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2017-10-13r-zlibbioc: added versioned dependency on r (#5674)Yifan Zhu1-0/+1
2017-10-13trilinos / oce : add missing if before calling macOS_version (#5743)Denis Davydov2-2/+3
* trilinos: add missing if before calling macOS_version * oce: add missing if before calling macOS_version
2017-10-13r-readr: created new package (#5741)Yifan Zhu1-0/+43
2017-10-13r-dorng: created new package (#5740)Yifan Zhu1-0/+46
2017-10-13r-stringr: added list_url and version 1.2.0 (#5738)Yifan Zhu1-0/+2
2017-10-13r-stringi: added list_url and version 1.1.5 and 1.1.3 (#5737)Yifan Zhu1-0/+3
2017-10-13r-summarizedexperiment: created new package (#5734)Yifan Zhu1-0/+47
2017-10-13r-yaqcaffy: added list_url and versioned dependency on r (#5730)Yifan Zhu1-0/+2
2017-10-13slepc: refine version constraints for petsc 3.8 (#5752)Denis Davydov1-4/+8
2017-10-13openblas: remove extra develop version (#5750)Denis Davydov1-2/+0
2017-10-13gettext: fix prefix (#5749)Denis Davydov1-1/+1
2017-10-12Lbann flags (#5747)Brian Van Essen2-3/+2
* Fixed the datatype flag in the LBANN package. Also added develop version to OpenBLAS. * Fixed where the datatype flag should be set.
2017-10-12r-gcrma: added versioned dependency on r (#5670)Yifan Zhu1-0/+1
2017-10-12r-simpleaffy: added versioned dependency on r (#5673)Yifan Zhu1-0/+1
2017-10-12petsc: add in maintainers (#5729)Satish Balay1-0/+2
2017-10-12Add the option for a versioned layout to boost (#5709)David Hows1-0/+6
2017-10-12kaks-calculator: new package (#5725)Audrey Thoma1-0/+59
* kaks-calculator: new package * kaks-calculator: new package * fixing homepage
2017-10-12petsc: update to latest 3.8 version [and include 3.7.7] (#5723)Satish Balay1-1/+3
Also fix flake8 warning "import os should be before import sys"
2017-10-12Add OpenFAST package (wind turbine simulation tool). (#5662)Jon Rood1-0/+93
* Add OpenFAST package (wind turbine simulator). * Adding maintainer to openfast package. * Fixing copyright date.
2017-10-12various fixes for macOS high sierra (#5647)Denis Davydov7-5/+52
* various fixes for macOS high sierra * add macOS_version() helper function * flake8 fixes * update oce and trilinos * fix bison
2017-10-12Make --trusted default when running spack gpg list (#5678)David Hows2-1/+2
* Make --trusted default when running spack gpg list Currently running `spack gpg list` with no arguments returns nothing. You must supply either the `--trusted` or the `--signing` options. The idea here is to return some initial data to the user when the command is run. The alternative is to return an error, telling the user to select one of the two options. * Add an extra test case for the empty list command Fixes the issue with code coverage
2017-10-12Speed up concretization (#5716)Todd Gamblin4-17/+23
This isn't a rework of the concretizer but it speeds things up a LOT. The main culprits were: 1. Variant code, `provider_index`, and `concretize.py` were calling `spec.package` when they could use `spec.package_class` - `spec.package` looks up a package instance by `Spec`, which requires a (fast-ish but not that fast) DAG compare. - `spec.package_class` just looks up the package's class by name, and you should use this when all you need is metadata (most of the time). - not really clear that the current way packages are looked up is necessary -- we can consider refactoring that in the future. 2. `Repository.repo_for_pkg` parses a `str` argument into a `Spec` when called with one, via `@_autospec`, but this is not needed. - Add some faster code to handle strings directly and avoid parsing This speeds up concretization 3-9x in my limited tests. Still not super fast but much more bearable: Before: - `spack spec xsdk` took 33.6s - `spack spec dealii` took 1m39s After: - `spack spec xsdk` takes 6.8s - `spack spec dealii` takes 10.8s
2017-10-12samtools: add version 1.6 + some fixes (#5715)Carlos Bederián3-9/+11
* htslib: add version 1.6 * samtools: add version 1.6, remove zlib dependency * bcftools: add version 1.6, switch to using standalone htslib
2017-10-12minimap2: new package (#5722)Audrey Thoma2-0/+77
2017-10-12Initial version of libpcap (#5710)David Hows1-0/+34
Add a package script for libpcap with the current version (1.8.1)
2017-10-12Better install output (#5714)Todd Gamblin6-20/+17
* Do not call setup_package for fake installs - setup package could fail if ``setup_dependent_environment`` or other routines expected to use executables from dependencies - xpetsc and boost try to get python config variables in `setup_dependent_package`; this would cause them not to be fake-installable * Remove vestigial deptype_query argument to Spec.traverse() - The `deptype_query` argument isn't used anymore -- it's only passed around and causes confusion when calling traverse. - Get rid of it and just keep the `deptypes` argument * Don't print redundant messages when installing dependencies - `do_install()` was originally depth-first recursive, and printed "<pkg> already installed in ..." multiple times for packages as recursive calls encountered them. - For much cleaner output, use spec.traverse(order='post') to install dependencies instead
2017-10-11r-affy: added versioned dependency on r (#5660)Yifan Zhu1-0/+1
2017-10-11r-affyio: added versioned dependency on r (#5661)Yifan Zhu1-0/+1
2017-10-11r-biocinstaller: added versioned dependency on r (#5663)Yifan Zhu1-1/+1
2017-10-11r-matrixstats: created new package (#5682)Yifan Zhu1-0/+40
2017-10-11r-biocgenerics: added version 0.22.1 and added versioned dependency on r (#5683)Yifan Zhu1-0/+4
2017-10-11r-genomeinfodbdata: added versioned dependency on r (#5685)Yifan Zhu1-0/+1
2017-10-11r-genomeinfodb: created new package (#5695)Yifan Zhu1-0/+46
2017-10-11r-genomicranges: added new package (#5697)Yifan Zhu1-0/+52
2017-10-11r-futile-options: created new package (#5699)Yifan Zhu1-0/+34
2017-10-11r-lambda-r: created new package (#5700)Yifan Zhu1-0/+36
2017-10-11r-futile-logger: created new package (#5701)Yifan Zhu1-0/+40
2017-10-11r-rsamtools: created new package (#5702)Yifan Zhu1-0/+50
2017-10-11r-biocparallel: created new package (#5703)Yifan Zhu1-0/+41
2017-10-11r-delayedarray: created new package (#5704)Yifan Zhu1-0/+54
2017-10-11r-biomart: added versioned dependency on r (#5666)Yifan Zhu1-0/+1
2017-10-11Strelka depends on boost 1.56.0 *or newer* (#5690)George Hartzell1-1/+1
Relax/correct the constraint on the version of boost used by Strelka to match the docs.
2017-10-11dealii: minor fixes (#5687)Denis Davydov1-3/+3
* dealii: fix minor bug in Assimp config * dealii: request sundials without pthreads
2017-10-11Add a bundle package for the ECP proxy applications suite (#5689)Christoph Junghans3-2/+57
* Add a bundle package for the ECP proxy applications suite * Update package.py
2017-10-10Add a package: dmlc/mxnet. (#3579)健美猫11-0/+573
* Add dmlc/mxnet packags. * Build mxnet+cuda+opencv with GCC-4.8.5 and GCC-5.4.0. * Build mxnet version 0.10.0, 0.10.0.post1 and 0.10.0.post2. * Add component version constrain for mxnet 0.10.0.x . * Go through flake8. * Replace commit hash with commit date as package version. * Go throught Travis-CI. * Update submodule version for 0.10.0.post2. * Add openmp variant for dmlc-core and mxnet. * Refine variant handling. * Fix filter_file for dmlc-core. * Cut long strings into multiple lies due to PEP8 requirements. * Fix for PEP8. * Add CUB_INCLUDE. * Add py-mxnet: Python binding for MXNet. * Remove distutils.dir_util. * Add the profiler variant for mxnet. * Add a shared variant for nnvm. * Set USE_OPENMP to OFF by default. * Fix flake8 errors. * Fix flake8 issues. * flake8 issues again.
2017-10-10Adding flang - a llvm based Fortran compiler (#5459)Christoph Junghans1-0/+80
* flang: initial commit * flang: added symlink to clang's flang * add flang wrapper * flang wrapper: inject rpath as well * flang wrapper: PATH -> -B
2017-10-10compilers/clang: add flang (#5503)Christoph Junghans3-10/+16
* compilers/clang: add flang * Update clang.py
2017-10-10ninja: add v1.8.2 (#5625)Christoph Junghans1-0/+1
2017-10-10plumed: reworked patching applications, added new version (#5680)Massimiliano Culpo1-47/+31
closes #5506 The application of patches to upstream executables has been reworked according to the suggestions of the main developer in #5506. In particular we are not maintaining a dictionary that maps plumed versions to the versions of patchable executables, and we are using a non-interactive command to patch applications. All the comments on substituting plumed at run-time do not apply here, since we use RPATH and we want to maintain a 1:1 relationship between the DAG hash and the plumed library used.
2017-10-10snap-korf: new package (#5589)Audrey Thoma1-0/+62
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