR. * In support of PR#10252, get rid of join_path for nexus. * In support of PR#10252, work around concretizer limitation. * In support of PR#10252, convert to conditionals to if-else clauses for compactness. * In support of PR#10252, get rid of extra space and new line in warning messages.
2019-01-26laghos: update version (#10420)Abhinav Bhatele2-1/+2
2019-01-26petsc: configure works with python3 in current petsc@develop - and will ↵Satish Balay1-1/+2
work in future releases [3.11+] (#10380)
2019-01-26diffutils: add version 3.7 (#10406)Matthias Diener1-0/+1
2019-01-26rust: add version 1.32.0 (#10407)Matthias Diener1-0/+1
2019-01-26bcftools: do not use bundled htslib (#10445)Ricardo Silva1-0/+6
* if the path to htslib is not specified the bundled one is built instead * additionally this fixes the build with the intel compiler
2019-01-26perl-data-dumper: New package (#10425)Chuck Atkins1-0/+15
This package is added to satisfy a build time dependency for llvm-openmp
2019-01-26libuv: Bump version to 1.25.0 (#10423)Chuck Atkins1-1/+2
2019-01-26cmake: Use system libs by default (#10424)Chuck Atkins1-2/+3
This also fixes the libuv version dependency for 3.11+
2019-01-26Added the py-send2trash package as a pre-req for py-jupyterhub (#10441)wspear1-0/+17
2019-01-26magma: add version 2.5.0 (#10438)Piotr Luszczek1-0/+1
2019-01-26capstone: new package (#10449)Levi Baber1-0/+16
2019-01-24Environments: fix bug for install of external packages (#10437)Peter Scheibel1-0/+1
"spack install" will install all packages added to the current environment. When this included external packages, the environment update would fail because it would attempt to copy log files that were only generated if Spack handled the install itself. This skips that step for external packages.
2019-01-24Allow `spack install --overwrite` for nonexistent or multiple packages (#9201)Greg Becker2-25/+78
* Allow overwrite nonexistent and multiple packages initial implementation give one prompt to users instead of a prompt per spec testing * flake * bugfix: install overwrite check each spec against installed * python3 compliance for filter/map
2019-01-24fix issue where docker images were being pushed without login (#10379)Omar Padron1-3/+1
2019-01-23Update ecp st tau pdt (#8192)sameershende2-34/+135
* Updated MPI and TAU versions in the TAU package * Updated PDT versions * Added support for Python (+python), default to `False` * Cleaned up binutils, python, mpi usage. * Updated binutils install to add additional header files to the include/extra directory. * Resolving review problems with TAU and binutils packages. The binutils package was updated to include support for installing the ELF headers as a +headers variant. The TAU package was updated to use all known Spack dependencies.
2019-01-22trinotate: remove perl-dbd-mysql, move runtime files to HOME (#9850)Justin Stanley1-1/+8
2019-01-22r-gamlss: new package (and data) at 5.1-2 (#10360)Justin Stanley3-0/+61
* r-gamlss-data: new package at 5.1-0 * r-gamlss-dist: new package at 5.1-1 * r-gamlss: new package at 5.1-2 * r-gamlss: add mass, survival, nlme imports
2019-01-22entrezdirect: new package (#10374)Justin Stanley1-0/+30
2019-01-22py-whatshap: new package at 0.17 (#10377)Justin Stanley1-0/+31
* py-whatshap: new package at 0.17 * py-whatshap: remove unused build_args
2019-01-22r-rrcov: new package at 1.4-7 (#10387)Justin Stanley1-0/+25
2019-01-22r-robust: new package at 0.4-18 (#10391)Justin Stanley1-0/+23
2019-01-22r-dynamictreecut: new package at 1.63-1 (#10388)Justin Stanley1-0/+19
2019-01-22Exclude system mkl installs from numpy (#10383)Peter Scheibel1-4/+28
Fixes #10361 Fixes #6634 When mkl isnt in the spec, still write an explicit mkl entry to prevent numpy from looking in system dirs and using a system install of mkl. Do the same for openblas and atlas (although mkl was the only system install reported to interfere with Spack's choice).
2019-01-22py-pyvcf: new package at 0.6.0 (#10375)Justin Stanley1-0/+17
2019-01-21Typo fixes in .flake8 comments (#10399)Adam J. Stewart2-11/+19
2019-01-20py-pyfaidx: new package at 0.5.5.2 (#10376)Justin Stanley1-0/+17
2019-01-20cmake: add version 3.13.3 (#10397)Matthias Diener1-0/+1
2019-01-18Update Nalu-Wind and dependencies (#10204)Jon Rood7-44/+131
* Updating nalu-wind, nalu, openfast, and tioga packages. Includes improved handling of +shared variant. * Add fftw and catalyst support to nalu-wind. * Restrict ParaView to use matplotlib versions before 3 (which require Python 3)
2019-01-18adding checksum for latest lmod release (#10381)Owen Solberg1-0/+1
2019-01-16Update templight pseudo-release to remove need for patching (#10290)Hadrien G1-2/+16
* Update templight+LLVM combo * Bring back old pseudo-release
2019-01-16Openblas: added version 0.3.5 (#10364)Massimiliano Culpo1-0/+1
2019-01-16Added latest version of singularity 2.x (#10354)sknigh1-0/+1
2019-01-16Add package for Hugo (static website generator) (#10358)George Hartzell1-0/+26
2019-01-15py-modred: New package (#10309)Tom Payerle2-0/+38
* py-modred: New package Parallelized python module for finding modal decompositions and reduced order models. * fix license I think? * Add dependency on py-numpy and remove commented out code
2019-01-15Added hpl 2.3 (#10345)sknigh1-3/+31
* Added hpl 2.3 * Added requested build fixes, added step to copy HPL.dat in 2.3+
2019-01-15r requires cairo+pdf (#10350)Adam J. Stewart1-1/+1
2019-01-15explicitly depend_on cairo with X **and** pdf variants (#10351)Owen Solberg1-0/+1
2019-01-15Add useful comment explaining why this is not needed for Python3. (#10326)Elizabeth Fischer1-0/+1
2019-01-15openPMD-api: Dependency Update (#10314)Axel Huebl1-14/+19
openPMD-api now only supports Python 3, needs a newer CMake and ADIOS1 and also learned to read & write JSON :-)
2019-01-14vigra: new package (#10337)Neil Flood1-0/+91
* vigra: new package * Better constraints and types on some depends_on. Use site_packages_dir variable for Python install dir. Explicit switch-offs where available. Change some local variables to suit style checks. * Take care of lines too long * Explicit WITH_HDF5=ON
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