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* add runtime deps
* revert to strict dep versions
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* new package starting at 4.0.2
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* gatk: added 4.0.8.1, fixed binary install
* gatk: fix flake8 conflict
* gatk: improve comments and modify install
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* add version 1.3.0
* change build parameters, install process
* mxnet will not compile against spack's nnvm and dmlc so we must use
the distributions provided by the source package.
* also removed 'bin' installation as mxnet is just a shared library.
* improve BLAS linking
* remove unnecessary args
* added variant for python bindings
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* Added kibana, updated elasticsearch
* Update elastic search to 6.4
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Signed-off-by: Daniel Topa <dantopa@lanl.gov>
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* py-colormath: new version requires newer networkx
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* r-nloptr: Explicit depends_on(nlopt). Previously there was a hidden dependency, masked by the package's configure script.
* r-nloptr: Change spelling of variables to satisfy pyflake8
* r-nloptr: Break a long line to satisfy pyflake8
* r-nloptr: larger indent on continuation, to satisfy pyflake8
* r-nloptr: another attempt at larger indent on continuation, to satisfy pyflake8
* r-nloptr: now a smaller indent on continuation, to satisfy pyflake8
* r-nloptr: Another attempt at right amount of indent.
* r-nloptr: Another attempt at right amount of indent.
* Use the correct attributes for finding the nlopt includes and libs.
* Lines too long, split into pieces
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Improve Spack's parsing of module show to eliminate some false
positives (e.g. accepting MODULEPATH when it is in fact looking for
PATH). This makes the following changes:
* Updates the pattern searching for several paths to avoid the case
where they are prefixes of unwanted paths
* Adds a warning message when an extracted path doesn't exist (which
may help catch future module parsing bugs faster)
* Adds a test with the content mentioned in #9083
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* mpiifort doesn't automatically link all run-time libraries
* scalapack was being picked up accidentaly if intel-mkl was in the spec
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Added v4.0.0 and workaround for cmake bug
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This patch does not apply cleanly anymore and breaks clang/Mac builds
balay@asterix /home/balay/git-repo/github/trilinos (develop=)
$ patch -Np1 < /home/balay/git-repo/github/spack/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
|+++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
--------------------------
File to patch:
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* assimp: fix compile issues with intel compilers on knl/linux [a dependency for dealii]
Fixes issue #9189
* assimp: add variant 'shared' with default value 'True'
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* libmesh: Added SLEPC eigensolver variant.
* libmesh: Added new versions.
* Corrected flake8 errors.
* Corrected SLEPc variant with proper config & conflicts.
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* Added jdk version, added r-ks and r-multicool packages, made some r packages less conservative in their r version requirement
* flake8 fixes
* fix formatting in jdk version cmd
* Added type=('build', 'run') to some R package dependencies,
added some missing dependencies to r-ks. Thanks Adam.
* fix flake8 error
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* xsdk: update xsdk@develop dependency on trilinos@develop
* trilinos: enable tpetra, ifpack2, zoltan2, amesos2
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Without this change, openssl's new perl dependency makes the tests fail.
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Due to an internal bug regarding the handling of scalars
(ndim must be 0) in numpy prior to 1.15.0, openPMD-api
will require the latest numpy 1.15+.
Since there is a small regression with datetime pickling in
1.15.0 from the required fix and spack only packages 1.15.1
currently, we depend on 1.15.1 in the recipe.
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Spack originally handled environment modifications in the following
order:
1. clear environment variables
(unless Spack was invoked with --dirty)
2. apply spack-specific environment variable updates,
including variables set by Spack core like CC/PKG_CONFIG_PATH
and those set by installed dependencies (e.g. in
setup_dependent_environment)
3. load all external/compiler modules
1 and 2 were done together. This splits 1 into its own function and
imposes the following order for environment modifications:
1. clear environment variables
2. load all external/compiler modules
3. apply spack-specific environment variable updates
As a result, prepend-path actions taken by Spack (or installed Spack
dependencies) take precedence over prepend-path actions from compiler
and external modules. Additionally, when Spack (or a package
dependency) sets/unsets an environment variable, that will override
the actions of external/compiler modules.
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* add 5 most recent versions and git master branch
* add trilinos, gmodel, throw, examples, optimize, symbols,
and warnings variants
* disable XSDK so that Trilinos dependencies are found.
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* Update dmd.
* Build dmd and druntime.
* Build dmd.
* Restore edit.
* Flake8.
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* skilion-onedrive: a new package.
* Fix flake8 issues.
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* Bamdst: a new package.
* Remove duplicate make() in install().
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* r-summarizedexperiment: new version
* r-summarizedexperiment: add ending range for r3.4 dep
* r-summarizedexperiment: fix range
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