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2019-10-04migrate: add zlib dependency. (#13039)Toyohisa Kameyama1-4/+8
* migrate: add zlib dependency. * flake8. * autotools related tools change to build.
2019-10-04LLVM 9.0.0 (#13050)Felix Thaler1-0/+16
2019-10-03fftw: simplify the recipe and make use of specific targets (#12889)Massimiliano Culpo1-123/+68
* fftw: grouped precisions in a single variant * fftw: simd options are now based on target features and not on variants * fftw: simplified computing the selected precisions
2019-10-03boost: Use gcc toolset for bootstrap with Fujitsu compiler. (#12876)t-karatsu1-1/+1
2019-10-03graphmap: add zlib dependency. (#13031)Toyohisa Kameyama1-0/+2
2019-10-03fastqvalidator: add zlib dependency and Removes erroneous deletes in ↵Toyohisa Kameyama2-0/+29
Chromosome (#13030)
2019-10-03hapcut2: add zlib dependency. (#13032)Toyohisa Kameyama1-0/+2
2019-10-03liblbxutil: Add zlib dependency. (#13033)Toyohisa Kameyama1-0/+1
2019-10-03metabat: Add zlib and ncurses dependency. (#13034)Toyohisa Kameyama1-0/+2
2019-10-03muse: add zlib dependency. (#13040)Toyohisa Kameyama1-0/+2
2019-10-03ngmlr: add zlib dependency. (#13041)Toyohisa Kameyama1-0/+2
2019-10-03fix ipykernel dependency, newer versions are python3-only (#13019)Andreas Baumbach1-2/+3
* fix ipykernel dependency, newer versions are python3-only * Update var/spack/repos/builtin/packages/py-ipykernel/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ipykernel/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-03Update cctools to v7.0.18 (#13037)George Hartzell1-1/+2
- add version/checksum info for v7.0.18 - update checksum for v6.1.1 to use sha256, while I have the editor open...
2019-10-03updated manta checksum (#13038)Owen Solberg1-0/+1
2019-10-03Add py-flye 2.6 (#13025)Adam J. Stewart1-2/+13
2019-10-03Update compilers.yaml location in Getting Started docs (#13029)Adam J. Stewart1-11/+14
2019-10-03Add EasyBuild 4.0.0 (#13024)Adam J. Stewart4-18/+41
* Add EasyBuild 4.0.0 * Update homepage, remove no longer required deps * Replace version ranges with fixed versions
2019-10-03Update ECP Data & Vis SDK packages (#13027)Chuck Atkins2-23/+22
* ecp-io-sdk: Add faodel and sort variants * ecp-viz-sdk: Re-enable catalyst, sort variants, turn on by default * ecp-io-sdk and ecp-viz-sdk: Fix dependency variants
2019-10-03Generic x86_64 code compiled with GCC uses non deprecated mtune flags (#13022)Massimiliano Culpo2-6/+15
fixes #12928
2019-10-02Remove support for generating dotkit files (#11986)Massimiliano Culpo34-426/+121
Dotkit is being used only at a few sites and has been deprecated on new machines. This commit removes all the code that provide support for the generation of dotkit module files. A new validator named "deprecatedProperties" has been added to the jsonschema validators. It permits to prompt a warning message or exit with an error if a property that has been marked as deprecated is encountered. * Removed references to dotkit in the docs * Removed references to dotkit in setup-env-test.sh * Added a unit test for the 'deprecatedProperties' schema validator
2019-10-02added tasmanian version 7.0 to spack (#13003)Miroslav Stoyanov3-4/+52
2019-10-02New package: mapnik (#12708)Sinan1-0/+54
2019-10-02libint + cp2k: 2-stage build with 'tune' and 'fortran' variants (#12475)Tiziano Müller2-20/+128
* libint: switch to 2-stage build for 2.6.0+ * libint: add tune and fortran variants * cp2k: add support for libint >= 2.0 * cp2k: use pkg-config for linking libxc
2019-10-02cdhit: add zlib dependency. (#13015)Toyohisa Kameyama1-3/+7
* cdhit: add zlib dependency. * Add zlib variant.
2019-10-02denovogear: Add missing zlib depenbdency and fix open handling error. (#13017)Toyohisa Kameyama2-0/+15
2019-10-02cnpy: add zlib dependency. (#13016)Toyohisa Kameyama1-0/+2
2019-10-02Add cuda to paraview build. (#12996)Dan Lipsa1-1/+11
2019-10-02Singularity 3.4.1 still needs the makefile patch (#13008)George Hartzell1-1/+1
* Singularity 3.4.1 still needs the makefile patch * Constrain build patch to 3.4.0:3.4.1
2019-10-02new package: openldap (#12748)Sinan1-0/+92
* new package: openldap * fix mistake * remove template text * fix build error involving perl * flake8 * improvements * introduce multi valued variant for tls support * improve tls variant * overwrite build phase as opposed install * improve style
2019-10-02ants: missing zlib dependency and fix working directory in install. (#13010)Toyohisa Kameyama1-1/+6
2019-10-02breakdancer: missing ncurses dependency. (#13011)Toyohisa Kameyama1-0/+2
2019-10-02breseq: fix dependency and limit compiler version. (#13013)Toyohisa Kameyama1-1/+4
2019-10-02fujitsu compiler: Add 'required_libs'. (#13014)t-karatsu1-0/+2
2019-10-02update py-jupyter-notebook to use the real releases (#13020)Andreas Baumbach1-13/+9
* github releases are not released versions, but from-source releases * they lack the mimification of the JS/CSS components and as such require node-js and npm, this conflicts with python@3: * this commit * drops the from-source dependencies on node-js and npm and * updates the checksums to the correct sha256 hashes of the pypi releases. The pypi-tarballs are different
2019-10-02Replace expensive store.reindex() call with db.add() call. (#13021)Patrick Gartung1-1/+1
2019-10-01ZFP: CMake Package (#12999)Axel Huebl4-38/+65
* ZFP: CMake Package ZFP is primarily build via CMake, which will have all install logic and configuration files generated. The 0.5.0 release did not support this yet, so we toss it. * Patch ADIOS1: ZFP 0.5.1+ support * ZFP: Expose all CMake variants
2019-10-01'spack buildcache list' should show all buildaches available. (#13002)Patrick Gartung1-5/+1
* binary cache: show all packages for compatible differing targets * Don't restrict spack buildcache list to arch or os * Fix from merge conflict
2019-10-01direnv: add info for version 2.20.0 (#13007)George Hartzell1-0/+1
2019-10-01Add all compatible system types directory to module pathsMassimiliano Culpo4-3/+21
fixes #12915 closes #12916 Since Spack has support for specific targets it might happen that software is built for targets that are not exactly the host because it was either an explicit user request or the compiler being used is too old to support the host. Modules for different targets are written into different directories and by default Spack was adding to MODULEPATH only the directory corresponding to the current host. This PR modifies this behavior to add all the directories that are **compatible** with the current host.
2019-10-01new package: py-python-ldap (#12599)Sinan1-0/+24
* new package: py-python-ldap * fix dependency types * improvements * Update var/spack/repos/builtin/packages/py-python-ldap/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-python-ldap/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * add openldap dependency
2019-10-01New package: py-python-mapnik (#12786)Sinan1-0/+29
2019-10-01picard: add 2.20.8codeandkey1-0/+1
2019-10-01go-md2man: disable module-mode (#12985)Daryl W. Grunau1-0/+1
* go-md2man: disable module-mode * Update var/spack/repos/builtin/packages/go-md2man/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01add singularity 3.4.1 (#12995)Eduardo Arango1-1/+3
* add singularity 3.4.1 Signed-off-by: ArangoGutierrez <eduardo@sylabs.io> * revert some changes Signed-off-by: ArangoGutierrez <eduardo@sylabs.io> * add maintainers list to pkg singularity Add @alalazo and me to the Singularity maintainers list * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/singularity/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01binary cache: show all packages for compatible differing targets (#12943)Greg Becker1-3/+6
2019-10-01Dataspaces: Fix Fetch URL, Savanna Spec (#13001)Axel Huebl2-2/+2
2019-10-01GCC package: don't set CC etc. based on bin dir if it doesn't exist (#13000)Peter Scheibel1-0/+4
7bcb306 updated setup_environment in the GCC package to examine the bin/ directory to find alternatively-named instances of CC, but this failed to account for when GCC was being installed and failed when it attempted to list the not-yet-existing installation prefix. This commit updates the logic to skip this search if the bin/ directory doesn't exist.
2019-10-01libaio: fixed a condition that checks whether we are running on OS X (#12976)Massimiliano Culpo4-37/+52
* libaio: fixed a condition that checks whether we are running on OS X * libaio: simplified package by adding an explicit conflict for darwin * libaio: added information to the docstring * fio: added version 3.16, added conflict when using libaio, docstring * lvm2: conflict due to libaio dep, improved docstring, simpler install * mariadb: conflict due to libaio dep, improved docstring, version 10.4.7 * mariadb: the dependency on libaio is now conditional, removed conflict * mariadb: fixed a typo in previous commit Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * libaio: turned into a MakefilePackage
2019-10-01When removing a file from a view, don't fail if it doesn't exist (#12960)Jeffrey Salmond1-0/+3
Sometimes when remove_file is called on a link, that link is missing (perhaps ctrl-C happened halfway through a previous action). As removing a non-existent file is no problem, this patch changes the behavior so Spack continues rather than stopping with an error. Currently you would see ValueError: /path/to/dir is not a link tree! and now it continues with a warning.
2019-10-01Kaldi package: add version 7637de7 and egs (#12911)Jimmy Tang1-0/+8
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