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2017-08-15nco: Add patch to fix invalid conversion from char to char* (#5102)Michael Kuhn2-0/+54
This patch is needed to be able to build nco with GCC 7.
2017-08-15ncview: Fix download URL (#5103)Michael Kuhn1-1/+1
2017-08-15add version 0.2.10 to py-lazyarray (#5093)healther1-1/+2
2017-08-15gcc: Add 7.2.0 (#5098)Michael Kuhn1-3/+4
2017-08-15Use correct variant syntax to build zfp (#5099)Mark C. Miller1-2/+1
`h5z-zfp` now builds zfp with correct bit stream word size; the syntax of the variant declaration did not work in previous versions of spack but does now
2017-08-15add older versions to package folly (#5088)healther1-0/+5
2017-08-14Create, install and relocate tarballs of installed packagesPatrick Gartung7-0/+1467
Adds the "buildcache" command to spack. The buildcache command is used to create gpg signatures for archives of installed spack packages; the signatures and archives are placed together in a directory that can be added to a spack mirror. A user can retrieve the archives from a mirror and verify their integrity using the buildcache command. It is often the case that the user's Spack instance is located in a different path compared to the Spack instance used to generate the package archive and signature, so this includes logic to relocate the RPATHs generated by Spack.
2017-08-14Added a custom action for --clean and --dirty. (#5081)Massimiliano Culpo3-9/+52
The action `CleanOrDirtyAction` has been added. It sets the default value for `dest` to `spack.dirty`, and changes it according to the flags passed via command line. Added unit tests to check that the arguments are parsed correctly. Removed lines in `PackageBase` that were setting the default value of dirty according to what was in the configuration.
2017-08-14Decode process stream only for python3scheibelp1-2/+17
Popen.communicate outputs a str object for python2 and a bytes object for python3. This updates the Executable.__call__ function to call .decode on the output of Popen.communicate only for python3. This ensures that Executable.__call__ returns a str for python2 and python3.
2017-08-11Opencv update (#5079)Brian Van Essen1-0/+1
* Added a package for the MDAnalysis toolkit. * Added version 3.3.0
2017-08-11patch: get correct package directory for a given packageMassimiliano Culpo1-3/+15
fixes #4236 fixes #5002 When a package is defined in more than one repository, RepoPath.dirname_for_package_name may return the path to either definition. This sidesteps that ambiguity by accessing the module associated with the package definition.
2017-08-11adding falcon (#5057)snehring7-0/+293
* py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-11mpest: new package (#5064)Audrey Thoma1-0/+50
* mpest: new package * adding architecture env var and making more version-flexible * fixing environment * fixed build directory * getting rid of duplicated code
2017-08-11packages need to reference self.spec instead of spec (#5075)Gregory Lee4-5/+6
2017-08-11signalp: new package (#5054)Audrey Thoma1-0/+61
* signalp: new package * fixed homepage * fixed url and phases * refixed phase * improved readability * making path in execuatble adaptable to new versions
2017-08-11sspace-standard: new pacakge (#5071)Audrey Thoma1-0/+56
* sspace-standard: new pacakge * fixing install versioning * fixing description
2017-08-11sspace-longread: new package (#5072)Audrey Thoma1-0/+52
* sspace-longread: new package * fixing description * fixing order
2017-08-11gapfiller: new package (#5073)Audrey Thoma1-0/+52
2017-08-11More variants for MFEM (#4533)Mark C. Miller3-131/+205
* fixes #967 * Version bump to 0.9.1 - Bugfixes for spack find - 0.9.1 can read specs from current develop. * Don't assume spack is in the path when building docs. * adding mfem variants; do not assume build defaults * adjusting format to clarify options * fixing some build issues * fixing mfem+sundials * removing mesquite variant...turns out it is obsolete * adding examples to mfem; fixing sundials darwin installs * adding some additional variants and setting some configure flags by fiat * switching most check_variants logic to conflicts() directives * adding comment about cmake config * fixing flake8 issues; thought I had already done that * moving func def into install method * switch yes_no to no_yes; fix miss-spelling of miniapps * switching make target all to lib * changing yes_no to function as requested; fix problem with same in sundials * fix missing import sys directive * adding master and develop versions to amrex
2017-08-11Elemental fix (#5067)Brian Van Essen2-2/+5
* Added a package for the MDAnalysis toolkit. * Added additional packages that Elemental depends on. * Changed LBANN to not ask for the scalapack variant in Elemental. * Removed variant control on scalapack
2017-08-10New package: qbox (#4711)EmreAtes3-3/+100
* New package: qbox * API changes * Use install instead of shutil for comd * Use any BLAS library * Fix typo * Python2 fix * python2 + fix backslashes * Modified to respond to ld_flags correctly * Modified to use ld_flags * Add ld_flags support
2017-08-10Add AMG2013 package (#4836)Akhil Reddy Patlolla1-0/+73
* Updated Changes * Updated AMG with required MPI * Updated AMG with Version ' changes' * Fixed Issues with flag's and variant checks * Updated with MPI Alone and Changes - NO Serial Variant * Updated with MPI Alone and Changes - NO Serial Variant * Fixed Flake 8 line length error * Updated Spack Issues
2017-08-10 Variants Serial MPI openmp (#4897)Akhil Reddy Patlolla2-79/+47
* Variants Serial MPI openmp * Fixed Flake8 Issue and remove Patch File * Fixed issues with openmp Flag * Edited Required Changes * Fixed issues with flake8 and Added Conditional GCC Flags * Fixed Flake 8 Issue * Fixed flag's issue with non GCC Compiler * Fixed condition and spacing issues
2017-08-10braker & genemark-et: new packages (#5058)Audrey Thoma3-0/+106
* braker & genemark-et: new packages * fixing install
2017-08-10fimpute: new package (#5060)Audrey Thoma1-0/+40
2017-08-10impute2: new package (#5062)Audrey Thoma1-0/+39
2017-08-10mothur: new package (#5055)Audrey Thoma1-0/+59
* mothur: new package * fixing mpi things
2017-08-10Update Krell products: Add new OpenSpeedShop gui package based on qt4/qt5 ↵Jim Galarowicz1-0/+97
gui toolkit. (#5056) * Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies. * Add libxml2+python depends on to get around issues with the libxml2 package file. * Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build. * Fix bad syntax in specifying the boost version range. * Update the version numbers for the krell institute components and tools: cbtf and openspeedshop. * Do not build glib for qt3, it is not needed and causes build problems at this time anyway. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH. * A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set. * Trim comments to fit more concisely. * Fix tabs versus spaces and swap if and else clause check from a negative to a positive check. * Add new OpenSpeedShop gui package based on qt4/qt5 gui toolkit. * Fix flake8 errors. * Fix flake8 errors.
2017-08-10gblocks: new package (#5061)Audrey Thoma1-0/+40
2017-08-10kallisto: new package (#5063)Audrey Thoma1-0/+39
2017-08-10fastphase: new package (#5059)Audrey Thoma1-0/+39
2017-08-10go: Fix cgo (#5052)Michael Kuhn1-0/+4
2017-08-09Add version 2.19.1.403 to bcl2fastq2 package (#5047)George Hartzell1-3/+10
* Update bcl2fastq2 with info for 2.19.1.403 Heads up, the download location changed (domain name AND protocol). * Flake8 fix What's one space between friends?
2017-08-09soapindel: new package (#5048)Audrey Thoma1-0/+53
* soapindel: new package * fixed versioning
2017-08-09Adding lower bound to pnetcdf conflict in Trilinos (#5039)Jon Rood1-1/+1
* Adding lower bound to pnetcdf conflict in Trilinos to allow for use of develop and master branch. * Using even lower bound for pnetcdf conflict in Trilinos.
2017-08-09soap2: new package (#5045)Audrey Thoma1-0/+42
2017-08-09haploview: new package (#5036)Audrey Thoma2-0/+57
2017-08-09soapsnp: new package (#5046)Audrey Thoma1-0/+42
2017-08-09Opencv fix (#5040)Brian Van Essen1-20/+22
* Added a package for the MDAnalysis toolkit. * Changed cmake_options to args to be consistent with the rest of the file and fix a cmake error about undefined errors. Additionally, added guards for both png and zlib to not include their cmake options when those variants are not specified.
2017-08-09shapeit: new package (#5042)Audrey Thoma1-0/+44
* shapeit: new package * fixing versioning
2017-08-09pipits: new package (#5041)Audrey Thoma4-0/+217
* pipits: new package and dependencies * fixing rdp-classifier java dep * adding resources to pipits and fixing deps for py-biom-format
2017-08-09bugfix for module_cmd (#5038)becker332-2/+2
* bugfix for modulecmd when bash is symlinked to sh * update test to make sure module_cmd can interpret sh
2017-08-09Merged 'purge' command with 'clean' and deleted 'purge' (#4970)Massimiliano Culpo7-95/+131
* Merged 'purge' command with 'clean'. Deleted 'purge'. fixes #2942 'spack purge' has been merged with 'spack clean'. Documentation has been updated accordingly. The 'clean' and 'purge' behavior are not mutually exclusive, and they log brief information to tty while they go. * Fixed a wrong reference to spack clean in the docs * Added tests for 'spack clean'. Updated bash completion.
2017-08-09OpenMC parallel build fix. (#5037)pkondamudi1-0/+2
2017-08-09alglib: add new package (#5035)Denis Davydov2-0/+81
2017-08-09Bugfixes for compiler detection on the Cray platform. (#3075)Sergey Kosukhin6-8/+81
* Typo fixes in docstrings. * Let OS classes know if the paths they get were explicitly specified by user. * Fixed regexp for cray compiler version matching. * Replaced LinuxDistro with CrayFrontend for the Cray platform's frontend.
2017-08-09slurm: added initial recipe (#4802)Massimiliano Culpo1-0/+109
* slurm: added initial recipe * Modified variants following Adam comment. The MV variant 'features' has been turned into a set of BV variants. The dependency on 'readline' has been made optional.
2017-08-08Fixed minor issues from Cmake conversion (#5024)Brian Homerding1-2/+2
2017-08-08Packages/cns nospec (#5023)jiseung1-1/+41
* new package: cns-nospec * made changes as suggested and added proxy-app tag * updated edit() * adjusted logic for '+debug' * install readme and license * install readme and license * install readme and license; fix mpi version build issues * fix build issues for ~mpi * pep8 compliant
2017-08-08xplor-nih: new package (#5030)Audrey Thoma1-0/+48
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