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2016-07-30New package - r-caretGlenn Johnson1-0/+50
Classification and Regression Training
2016-07-30New package - r-glmnetGlenn Johnson1-0/+49
Lasso and Elastic-Net Regularized Generalized Linear Models
2016-07-30New package - r-vcdGlenn Johnson2-0/+95
Visualizing Categorical Data
2016-07-30New package - r-multcompGlenn Johnson5-0/+226
Simultaneous Inference in General Parametric Models.
2016-07-30New package r-randomforestGlenn Johnson1-0/+42
Breiman and Cutler's Random Forests for Classification and Regression.
2016-07-30Have R extensions build in parallel.Glenn Johnson1-0/+4
Set `MAKEFLAGS` so R extensions can be built in parallel if that is set in spack.
2016-07-30New package r-carGlenn Johnson11-0/+510
Companion to Applied Regression.
2016-07-29GTK+3: Provide updates to package dependencies.Kelly (KT) Thompson5-5/+49
WIP: I started trying to build gtkplus@3.20, but this package has many more dependencies than v2 and it requires newer versions of existing packages. This commit provides updates for 5 packages that are required by GTK+3. This is not the complete set of changes required for GTK+3. atk - move default version from 2.14 -> 2.20. glib - move default version from 2.42 -> 2.49 - v2.49 requires pcre+utf as a new dependency. pcre - if variant +utf is selected, add '--enable-unicode-properties' to the configure options. libepoxy - new package to spack - manages OpenGL function pointers. pango - move default version from 1.36 -> 1.40
2016-07-29mkl: flake8 fixes; minor docu updateDenis Davydov1-5/+5
2016-07-29trilinos: make sure hdf5 is picked up from SpackDenis Davydov1-3/+10
2016-07-29trilinos: fix lapack lib dirDenis Davydov1-1/+1
2016-07-29hypre: minor cleanup related to blas/lapackDenis Davydov1-2/+2
2016-07-29mkl: symlink libs to prefix.libDenis Davydov1-0/+8
2016-07-28Merge pull request #1344 from LLNL/bugfix/py-nose-nosetestsTodd Gamblin1-1/+1
do not ignore nosetests script in py-nose
2016-07-28Merge pull request #1331 from adamjstewart/fixes/mvapich2becker331-0/+1
MVAPICH2 depends on libpciaccess
2016-07-27Merge pull request #1235 from davydden/pkg/p4est_run_testsbecker331-22/+18
p4est: use run_tests instead of a variant
2016-07-27Add package for treeGeorge Hartzell1-0/+46
Add a package for [tree](http://mama.indstate.edu/users/ice/tree/). It has a Makefile that hardcodes a prefix and some CFLAGS. Used filter_file to: - set the make variable *prefix* to `prefix`; and - comment out their CFLAGS, just use ours.... It installs, runs on CentOS7, and uninstalls cleanly.
2016-07-27Merge pull request #1350 from adamjstewart/fixes/opensslTodd Gamblin1-1/+1
Fix OpenSSL url_for_version
2016-07-25intel parallel studio itac fixesGreg Lee1-1/+7
2016-07-25intel parallel studio setup mkl environmentGreg Lee1-0/+25
2016-07-25Added libhio packageSamuel Knight1-0/+45
2016-07-25Merge pull request #1352 from glennpj/r_googlevisbecker331-0/+47
New package - r-googlevis
2016-07-25Merge pull request #1351 from glennpj/r_htmlwidgetsbecker3330-0/+1359
New packages - R htmlwidgets
2016-07-25Add py-setuptools as dependencyGlenn Johnson4-0/+4
With the addition of dependency types and with `py-setuptools` set as type='build' there are more packages that need to have `py-setuptools` added as a dependency. This PR adds that dependency for the following packages: - py-h5py - py-networkx - py-pytables - py-scikit-image
2016-07-24r-curl update and chaged remote archiveGlenn Johnson1-1/+2
This updates to the 1.0 version of r-curl. The remote archive directory name also changed so change that here as well.
2016-07-24New packages - R htmlwidgetsGlenn Johnson30-0/+1359
2016-07-24New package - r-googlevisGlenn Johnson1-0/+47
2016-07-24Fix OpenSSL url_for_versionAdam J. Stewart1-1/+1
2016-07-23Add dependency type tp r- packagesGlenn Johnson29-93/+95
This PR adds the `nolink` dependency type to r- package dependencies. This is needed due to the new dependency types in Spack. A couple of packages were updated with new versions as well.
2016-07-22do not ignore nosetests script in py-noseGreg Lee1-1/+1
2016-07-22R extension dependencies with compiler wrapperGlenn Johnson1-15/+25
This commit introduces a mechanism to insure that R package dependencies are built with the Spack compiler wrapper. A copy of Makeconf is made before `filter_compilers` is called. This is then pointed to by the R_MAKEVARS_SITE environment variable set up in `setup_dependent_environment`. With this the normal compilers are used outside of spack and the spack wrapper compilers are used inside of spack. This commit also standardizes on the `join_path` call. It also sets the commented build command to reflect what is actually used with the newer string formatting.
2016-07-22Add CGNS packageAdam J. Stewart1-0/+73
2016-07-22Merge pull request #950 from xjrc/packages/pythonTodd Gamblin2-38/+43
Enhancement Proposal: Make Python Spack Installs Ignore User Configuration
2016-07-22Adding temporary script that fixes all Python extensions w/ 'setup_py'.Joseph Ciurej1-2/+5
2016-07-22Improved the build flag construction code in the python install method.Joseph Ciurej1-27/+7
2016-07-22Fixed a bug that was causing Python installs to be affected by user config.Joseph Ciurej1-9/+31
2016-07-22Merge pull request #1336 from glennpj/rcaseTodd Gamblin9-11/+15
Fix alpha case of dependencies for some r-packages
2016-07-21Merge pull request #1230 from hartzell/update-jdkTodd Gamblin1-10/+10
Add URL and md5 for jdk-8u92.
2016-07-21Fix alpha case of dependencies.Glenn Johnson9-11/+15
A while ago I was asked to convert packages to all lowercase. That was done but some dependencies did not get converted in the specification. This commit fixes that as well as a couple of urls that need to be made explicit and a missing dependency on jdk.
2016-07-21Merge pull request #1333 from LLNL/features/no-openssl-pingingTodd Gamblin1-56/+9
Remove remote website pinging from OpenSSL
2016-07-21Merge pull request #1334 from hartzell/add-gcc-5.4.0Todd Gamblin1-0/+1
Update gcc package with info about gcc-5.4.0
2016-07-21Remove remote website pinging from OpenSSLTodd Gamblin1-56/+9
- OpenSSL no longer checks remote versions on the openssl site. - Spack is used on systems that aren't connected to the internet, and this check is probably in the wrong place and affects too many commands. We can work on figuring out a better, more configurable place to put a check like this.
2016-07-21Update with info about gcc-5.4.0George Hartzell1-0/+1
2016-07-21editMitchell Devlin1-5/+18
2016-07-21Fix flake8 violationsGeorge Hartzell1-0/+2
2016-07-21Fix shebang line in tcl scriptsGeorge Hartzell2-1/+20
Lmod's configure script goes to the trouble of finding tclsh. This change uses that info to rewrite the #! lines in the tcl scripts so that they call the tclsh that the configure script discovered. It needs to massage the existing shebang lines into something that the sed statement in the makefile can manipulate and it needs to add the path_to_tclsh info into the set of sed statements. Checked with versions 6.4.1 and 6.3.7 (the checksum for 6.0.1 is incorrect, a fix for another time).
2016-07-21tcl is actually a runtime dependency.George Hartzell1-1/+1
lmod uses tclsh at runtime, so adjust the depends_on accordingly (thanks @davydden!).
2016-07-21The lmod package should depend_on('tcl')George Hartzell2-0/+3
The lmod package needs a tclsh. Up until now it just assumed that one was available on the system. This change adds a depends_on('tcl') to the lmod package. The tcl package installs a tclsh script with an embedded version number (e.g. tclsh8.6) but the lmod configuration looks for tclsh. This change extends the tcl package to symlink tclshX.Y to tclsh in the tcl package bin directory.
2016-07-21MVAPICH2 depends on libpciaccessAdam J. Stewart1-0/+1
2016-07-20MPI related changesGlenn Johnson1-26/+22
- Redid the code for setting the itac symlink for the cluster edition. - Removed the *PATH variables for MPI to avoid a conflict with other MPI environment modules. - Added missing test for `+all` when checking variants.
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