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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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* added py-pycogent
* flake8 edits
* added type=('build', 'run') to deps, changed py-matplotlib and mpi4py
* changed python min version to 2.6
* fixed cython to py-cython dep
* fixed mpi4py to py-mpi4py
* fixed py-sqlalchemy
* added 1.5.3 version
* fixed version 1.5.3 install
* changed deps names to reflect convention
* added variants
* changed download URL and added SHA256 hash
* fixed deps
* added github url for 1.5.3
* removed unneeded deps
* doesn't require py-setuptools
* fixed url and added py-setuptools specific to version 1.9
* fixed variant names and changed cython to normal dependency instead of variant
* removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi
* fixed dependencies and added py-pymysql dep
* added setup-environment step
* changed download url for 1.5.3 to pypi
* fixed flake8 issue
* updated
* added changes
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* Addition of latest maestrowf releases.
* Addition of filelock to dependencies.
* Addition of when clause to depends_on for filelock and tabulate.
* Correction of the tar url.
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* Add 'extra_env' argument to Executable.__call__: this will be added
to the environment but does not affect whether the current
environment is reused. If 'env' is not set, then the current
environment is copied and the variables from 'extra_env' are added
to it.
* MakeExecutable can take a 'jobs_env' parameter that specifies the
name of an environment variable used to set the level of parallelism.
This is added to 'extra_env' (so does not affect whether the current
environment is reused).
* CMake-based Spack packages set 'jobs_env' when executing the 'test'
target for make and ninja (which does not use -j)
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* r-genomicalignments: new version
* r-genomicalignments: ending range for r3.4 dep
* r-genomicalignments: fix range
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* r-biomart: new version;
* r-biomart: ending range for r3.4 dep
* r-biomart: fix version range
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* r-deseq2: new version
* r-deseq2: fix r 3.4 dep range
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* Trying to package old AIDA
* Document the incompleteness
* Install the jars too
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* added py-picrust
* flake8 edits
* fixed boilerplate, added type='build', 'run'
* fixed errors
* added deps
* fixed error
* fixed numpy max version
* fixed future version
* fixed version issues
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actually AutoTools, not CMake. (#9110)
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* py-pymysql: new package
* added type build and run
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* openblas@0.3.1:0.3.2: patch CMake export bug
See https://github.com/xianyi/OpenBLAS/pull/1703.
* openblas@0.3.1: new version
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* New package: CODES simulation framework
* CODES: add comments
* CODES: remove -fi from extra autoreconf flags
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Update the version numbers and now depend on
the develop version of dyninst because of a
feature in openspeedshop depends on new code
in the dyninst develop tree. Without dyninst
develop, openspeedshop will not build.
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* py-matplotlib: Add patch to fix FreeType library detection
Adds patch to add $CPATH to locations searched for FreeType header file
Patch has been upstreamed:
https://github.com/matplotlib/matplotlib/pull/11457
* py-matplotlib: Add patch to fix FreeType library detection
* Make patch only apply to versin 2.2.2 (as already upstreamed)
* Fix flake8 format issue
* py-matplotlib: add range to freetype patch
* py-matplotlib: whitespace
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