From 3dd4a01a5e737a08a211f4e0f58da0a725e70818 Mon Sep 17 00:00:00 2001 From: Elizabeth Fischer Date: Wed, 4 Jan 2017 21:24:07 -0500 Subject: Standardize package names: lower-case, not Mixed_CASE (#2475) * Rename packages * Upcasing depends_on() in packages. * Downcased extends('r') * Fixed erroneously changed URL that had slipped through. * Fixed typo * Fixed link from documentation into package source code. * Fixed another doc problem. * Changed underscores to dashes in package names. * Added test to enforce lowercase, no-underscore naming convention. * Fix r-xgboost * Downcase more instances of 'R' in package auto-creation. * Fix test. * Converted unit test packages to use dashes not underscores * Downcase `r` in the docs. * Update module_file_support.rst Fix r->R for class R. --- lib/spack/docs/module_file_support.rst | 10 +- lib/spack/spack/cmd/create.py | 6 +- lib/spack/spack/test/build_system_guess.py | 2 +- lib/spack/spack/test/concretize.py | 2 +- lib/spack/spack/test/install.py | 2 +- lib/spack/spack/test/mirror.py | 4 +- lib/spack/spack/test/package_sanity.py | 11 ++ lib/spack/spack/test/packages.py | 6 +- .../builtin.mock/packages/direct-mpich/package.py | 37 +++++ .../builtin.mock/packages/direct_mpich/package.py | 37 ----- .../packages/indirect-mpich/package.py | 42 +++++ .../packages/indirect_mpich/package.py | 42 ----- .../packages/simple-inheritance/package.py | 24 +++ .../packages/simple_inheritance/package.py | 24 --- .../trivial-install-test-package/package.py | 39 +++++ .../trivial_install_test_package/package.py | 39 ----- .../repos/builtin/packages/ImageMagick/package.py | 57 ------- var/spack/repos/builtin/packages/LuaJIT/package.py | 40 ----- var/spack/repos/builtin/packages/Mitos/package.py | 50 ------ var/spack/repos/builtin/packages/R/package.py | 184 --------------------- .../builtin/packages/SAMRAI/no-tool-build.patch | 20 --- var/spack/repos/builtin/packages/SAMRAI/package.py | 77 --------- .../repos/builtin/packages/cleverleaf/package.py | 2 +- .../repos/builtin/packages/etsf-io/package.py | 67 ++++++++ .../repos/builtin/packages/etsf_io/package.py | 67 -------- .../builtin/packages/fastx-toolkit/package.py | 43 +++++ .../builtin/packages/fastx_toolkit/package.py | 43 ----- .../builtin/packages/globus-toolkit/package.py | 40 +++++ .../builtin/packages/globus_toolkit/package.py | 40 ----- var/spack/repos/builtin/packages/gource/package.py | 2 +- .../repos/builtin/packages/image-magick/package.py | 57 +++++++ var/spack/repos/builtin/packages/julia/package.py | 2 +- var/spack/repos/builtin/packages/libNBC/package.py | 44 ----- var/spack/repos/builtin/packages/libnbc/package.py | 44 +++++ .../repos/builtin/packages/lua-jit/package.py | 40 +++++ var/spack/repos/builtin/packages/mitos/package.py | 50 ++++++ var/spack/repos/builtin/packages/octave/package.py | 4 +- .../repos/builtin/packages/octopus/package.py | 4 +- .../builtin/packages/pmgr-collective/package.py | 38 +++++ .../builtin/packages/pmgr_collective/package.py | 38 ----- .../builtin/packages/py-SQLAlchemy/package.py | 39 ----- .../repos/builtin/packages/py-csvkit/package.py | 2 +- .../builtin/packages/py-matplotlib/package.py | 2 +- .../builtin/packages/py-sqlalchemy/package.py | 39 +++++ .../builtin/packages/r-BiocGenerics/package.py | 56 ------- var/spack/repos/builtin/packages/r-R6/package.py | 46 ------ .../repos/builtin/packages/r-abind/package.py | 2 +- .../repos/builtin/packages/r-assertthat/package.py | 2 +- .../repos/builtin/packages/r-base64enc/package.py | 2 +- var/spack/repos/builtin/packages/r-bh/package.py | 2 +- .../builtin/packages/r-biocgenerics/package.py | 56 +++++++ .../repos/builtin/packages/r-bitops/package.py | 2 +- var/spack/repos/builtin/packages/r-boot/package.py | 2 +- var/spack/repos/builtin/packages/r-brew/package.py | 2 +- var/spack/repos/builtin/packages/r-c50/package.py | 2 +- var/spack/repos/builtin/packages/r-car/package.py | 2 +- .../repos/builtin/packages/r-caret/package.py | 2 +- .../repos/builtin/packages/r-catools/package.py | 2 +- .../repos/builtin/packages/r-chron/package.py | 2 +- .../repos/builtin/packages/r-class/package.py | 2 +- .../repos/builtin/packages/r-cluster/package.py | 2 +- .../repos/builtin/packages/r-codetools/package.py | 2 +- .../repos/builtin/packages/r-colorspace/package.py | 2 +- .../repos/builtin/packages/r-crayon/package.py | 2 +- .../repos/builtin/packages/r-cubature/package.py | 2 +- var/spack/repos/builtin/packages/r-curl/package.py | 2 +- .../repos/builtin/packages/r-datatable/package.py | 2 +- var/spack/repos/builtin/packages/r-dbi/package.py | 2 +- .../repos/builtin/packages/r-deoptim/package.py | 2 +- .../repos/builtin/packages/r-devtools/package.py | 2 +- .../repos/builtin/packages/r-diagrammer/package.py | 2 +- .../repos/builtin/packages/r-dichromat/package.py | 2 +- .../repos/builtin/packages/r-digest/package.py | 2 +- .../repos/builtin/packages/r-doparallel/package.py | 2 +- .../repos/builtin/packages/r-dplyr/package.py | 4 +- var/spack/repos/builtin/packages/r-dt/package.py | 2 +- .../repos/builtin/packages/r-dygraphs/package.py | 2 +- .../repos/builtin/packages/r-e1071/package.py | 2 +- .../repos/builtin/packages/r-evaluate/package.py | 2 +- .../repos/builtin/packages/r-filehash/package.py | 2 +- .../repos/builtin/packages/r-foreach/package.py | 2 +- .../repos/builtin/packages/r-foreign/package.py | 2 +- .../repos/builtin/packages/r-formatr/package.py | 2 +- .../repos/builtin/packages/r-formula/package.py | 2 +- .../repos/builtin/packages/r-gdata/package.py | 2 +- .../repos/builtin/packages/r-geosphere/package.py | 2 +- .../repos/builtin/packages/r-ggmap/package.py | 2 +- .../repos/builtin/packages/r-ggplot2/package.py | 2 +- .../repos/builtin/packages/r-ggvis/package.py | 2 +- .../repos/builtin/packages/r-gistr/package.py | 2 +- .../repos/builtin/packages/r-git2r/package.py | 2 +- .../repos/builtin/packages/r-glmnet/package.py | 2 +- .../repos/builtin/packages/r-googlevis/package.py | 2 +- .../repos/builtin/packages/r-gridbase/package.py | 2 +- .../repos/builtin/packages/r-gridextra/package.py | 2 +- .../repos/builtin/packages/r-gtable/package.py | 2 +- .../repos/builtin/packages/r-gtools/package.py | 2 +- .../repos/builtin/packages/r-hexbin/package.py | 2 +- .../repos/builtin/packages/r-highr/package.py | 2 +- .../repos/builtin/packages/r-htmltools/package.py | 2 +- .../builtin/packages/r-htmlwidgets/package.py | 2 +- .../repos/builtin/packages/r-httpuv/package.py | 2 +- var/spack/repos/builtin/packages/r-httr/package.py | 4 +- .../repos/builtin/packages/r-igraph/package.py | 2 +- .../repos/builtin/packages/r-influencer/package.py | 2 +- .../repos/builtin/packages/r-inline/package.py | 2 +- .../repos/builtin/packages/r-irdisplay/package.py | 2 +- .../repos/builtin/packages/r-irkernel/package.py | 2 +- .../repos/builtin/packages/r-irlba/package.py | 2 +- .../repos/builtin/packages/r-iterators/package.py | 2 +- var/spack/repos/builtin/packages/r-jpeg/package.py | 2 +- .../repos/builtin/packages/r-jsonlite/package.py | 2 +- .../repos/builtin/packages/r-knitr/package.py | 2 +- .../repos/builtin/packages/r-labeling/package.py | 2 +- .../repos/builtin/packages/r-lattice/package.py | 2 +- .../repos/builtin/packages/r-lazyeval/package.py | 2 +- .../repos/builtin/packages/r-leaflet/package.py | 2 +- var/spack/repos/builtin/packages/r-lme4/package.py | 2 +- .../repos/builtin/packages/r-lmtest/package.py | 2 +- .../repos/builtin/packages/r-lubridate/package.py | 2 +- .../repos/builtin/packages/r-magic/package.py | 2 +- .../repos/builtin/packages/r-magrittr/package.py | 2 +- .../repos/builtin/packages/r-mapproj/package.py | 2 +- var/spack/repos/builtin/packages/r-maps/package.py | 2 +- .../repos/builtin/packages/r-maptools/package.py | 2 +- .../repos/builtin/packages/r-markdown/package.py | 2 +- var/spack/repos/builtin/packages/r-mass/package.py | 2 +- .../repos/builtin/packages/r-matrix/package.py | 2 +- .../builtin/packages/r-matrixmodels/package.py | 2 +- .../repos/builtin/packages/r-memoise/package.py | 2 +- var/spack/repos/builtin/packages/r-mgcv/package.py | 2 +- var/spack/repos/builtin/packages/r-mime/package.py | 2 +- .../repos/builtin/packages/r-minqa/package.py | 2 +- .../repos/builtin/packages/r-multcomp/package.py | 2 +- .../repos/builtin/packages/r-munsell/package.py | 2 +- .../repos/builtin/packages/r-mvtnorm/package.py | 2 +- .../repos/builtin/packages/r-ncdf4/package.py | 2 +- .../repos/builtin/packages/r-networkd3/package.py | 2 +- var/spack/repos/builtin/packages/r-nlme/package.py | 2 +- .../repos/builtin/packages/r-nloptr/package.py | 2 +- var/spack/repos/builtin/packages/r-nmf/package.py | 2 +- var/spack/repos/builtin/packages/r-nnet/package.py | 2 +- var/spack/repos/builtin/packages/r-np/package.py | 2 +- .../repos/builtin/packages/r-openssl/package.py | 2 +- .../repos/builtin/packages/r-packrat/package.py | 2 +- .../repos/builtin/packages/r-partykit/package.py | 2 +- .../repos/builtin/packages/r-pbdzmq/package.py | 4 +- .../repos/builtin/packages/r-pbkrtest/package.py | 2 +- .../repos/builtin/packages/r-pkgmaker/package.py | 2 +- .../repos/builtin/packages/r-plotrix/package.py | 2 +- var/spack/repos/builtin/packages/r-plyr/package.py | 2 +- var/spack/repos/builtin/packages/r-png/package.py | 2 +- .../repos/builtin/packages/r-praise/package.py | 2 +- .../repos/builtin/packages/r-proto/package.py | 2 +- var/spack/repos/builtin/packages/r-pryr/package.py | 2 +- .../repos/builtin/packages/r-quantmod/package.py | 2 +- .../repos/builtin/packages/r-quantreg/package.py | 2 +- var/spack/repos/builtin/packages/r-r6/package.py | 46 ++++++ .../builtin/packages/r-randomforest/package.py | 2 +- .../repos/builtin/packages/r-raster/package.py | 2 +- .../repos/builtin/packages/r-rbokeh/package.py | 2 +- .../builtin/packages/r-rcolorbrewer/package.py | 2 +- var/spack/repos/builtin/packages/r-rcpp/package.py | 2 +- .../repos/builtin/packages/r-rcppeigen/package.py | 2 +- .../repos/builtin/packages/r-registry/package.py | 2 +- var/spack/repos/builtin/packages/r-repr/package.py | 2 +- .../repos/builtin/packages/r-reshape2/package.py | 2 +- .../builtin/packages/r-rgooglemaps/package.py | 2 +- .../repos/builtin/packages/r-rinside/package.py | 2 +- .../repos/builtin/packages/r-rjava/package.py | 2 +- .../repos/builtin/packages/r-rjson/package.py | 2 +- .../repos/builtin/packages/r-rjsonio/package.py | 2 +- .../repos/builtin/packages/r-rmarkdown/package.py | 2 +- .../repos/builtin/packages/r-rmysql/package.py | 2 +- .../repos/builtin/packages/r-rngtools/package.py | 2 +- .../repos/builtin/packages/r-rodbc/package.py | 2 +- .../repos/builtin/packages/r-roxygen2/package.py | 2 +- .../builtin/packages/r-rpostgresql/package.py | 2 +- .../repos/builtin/packages/r-rsnns/package.py | 2 +- .../repos/builtin/packages/r-rsqlite/package.py | 2 +- .../repos/builtin/packages/r-rstan/package.py | 2 +- .../repos/builtin/packages/r-rstudioapi/package.py | 2 +- var/spack/repos/builtin/packages/r-rzmq/package.py | 2 +- .../repos/builtin/packages/r-sandwich/package.py | 2 +- .../repos/builtin/packages/r-scales/package.py | 2 +- .../repos/builtin/packages/r-shiny/package.py | 4 +- var/spack/repos/builtin/packages/r-sp/package.py | 2 +- .../repos/builtin/packages/r-sparsem/package.py | 2 +- .../builtin/packages/r-stanheaders/package.py | 2 +- .../repos/builtin/packages/r-stringi/package.py | 2 +- .../repos/builtin/packages/r-stringr/package.py | 2 +- .../repos/builtin/packages/r-survey/package.py | 2 +- .../repos/builtin/packages/r-survival/package.py | 2 +- .../repos/builtin/packages/r-tarifx/package.py | 2 +- .../repos/builtin/packages/r-testit/package.py | 2 +- .../repos/builtin/packages/r-testthat/package.py | 4 +- .../repos/builtin/packages/r-thdata/package.py | 2 +- .../repos/builtin/packages/r-threejs/package.py | 2 +- .../repos/builtin/packages/r-tibble/package.py | 2 +- .../repos/builtin/packages/r-tidyr/package.py | 2 +- var/spack/repos/builtin/packages/r-ttr/package.py | 2 +- var/spack/repos/builtin/packages/r-uuid/package.py | 2 +- var/spack/repos/builtin/packages/r-vcd/package.py | 2 +- .../repos/builtin/packages/r-visnetwork/package.py | 2 +- .../repos/builtin/packages/r-whisker/package.py | 2 +- .../repos/builtin/packages/r-withr/package.py | 2 +- .../repos/builtin/packages/r-xgboost/package.py | 2 +- .../repos/builtin/packages/r-xlconnect/package.py | 2 +- .../builtin/packages/r-xlconnectjars/package.py | 2 +- var/spack/repos/builtin/packages/r-xlsx/package.py | 2 +- .../repos/builtin/packages/r-xlsxjars/package.py | 2 +- var/spack/repos/builtin/packages/r-xml/package.py | 2 +- .../repos/builtin/packages/r-xtable/package.py | 2 +- var/spack/repos/builtin/packages/r-xts/package.py | 2 +- var/spack/repos/builtin/packages/r-yaml/package.py | 2 +- var/spack/repos/builtin/packages/r-zoo/package.py | 2 +- var/spack/repos/builtin/packages/r/package.py | 184 +++++++++++++++++++++ .../builtin/packages/samrai/no-tool-build.patch | 20 +++ var/spack/repos/builtin/packages/samrai/package.py | 77 +++++++++ .../repos/builtin/packages/sdl2-image/package.py | 43 +++++ .../repos/builtin/packages/sdl2_image/package.py | 43 ----- .../packages/the-platinum-searcher/package.py | 45 +++++ .../packages/the-silver-searcher/package.py | 44 +++++ .../packages/the_platinum_searcher/package.py | 45 ----- .../packages/the_silver_searcher/package.py | 44 ----- .../repos/builtin/packages/uberftp/package.py | 2 +- 226 files changed, 1285 insertions(+), 1274 deletions(-) create mode 100644 var/spack/repos/builtin.mock/packages/direct-mpich/package.py delete mode 100644 var/spack/repos/builtin.mock/packages/direct_mpich/package.py create mode 100644 var/spack/repos/builtin.mock/packages/indirect-mpich/package.py delete mode 100644 var/spack/repos/builtin.mock/packages/indirect_mpich/package.py create mode 100644 var/spack/repos/builtin.mock/packages/simple-inheritance/package.py delete mode 100644 var/spack/repos/builtin.mock/packages/simple_inheritance/package.py create mode 100644 var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py delete mode 100644 var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py delete mode 100644 var/spack/repos/builtin/packages/ImageMagick/package.py delete mode 100644 var/spack/repos/builtin/packages/LuaJIT/package.py delete mode 100644 var/spack/repos/builtin/packages/Mitos/package.py delete mode 100644 var/spack/repos/builtin/packages/R/package.py delete mode 100644 var/spack/repos/builtin/packages/SAMRAI/no-tool-build.patch delete mode 100644 var/spack/repos/builtin/packages/SAMRAI/package.py create mode 100644 var/spack/repos/builtin/packages/etsf-io/package.py delete mode 100644 var/spack/repos/builtin/packages/etsf_io/package.py create mode 100644 var/spack/repos/builtin/packages/fastx-toolkit/package.py delete mode 100644 var/spack/repos/builtin/packages/fastx_toolkit/package.py create mode 100644 var/spack/repos/builtin/packages/globus-toolkit/package.py delete mode 100644 var/spack/repos/builtin/packages/globus_toolkit/package.py create mode 100644 var/spack/repos/builtin/packages/image-magick/package.py delete mode 100644 var/spack/repos/builtin/packages/libNBC/package.py create mode 100644 var/spack/repos/builtin/packages/libnbc/package.py create mode 100644 var/spack/repos/builtin/packages/lua-jit/package.py create mode 100644 var/spack/repos/builtin/packages/mitos/package.py create mode 100644 var/spack/repos/builtin/packages/pmgr-collective/package.py delete mode 100644 var/spack/repos/builtin/packages/pmgr_collective/package.py delete mode 100644 var/spack/repos/builtin/packages/py-SQLAlchemy/package.py create mode 100644 var/spack/repos/builtin/packages/py-sqlalchemy/package.py delete mode 100644 var/spack/repos/builtin/packages/r-BiocGenerics/package.py delete mode 100644 var/spack/repos/builtin/packages/r-R6/package.py create mode 100644 var/spack/repos/builtin/packages/r-biocgenerics/package.py create mode 100644 var/spack/repos/builtin/packages/r-r6/package.py create mode 100644 var/spack/repos/builtin/packages/r/package.py create mode 100644 var/spack/repos/builtin/packages/samrai/no-tool-build.patch create mode 100644 var/spack/repos/builtin/packages/samrai/package.py create mode 100644 var/spack/repos/builtin/packages/sdl2-image/package.py delete mode 100644 var/spack/repos/builtin/packages/sdl2_image/package.py create mode 100644 var/spack/repos/builtin/packages/the-platinum-searcher/package.py create mode 100644 var/spack/repos/builtin/packages/the-silver-searcher/package.py delete mode 100644 var/spack/repos/builtin/packages/the_platinum_searcher/package.py delete mode 100644 var/spack/repos/builtin/packages/the_silver_searcher/package.py diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst index 5db2ca0285..93c2ee33c6 100644 --- a/lib/spack/docs/module_file_support.rst +++ b/lib/spack/docs/module_file_support.rst @@ -353,9 +353,9 @@ and has similar effects on module file of dependees. Even in this case ``run_env`` must be filled with the desired list of environment modifications. .. note:: - The ``R`` package and callback APIs + The ``r`` package and callback APIs A typical example in which overriding both methods prove to be useful - is given by the ``R`` package. This package installs libraries and headers + is given by the ``r`` package. This package installs libraries and headers in non-standard locations and it is possible to prepend the appropriate directory to the corresponding environment variables: @@ -367,14 +367,14 @@ and has similar effects on module file of dependees. Even in this case with the following snippet: - .. literalinclude:: ../../../var/spack/repos/builtin/packages/R/package.py + .. literalinclude:: ../../../var/spack/repos/builtin/packages/r/package.py :pyobject: R.setup_environment - The ``R`` package also knows which environment variable should be modified + The ``r`` package also knows which environment variable should be modified to make language extensions provided by other packages available, and modifies it appropriately in the override of the second method: - .. literalinclude:: ../../../var/spack/repos/builtin/packages/R/package.py + .. literalinclude:: ../../../var/spack/repos/builtin/packages/r/package.py :lines: 128-129,146-151 .. _modules-yaml: diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index bee75cec4b..f1a5bc5cdb 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -215,7 +215,7 @@ class PythonGuess(DefaultGuess): class RGuess(DefaultGuess): """Provides appropriate overrides for R extensions""" dependencies = """\ - extends('R') + extends('r') # FIXME: Add additional dependencies if required. # depends_on('r-foo', type=nolink)""" @@ -283,7 +283,7 @@ class BuildSystemGuesser(object): 'scons': SconsGuess, 'bazel': BazelGuess, 'python': PythonGuess, - 'R': RGuess, + 'r': RGuess, 'octave': OctaveGuess } @@ -306,7 +306,7 @@ class BuildSystemGuesser(object): (r'/CMakeLists.txt$', 'cmake'), (r'/SConstruct$', 'scons'), (r'/setup.py$', 'python'), - (r'/NAMESPACE$', 'R'), + (r'/NAMESPACE$', 'r'), (r'/WORKSPACE$', 'bazel') ] diff --git a/lib/spack/spack/test/build_system_guess.py b/lib/spack/spack/test/build_system_guess.py index 97a9d67b47..86c1c9da13 100644 --- a/lib/spack/spack/test/build_system_guess.py +++ b/lib/spack/spack/test/build_system_guess.py @@ -36,7 +36,7 @@ import spack.stage ('CMakeLists.txt', 'cmake'), ('SConstruct', 'scons'), ('setup.py', 'python'), - ('NAMESPACE', 'R'), + ('NAMESPACE', 'r'), ('foobar', 'unknown') ] ) diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index 3cc5c70a5f..b7cad503a3 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -240,7 +240,7 @@ class TestConcretize(object): assert 'mpi' in spec def test_my_dep_depends_on_provider_of_my_virtual_dep(self): - spec = Spec('indirect_mpich') + spec = Spec('indirect-mpich') spec.normalize() spec.concretize() diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index d2ebf8dfb4..f10c3a37e9 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -60,7 +60,7 @@ def fake_fetchify(url, pkg): @pytest.mark.usefixtures('install_mockery') def test_install_and_uninstall(mock_archive): # Get a basic concrete spec for the trivial install package. - spec = Spec('trivial_install_test_package') + spec = Spec('trivial-install-test-package') spec.concretize() assert spec.concrete diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py index 13219ef878..e5e60e3045 100644 --- a/lib/spack/spack/test/mirror.py +++ b/lib/spack/spack/test/mirror.py @@ -129,7 +129,7 @@ class TestMirror(object): repos.clear() def test_url_mirror(self, mock_archive): - set_up_package('trivial_install_test_package', mock_archive, 'url') + set_up_package('trivial-install-test-package', mock_archive, 'url') check_mirror() repos.clear() @@ -143,6 +143,6 @@ class TestMirror(object): set_up_package('git-test', mock_git_repository, 'git') set_up_package('svn-test', mock_svn_repository, 'svn') set_up_package('hg-test', mock_hg_repository, 'hg') - set_up_package('trivial_install_test_package', mock_archive, 'url') + set_up_package('trivial-install-test-package', mock_archive, 'url') check_mirror() repos.clear() diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py index c3c3923855..c75d7cdcc7 100644 --- a/lib/spack/spack/test/package_sanity.py +++ b/lib/spack/spack/test/package_sanity.py @@ -26,6 +26,7 @@ This test does sanity checks on Spack's builtin package database. """ import unittest +import re import spack from spack.repository import RepoPath @@ -57,3 +58,13 @@ class PackageSanityTest(unittest.TestCase): # If there is a url for the version check it. v_url = pkg.url_for_version(v) self.assertEqual(vattrs['url'], v_url) + + def test_all_versions_are_lowercase(self): + """Spack package names must be lowercase, and use `-` instead of `_`. + """ + errors = [] + for name in spack.repo.all_package_names(): + if re.search(r'[_A-Z]', name): + errors.append(name) + + self.assertEqual([], errors) diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py index 39bbe4a954..6ae8a33a24 100644 --- a/lib/spack/spack/test/packages.py +++ b/lib/spack/spack/test/packages.py @@ -83,7 +83,7 @@ def test_import_package_as(builtin_mock): def test_inheritance_of_diretives(): - p = spack.repo.get('simple_inheritance') + p = spack.repo.get('simple-inheritance') # Check dictionaries that should have been filled by directives assert len(p.dependencies) == 3 @@ -93,14 +93,14 @@ def test_inheritance_of_diretives(): assert len(p.provided) == 2 # Check that Spec instantiation behaves as we expect - s = Spec('simple_inheritance') + s = Spec('simple-inheritance') s.concretize() assert '^cmake' in s assert '^openblas' in s assert '+openblas' in s assert 'mpi' in s - s = Spec('simple_inheritance~openblas') + s = Spec('simple-inheritance~openblas') s.concretize() assert '^cmake' in s assert '^openblas' not in s diff --git a/var/spack/repos/builtin.mock/packages/direct-mpich/package.py b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py new file mode 100644 index 0000000000..f38589ad4d --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class DirectMpich(Package): + homepage = "http://www.example.com" + url = "http://www.example.com/direct_mpich-1.0.tar.gz" + + version('1.0', 'foobarbaz') + + depends_on('mpich') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/direct_mpich/package.py b/var/spack/repos/builtin.mock/packages/direct_mpich/package.py deleted file mode 100644 index f38589ad4d..0000000000 --- a/var/spack/repos/builtin.mock/packages/direct_mpich/package.py +++ /dev/null @@ -1,37 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class DirectMpich(Package): - homepage = "http://www.example.com" - url = "http://www.example.com/direct_mpich-1.0.tar.gz" - - version('1.0', 'foobarbaz') - - depends_on('mpich') - - def install(self, spec, prefix): - pass diff --git a/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py new file mode 100644 index 0000000000..77b8022b1c --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class IndirectMpich(Package): + """Test case for a package that depends on MPI and one of its + dependencies requires a *particular version* of MPI. + """ + + homepage = "http://www.example.com" + url = "http://www.example.com/indirect_mpich-1.0.tar.gz" + + version(1.0, 'foobarbaz') + + depends_on('mpi') + depends_on('direct-mpich') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py b/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py deleted file mode 100644 index bbbf196129..0000000000 --- a/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py +++ /dev/null @@ -1,42 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class IndirectMpich(Package): - """Test case for a package that depends on MPI and one of its - dependencies requires a *particular version* of MPI. - """ - - homepage = "http://www.example.com" - url = "http://www.example.com/indirect_mpich-1.0.tar.gz" - - version(1.0, 'foobarbaz') - - depends_on('mpi') - depends_on('direct_mpich') - - def install(self, spec, prefix): - pass diff --git a/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py new file mode 100644 index 0000000000..3f135b002e --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py @@ -0,0 +1,24 @@ +from spack import * + + +class BaseWithDirectives(Package): + + depends_on('cmake', type='build') + depends_on('mpi') + variant('openblas', description='Activates openblas', default=True) + provides('service1') + + +class SimpleInheritance(BaseWithDirectives): + """Simple package which acts as a build dependency""" + + homepage = "http://www.example.com" + url = "http://www.example.com/simple-1.0.tar.gz" + + version('1.0', '0123456789abcdef0123456789abcdef') + + depends_on('openblas', when='+openblas') + provides('lapack', when='+openblas') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/simple_inheritance/package.py b/var/spack/repos/builtin.mock/packages/simple_inheritance/package.py deleted file mode 100644 index 3f135b002e..0000000000 --- a/var/spack/repos/builtin.mock/packages/simple_inheritance/package.py +++ /dev/null @@ -1,24 +0,0 @@ -from spack import * - - -class BaseWithDirectives(Package): - - depends_on('cmake', type='build') - depends_on('mpi') - variant('openblas', description='Activates openblas', default=True) - provides('service1') - - -class SimpleInheritance(BaseWithDirectives): - """Simple package which acts as a build dependency""" - - homepage = "http://www.example.com" - url = "http://www.example.com/simple-1.0.tar.gz" - - version('1.0', '0123456789abcdef0123456789abcdef') - - depends_on('openblas', when='+openblas') - provides('lapack', when='+openblas') - - def install(self, spec, prefix): - pass diff --git a/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py new file mode 100644 index 0000000000..2129d9788b --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class TrivialInstallTestPackage(Package): + """This package is a stub with a trivial install method. It allows us + to test the install and uninstall logic of spack.""" + homepage = "http://www.example.com/trivial_install" + url = "http://www.unit-test-should-replace-this-url/trivial_install-1.0.tar.gz" + + version('1.0', 'foobarbaz') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make('install') diff --git a/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py b/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py deleted file mode 100644 index 2129d9788b..0000000000 --- a/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py +++ /dev/null @@ -1,39 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class TrivialInstallTestPackage(Package): - """This package is a stub with a trivial install method. It allows us - to test the install and uninstall logic of spack.""" - homepage = "http://www.example.com/trivial_install" - url = "http://www.unit-test-should-replace-this-url/trivial_install-1.0.tar.gz" - - version('1.0', 'foobarbaz') - - def install(self, spec, prefix): - configure('--prefix=%s' % prefix) - make() - make('install') diff --git a/var/spack/repos/builtin/packages/ImageMagick/package.py b/var/spack/repos/builtin/packages/ImageMagick/package.py deleted file mode 100644 index 0b474285ce..0000000000 --- a/var/spack/repos/builtin/packages/ImageMagick/package.py +++ /dev/null @@ -1,57 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class Imagemagick(Package): - """ImageMagick is a software suite to create, edit, compose, - or convert bitmap images.""" - - homepage = "http://www.imagemagick.org" - url = "https://github.com/ImageMagick/ImageMagick/archive/7.0.2-7.tar.gz" - - version('7.0.2-7', 'c59cdc8df50e481b2bd1afe09ac24c08') - version('7.0.2-6', 'aa5689129c39a5146a3212bf5f26d478') - - depends_on('jpeg') - depends_on('pango') - depends_on('libtool', type='build') - depends_on('libpng') - depends_on('freetype') - depends_on('fontconfig') - depends_on('libtiff') - depends_on('ghostscript') - depends_on('ghostscript-fonts') - - def url_for_version(self, version): - return "https://github.com/ImageMagick/ImageMagick/archive/{0}.tar.gz".format(version) - - def install(self, spec, prefix): - gs_font_dir = join_path(spec['ghostscript-fonts'].prefix.share, "font") - configure('--prefix={0}'.format(prefix), - '--with-gs-font-dir={0}'.format(gs_font_dir)) - make() - make('check') - make('install') diff --git a/var/spack/repos/builtin/packages/LuaJIT/package.py b/var/spack/repos/builtin/packages/LuaJIT/package.py deleted file mode 100644 index 244c63c8fb..0000000000 --- a/var/spack/repos/builtin/packages/LuaJIT/package.py +++ /dev/null @@ -1,40 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -import os -from spack import * - - -class Luajit(Package): - """Flast flexible JITed lua""" - homepage = "http://www.luajit.org" - url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz" - - version('2.0.4', 'dd9c38307f2223a504cbfb96e477eca0') - - def install(self, spec, prefix): - # Linking with the C++ compiler is a dirty hack to deal with the fact - # that unwinding symbols are not included by libc, this is necessary - # on some platforms for the final link stage to work - make("install", "PREFIX=" + prefix, "TARGET_LD=" + os.environ['CXX']) diff --git a/var/spack/repos/builtin/packages/Mitos/package.py b/var/spack/repos/builtin/packages/Mitos/package.py deleted file mode 100644 index d577a1b285..0000000000 --- a/var/spack/repos/builtin/packages/Mitos/package.py +++ /dev/null @@ -1,50 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class Mitos(Package): - """Mitos is a library and a tool for collecting sampled memory - performance data to view with MemAxes""" - - homepage = "https://github.com/llnl/Mitos" - url = "https://github.com/llnl/Mitos" - - version('0.9.2', - git='https://github.com/llnl/Mitos.git', - commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d') - - version('0.9.1', git='https://github.com/llnl/Mitos.git', tag='v0.9.1') - - depends_on('dyninst@8.2.1:') - depends_on('hwloc') - depends_on('mpi') - depends_on('cmake', type='build') - - def install(self, spec, prefix): - with working_dir('spack-build', create=True): - cmake('..', *std_cmake_args) - make() - make("install") diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py deleted file mode 100644 index a60fa8122c..0000000000 --- a/var/spack/repos/builtin/packages/R/package.py +++ /dev/null @@ -1,184 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * -from spack.util.environment import * -import shutil - - -class R(Package): - """R is 'GNU S', a freely available language and environment for - statistical computing and graphics which provides a wide variety of - statistical and graphical techniques: linear and nonlinear modelling, - statistical tests, time series analysis, classification, clustering, etc. - Please consult the R project homepage for further information.""" - - homepage = "https://www.r-project.org" - url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz" - - extendable = True - - version('3.3.1', 'f50a659738b73036e2f5635adbd229c5') - version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') - version('3.2.3', '1ba3dac113efab69e706902810cc2970') - version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') - version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3') - version('3.2.0', '66fa17ad457d7e618191aa0f52fc402e') - version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4') - version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74') - - variant('external-lapack', default=False, - description='Links to externally installed BLAS/LAPACK') - variant('X', default=False, - description='Enable X11 support (call configure --with-x)') - - # Virtual dependencies - depends_on('blas', when='+external-lapack') - depends_on('lapack', when='+external-lapack') - - # Concrete dependencies - depends_on('readline') - depends_on('ncurses') - depends_on('icu4c') - depends_on('glib') - depends_on('zlib') - depends_on('zlib@:1.2.8', when='@:3.3.1') - depends_on('bzip2') - depends_on('libtiff') - depends_on('jpeg') - depends_on('cairo') - depends_on('cairo+X', when='+X') - depends_on('cairo~X', when='~X') - depends_on('pango') - depends_on('freetype') - depends_on('tcl') - depends_on('tk') - depends_on('tk+X', when='+X') - depends_on('tk~X', when='~X') - depends_on('libx11', when='+X') - depends_on('libxt', when='+X') - depends_on('curl') - depends_on('pcre') - depends_on('jdk') - - @property - def etcdir(self): - return join_path(prefix, 'rlib', 'R', 'etc') - - def install(self, spec, prefix): - rlibdir = join_path(prefix, 'rlib') - configure_args = ['--prefix=%s' % prefix, - '--libdir=%s' % rlibdir, - '--enable-R-shlib', - '--enable-BLAS-shlib', - '--enable-R-framework=no'] - if '+external-lapack' in spec: - configure_args.extend(['--with-blas', '--with-lapack']) - - configure(*configure_args) - make() - make('install') - - # Make a copy of Makeconf because it will be needed to properly build R - # dependencies in Spack. - src_makeconf = join_path(self.etcdir, 'Makeconf') - dst_makeconf = join_path(self.etcdir, 'Makeconf.spack') - shutil.copy(src_makeconf, dst_makeconf) - - self.filter_compilers(spec, prefix) - - def filter_compilers(self, spec, prefix): - """Run after install to tell the configuration files and Makefiles - to use the compilers that Spack built the package with. - - If this isn't done, they'll have CC and CXX set to Spack's generic - cc and c++. We want them to be bound to whatever compiler - they were built with.""" - - kwargs = {'ignore_absent': True, 'backup': False, 'string': True} - - filter_file(env['CC'], self.compiler.cc, - join_path(self.etcdir, 'Makeconf'), **kwargs) - filter_file(env['CXX'], self.compiler.cxx, - join_path(self.etcdir, 'Makeconf'), **kwargs) - filter_file(env['F77'], self.compiler.f77, - join_path(self.etcdir, 'Makeconf'), **kwargs) - filter_file(env['FC'], self.compiler.fc, - join_path(self.etcdir, 'Makeconf'), **kwargs) - - # ======================================================================== - # Set up environment to make install easy for R extensions. - # ======================================================================== - - @property - def r_lib_dir(self): - return join_path('rlib', 'R', 'library') - - def setup_dependent_environment(self, spack_env, run_env, extension_spec): - # Set R_LIBS to include the library dir for the - # extension and any other R extensions it depends on. - r_libs_path = [] - for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): - if d.package.extends(self.spec): - r_libs_path.append(join_path(d.prefix, self.r_lib_dir)) - - r_libs_path = ':'.join(r_libs_path) - spack_env.set('R_LIBS', r_libs_path) - spack_env.set('R_MAKEVARS_SITE', - join_path(self.etcdir, 'Makeconf.spack')) - - # Use the number of make_jobs set in spack. The make program will - # determine how many jobs can actually be started. - spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) - - # For run time environment set only the path for extension_spec and - # prepend it to R_LIBS - if extension_spec.package.extends(self.spec): - run_env.prepend_path('R_LIBS', join_path( - extension_spec.prefix, self.r_lib_dir)) - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('LIBRARY_PATH', - join_path(self.prefix, 'rlib', 'R', 'lib')) - run_env.prepend_path('LD_LIBRARY_PATH', - join_path(self.prefix, 'rlib', 'R', 'lib')) - run_env.prepend_path('CPATH', - join_path(self.prefix, 'rlib', 'R', 'include')) - - def setup_dependent_package(self, module, ext_spec): - """Called before R modules' install() methods. In most cases, - extensions will only need to have one line: - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path)""" - - # R extension builds can have a global R executable function - module.R = Executable(join_path(self.spec.prefix.bin, 'R')) - - # Add variable for library directry - module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir) - - # Make the site packages directory for extensions, if it does not exist - # already. - if ext_spec.package.is_extension: - mkdirp(module.r_lib_dir) diff --git a/var/spack/repos/builtin/packages/SAMRAI/no-tool-build.patch b/var/spack/repos/builtin/packages/SAMRAI/no-tool-build.patch deleted file mode 100644 index 1adf0cf721..0000000000 --- a/var/spack/repos/builtin/packages/SAMRAI/no-tool-build.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- SAMRAI/Makefile.in 2013-05-31 11:04:32.000000000 -0700 -+++ SAMRAI/Makefile.in.notools 2014-05-30 10:31:15.135979900 -0700 -@@ -8,7 +8,7 @@ - ## - ######################################################################### - --default: library tools -+default: library - - SAMRAI = @top_srcdir@ - SUBDIR = . -@@ -135,7 +135,7 @@ - done - $(MAKE) archive_remove_obj_names - --install: library tools -+install: library - $(INSTALL) -d -m 755 $(INSTDIR)/config - $(INSTALL) -d -m 755 $(INSTDIR)/lib - $(INSTALL) -d -m 755 $(INSTDIR)/bin diff --git a/var/spack/repos/builtin/packages/SAMRAI/package.py b/var/spack/repos/builtin/packages/SAMRAI/package.py deleted file mode 100644 index e0648290d6..0000000000 --- a/var/spack/repos/builtin/packages/SAMRAI/package.py +++ /dev/null @@ -1,77 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class Samrai(Package): - """SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) - is an object-oriented C++ software library enables exploration of - numerical, algorithmic, parallel computing, and software issues - associated with applying structured adaptive mesh refinement - (SAMR) technology in large-scale parallel application development. - - """ - homepage = "https://computation.llnl.gov/project/SAMRAI/" - url = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz" - list_url = homepage - - version('3.9.1', '232d04d0c995f5abf20d94350befd0b2') - version('3.8.0', 'c18fcffa706346bfa5828b36787ce5fe') - version('3.7.3', '12d574eacadf8c9a70f1bb4cd1a69df6') - version('3.7.2', 'f6a716f171c9fdbf3cb12f71fa6e2737') - version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce') - version('3.5.2-beta', 'd072d9d681eeb9ada15ce91bea784274') - version('3.5.0-beta', '1ad18a319fc573e12e2b1fbb6f6b0a19') - version('3.4.1-beta', '00814cbee2cb76bf8302aff56bbb385b') - version('3.3.3-beta', '1db3241d3e1cab913dc310d736c34388') - version('3.3.2-beta', 'e598a085dab979498fcb6c110c4dd26c') - version('2.4.4', '04fb048ed0efe7c531ac10c81cc5f6ac') - - depends_on("mpi") - depends_on("zlib") - depends_on("hdf5+mpi") - depends_on("boost") - - # don't build tools with gcc - patch('no-tool-build.patch', when='%gcc') - - # TODO: currently hard-coded to use openmpi - be careful! - def install(self, spec, prefix): - configure( - "--prefix=%s" % prefix, - "--with-CXX=%s" % spec['mpi'].prefix.bin + "/mpic++", - "--with-CC=%s" % spec['mpi'].prefix.bin + "/mpicc", - "--with-hdf5=%s" % spec['hdf5'].prefix, - "--with-boost=%s" % spec['boost'].prefix, - "--with-zlib=%s" % spec['zlib'].prefix, - "--without-blas", - "--without-lapack", - "--with-hypre=no", - "--with-petsc=no", - "--enable-opt", - "--disable-debug") - - make() - make("install") diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py index 61e6dca433..3bd1f0b5d0 100644 --- a/var/spack/repos/builtin/packages/cleverleaf/package.py +++ b/var/spack/repos/builtin/packages/cleverleaf/package.py @@ -40,7 +40,7 @@ class Cleverleaf(Package): version('develop', git='https://github.com/UK-MAC/CleverLeaf_ref.git', branch='develop') - depends_on("SAMRAI@3.8.0:") + depends_on("samrai@3.8.0:") depends_on("hdf5+mpi") depends_on("boost") depends_on('cmake', type='build') diff --git a/var/spack/repos/builtin/packages/etsf-io/package.py b/var/spack/repos/builtin/packages/etsf-io/package.py new file mode 100644 index 0000000000..c1e6f2eded --- /dev/null +++ b/var/spack/repos/builtin/packages/etsf-io/package.py @@ -0,0 +1,67 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## + +from spack import * + + +class EtsfIo(Package): + """ETSF_IO is a library implementing the Nanoquanta/ETSF file + format specifications. + + ETSF_IO enables an architecture-independent exchange of crystallographic + data, electronic wavefunctions, densities and potentials, as well as + spectroscopic data. It is meant to be used by quantum-physical and + quantum-chemical applications relying upon Density Functional Theory (DFT). + """ + + homepage = "http://www.etsf.eu/resources/software/libraries_and_tools" + url = "https://launchpad.net/etsf-io/1.0/1.0.4/+download/etsf_io-1.0.4.tar.gz" + + version('1.0.4', '32d0f7143278bd925b334c69fa425da1') + + depends_on("netcdf-fortran") + depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support + + def install(self, spec, prefix): + options = ['--prefix=%s' % prefix] + oapp = options.append + + # Specify installation directory for Fortran module files + # Default is [INCLUDEDIR/FC_TYPE] + oapp("--with-moduledir=%s" % prefix.include) + + # Netcdf4/HDF + hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib + options.extend([ + "--with-netcdf-incs=-I%s" % spec["netcdf-fortran"].prefix.include, + "--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % ( + spec["netcdf-fortran"].prefix.lib, hdf_libs), + ]) + + configure(*options) + + make() + make("check") + make("install") diff --git a/var/spack/repos/builtin/packages/etsf_io/package.py b/var/spack/repos/builtin/packages/etsf_io/package.py deleted file mode 100644 index c1e6f2eded..0000000000 --- a/var/spack/repos/builtin/packages/etsf_io/package.py +++ /dev/null @@ -1,67 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## - -from spack import * - - -class EtsfIo(Package): - """ETSF_IO is a library implementing the Nanoquanta/ETSF file - format specifications. - - ETSF_IO enables an architecture-independent exchange of crystallographic - data, electronic wavefunctions, densities and potentials, as well as - spectroscopic data. It is meant to be used by quantum-physical and - quantum-chemical applications relying upon Density Functional Theory (DFT). - """ - - homepage = "http://www.etsf.eu/resources/software/libraries_and_tools" - url = "https://launchpad.net/etsf-io/1.0/1.0.4/+download/etsf_io-1.0.4.tar.gz" - - version('1.0.4', '32d0f7143278bd925b334c69fa425da1') - - depends_on("netcdf-fortran") - depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support - - def install(self, spec, prefix): - options = ['--prefix=%s' % prefix] - oapp = options.append - - # Specify installation directory for Fortran module files - # Default is [INCLUDEDIR/FC_TYPE] - oapp("--with-moduledir=%s" % prefix.include) - - # Netcdf4/HDF - hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib - options.extend([ - "--with-netcdf-incs=-I%s" % spec["netcdf-fortran"].prefix.include, - "--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % ( - spec["netcdf-fortran"].prefix.lib, hdf_libs), - ]) - - configure(*options) - - make() - make("check") - make("install") diff --git a/var/spack/repos/builtin/packages/fastx-toolkit/package.py b/var/spack/repos/builtin/packages/fastx-toolkit/package.py new file mode 100644 index 0000000000..04b4d24b39 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastx-toolkit/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class FastxToolkit(Package): + """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + + homepage = "http://hannonlab.cshl.edu/fastx_toolkit/" + url = "https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2" + + version('0.0.14', 'bf1993c898626bb147de3d6695c20b40') + + depends_on('libgtextutils') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/fastx_toolkit/package.py b/var/spack/repos/builtin/packages/fastx_toolkit/package.py deleted file mode 100644 index 04b4d24b39..0000000000 --- a/var/spack/repos/builtin/packages/fastx_toolkit/package.py +++ /dev/null @@ -1,43 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class FastxToolkit(Package): - """The FASTX-Toolkit is a collection of command line tools for - Short-Reads FASTA/FASTQ files preprocessing.""" - - homepage = "http://hannonlab.cshl.edu/fastx_toolkit/" - url = "https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2" - - version('0.0.14', 'bf1993c898626bb147de3d6695c20b40') - - depends_on('libgtextutils') - - def install(self, spec, prefix): - configure('--prefix={0}'.format(prefix)) - - make() - make('install') diff --git a/var/spack/repos/builtin/packages/globus-toolkit/package.py b/var/spack/repos/builtin/packages/globus-toolkit/package.py new file mode 100644 index 0000000000..5cec13a5af --- /dev/null +++ b/var/spack/repos/builtin/packages/globus-toolkit/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class GlobusToolkit(Package): + """The Globus Toolkit is an open source software toolkit used for building + grids""" + + homepage = "http://toolkit.globus.org" + url = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1470089956.tar.gz" + + version('6.0.1470089956', 'b77fe3cc5a5844df995688b0e630d077') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/globus_toolkit/package.py b/var/spack/repos/builtin/packages/globus_toolkit/package.py deleted file mode 100644 index 5cec13a5af..0000000000 --- a/var/spack/repos/builtin/packages/globus_toolkit/package.py +++ /dev/null @@ -1,40 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class GlobusToolkit(Package): - """The Globus Toolkit is an open source software toolkit used for building - grids""" - - homepage = "http://toolkit.globus.org" - url = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1470089956.tar.gz" - - version('6.0.1470089956', 'b77fe3cc5a5844df995688b0e630d077') - - def install(self, spec, prefix): - configure("--prefix=%s" % prefix) - make() - make('install') diff --git a/var/spack/repos/builtin/packages/gource/package.py b/var/spack/repos/builtin/packages/gource/package.py index d8ae8b6506..dda00420a3 100644 --- a/var/spack/repos/builtin/packages/gource/package.py +++ b/var/spack/repos/builtin/packages/gource/package.py @@ -47,7 +47,7 @@ class Gource(Package): depends_on('libpng') depends_on('pcre') depends_on('sdl2') - depends_on('sdl2_image') + depends_on('sdl2-image') def install(self, spec, prefix): make_args = ['--prefix=%s' % prefix, diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/image-magick/package.py new file mode 100644 index 0000000000..9efb0cd368 --- /dev/null +++ b/var/spack/repos/builtin/packages/image-magick/package.py @@ -0,0 +1,57 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class ImageMagick(Package): + """ImageMagick is a software suite to create, edit, compose, + or convert bitmap images.""" + + homepage = "http://www.imagemagick.org" + url = "https://github.com/ImageMagick/ImageMagick/archive/7.0.2-7.tar.gz" + + version('7.0.2-7', 'c59cdc8df50e481b2bd1afe09ac24c08') + version('7.0.2-6', 'aa5689129c39a5146a3212bf5f26d478') + + depends_on('jpeg') + depends_on('pango') + depends_on('libtool', type='build') + depends_on('libpng') + depends_on('freetype') + depends_on('fontconfig') + depends_on('libtiff') + depends_on('ghostscript') + depends_on('ghostscript-fonts') + + def url_for_version(self, version): + return "https://github.com/ImageMagick/ImageMagick/archive/{0}.tar.gz".format(version) + + def install(self, spec, prefix): + gs_font_dir = join_path(spec['ghostscript-fonts'].prefix.share, "font") + configure('--prefix={0}'.format(prefix), + '--with-gs-font-dir={0}'.format(gs_font_dir)) + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 3725724ee3..89db570b81 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -222,7 +222,7 @@ class Julia(Package): if "+plot" in spec: julia("-e", 'Pkg.add("PyPlot"); using PyPlot') julia("-e", 'Pkg.add("Colors"); using Colors') - # These require maybe Gtk and ImageMagick + # These require maybe gtk and image-magick julia("-e", 'Pkg.add("Plots"); using Plots') julia("-e", 'Pkg.add("PlotRecipes"); using PlotRecipes') julia("-e", 'Pkg.add("UnicodePlots"); using UnicodePlots') diff --git a/var/spack/repos/builtin/packages/libNBC/package.py b/var/spack/repos/builtin/packages/libNBC/package.py deleted file mode 100644 index 414498a37a..0000000000 --- a/var/spack/repos/builtin/packages/libNBC/package.py +++ /dev/null @@ -1,44 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class Libnbc(Package): - """LibNBC is a prototypic implementation of a nonblocking - interface for MPI collective operations. Based on ANSI C and - MPI-1, it supports all MPI-1 collective operations in a - nonblocking manner. LibNBC is distributed under the BSD license. - """ - homepage = "http://unixer.de/research/nbcoll/libnbc/" - url = "http://unixer.de/research/nbcoll/libnbc/libNBC-1.1.1.tar.gz" - - version('1.1.1', 'ece5c94992591a9fa934a90e5dbe50ce') - - depends_on("mpi") - - def install(self, spec, prefix): - configure("--prefix=%s" % prefix) - make() - make("install") diff --git a/var/spack/repos/builtin/packages/libnbc/package.py b/var/spack/repos/builtin/packages/libnbc/package.py new file mode 100644 index 0000000000..414498a37a --- /dev/null +++ b/var/spack/repos/builtin/packages/libnbc/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libnbc(Package): + """LibNBC is a prototypic implementation of a nonblocking + interface for MPI collective operations. Based on ANSI C and + MPI-1, it supports all MPI-1 collective operations in a + nonblocking manner. LibNBC is distributed under the BSD license. + """ + homepage = "http://unixer.de/research/nbcoll/libnbc/" + url = "http://unixer.de/research/nbcoll/libnbc/libNBC-1.1.1.tar.gz" + + version('1.1.1', 'ece5c94992591a9fa934a90e5dbe50ce') + + depends_on("mpi") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/lua-jit/package.py b/var/spack/repos/builtin/packages/lua-jit/package.py new file mode 100644 index 0000000000..5f7de8ff06 --- /dev/null +++ b/var/spack/repos/builtin/packages/lua-jit/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import os +from spack import * + + +class LuaJit(Package): + """Flast flexible JITed lua""" + homepage = "http://www.luajit.org" + url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz" + + version('2.0.4', 'dd9c38307f2223a504cbfb96e477eca0') + + def install(self, spec, prefix): + # Linking with the C++ compiler is a dirty hack to deal with the fact + # that unwinding symbols are not included by libc, this is necessary + # on some platforms for the final link stage to work + make("install", "PREFIX=" + prefix, "TARGET_LD=" + os.environ['CXX']) diff --git a/var/spack/repos/builtin/packages/mitos/package.py b/var/spack/repos/builtin/packages/mitos/package.py new file mode 100644 index 0000000000..d577a1b285 --- /dev/null +++ b/var/spack/repos/builtin/packages/mitos/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Mitos(Package): + """Mitos is a library and a tool for collecting sampled memory + performance data to view with MemAxes""" + + homepage = "https://github.com/llnl/Mitos" + url = "https://github.com/llnl/Mitos" + + version('0.9.2', + git='https://github.com/llnl/Mitos.git', + commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d') + + version('0.9.1', git='https://github.com/llnl/Mitos.git', tag='v0.9.1') + + depends_on('dyninst@8.2.1:') + depends_on('hwloc') + depends_on('mpi') + depends_on('cmake', type='build') + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index aa521899e5..df144c8bbb 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -85,7 +85,7 @@ class Octave(Package): depends_on('glpk', when='+glpk') depends_on('gl2ps', when='+gl2ps') depends_on('gnuplot', when='+gnuplot') - depends_on('ImageMagick', when='+magick') + depends_on('image-magick', when='+magick') depends_on('hdf5', when='+hdf5') depends_on('jdk', when='+jdk') depends_on('llvm', when='+llvm') @@ -162,7 +162,7 @@ class Octave(Package): if '+magick' in spec: config_args.append("--with-magick=%s" - % spec['ImageMagick'].prefix.lib) + % spec['image-magick'].prefix.lib) if '+hdf5' in spec: config_args.extend([ diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py index adb760f06d..a100f7896a 100644 --- a/var/spack/repos/builtin/packages/octopus/package.py +++ b/var/spack/repos/builtin/packages/octopus/package.py @@ -42,8 +42,8 @@ class Octopus(Package): depends_on('fftw+mpi') # optional dependencies: - # TODO: scalapack, metis, parmetis, netcdf, etsf_io, SPARSKIT, ARPACK, - # FEAST, Libfm, PFFT, ISF, PNFFT + # TODO: scalapack, metis, parmetis, netcdf, etsf-io, sparskit, arpack, + # feast, libfm, pfft, isf, pnfft def install(self, spec, prefix): lapack = spec['lapack'].lapack_libs diff --git a/var/spack/repos/builtin/packages/pmgr-collective/package.py b/var/spack/repos/builtin/packages/pmgr-collective/package.py new file mode 100644 index 0000000000..f6466a7954 --- /dev/null +++ b/var/spack/repos/builtin/packages/pmgr-collective/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PmgrCollective(Package): + """PMGR_COLLECTIVE provides a scalable network for bootstrapping + MPI jobs.""" + homepage = "http://www.sourceforge.net/projects/pmgrcollective" + url = "http://downloads.sourceforge.net/project/pmgrcollective/pmgrcollective/PMGR_COLLECTIVE-1.0/pmgr_collective-1.0.tgz" + + version('1.0', '0384d008774274cc3fc7b4d810dfd07e') + + def install(self, spec, prefix): + make('PREFIX="' + prefix + '"') + make('PREFIX="' + prefix + '"', "install") diff --git a/var/spack/repos/builtin/packages/pmgr_collective/package.py b/var/spack/repos/builtin/packages/pmgr_collective/package.py deleted file mode 100644 index f6466a7954..0000000000 --- a/var/spack/repos/builtin/packages/pmgr_collective/package.py +++ /dev/null @@ -1,38 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class PmgrCollective(Package): - """PMGR_COLLECTIVE provides a scalable network for bootstrapping - MPI jobs.""" - homepage = "http://www.sourceforge.net/projects/pmgrcollective" - url = "http://downloads.sourceforge.net/project/pmgrcollective/pmgrcollective/PMGR_COLLECTIVE-1.0/pmgr_collective-1.0.tgz" - - version('1.0', '0384d008774274cc3fc7b4d810dfd07e') - - def install(self, spec, prefix): - make('PREFIX="' + prefix + '"') - make('PREFIX="' + prefix + '"', "install") diff --git a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py deleted file mode 100644 index 73e144b00e..0000000000 --- a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py +++ /dev/null @@ -1,39 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class PySqlalchemy(Package): - """The Python SQL Toolkit and Object Relational Mapper""" - - homepage = 'http://www.sqlalchemy.org/' - url = "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz" - - version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4') - - extends('python') - - def install(self, spec, prefix): - setup_py('install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py index 5b0394a138..904f138d12 100644 --- a/var/spack/repos/builtin/packages/py-csvkit/package.py +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -39,7 +39,7 @@ class PyCsvkit(Package): depends_on('py-dateutil', type=nolink) depends_on('py-dbf', type=nolink) depends_on('py-xlrd', type=nolink) - depends_on('py-SQLAlchemy', type=nolink) + depends_on('py-sqlalchemy', type=nolink) depends_on('py-six', type=nolink) depends_on('py-openpyxl', type=nolink) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 38859ebe15..8661a3f721 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -76,7 +76,7 @@ class PyMatplotlib(Package): # --------- Optional external programs # ffmpeg/avconv or mencoder - depends_on('ImageMagick', when='+animation') + depends_on('image-magick', when='+animation') # --------- Optional dependencies depends_on('pkg-config', type='build') # why not... diff --git a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py new file mode 100644 index 0000000000..73e144b00e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PySqlalchemy(Package): + """The Python SQL Toolkit and Object Relational Mapper""" + + homepage = 'http://www.sqlalchemy.org/' + url = "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz" + + version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4') + + extends('python') + + def install(self, spec, prefix): + setup_py('install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py deleted file mode 100644 index 5a6ce72a4b..0000000000 --- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py +++ /dev/null @@ -1,56 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class RBiocgenerics(Package): - """S4 generic functions needed by many Bioconductor packages.""" - - homepage = 'https://bioconductor.org/packages/BiocGenerics/' - version('bioc-3.3', - git='https://github.com/Bioconductor-mirror/BiocGenerics.git', - branch='release-3.3') - version('bioc-3.2', - git='https://github.com/Bioconductor-mirror/BiocGenerics.git', - branch='release-3.2') - - extends('R') - - def validate(self, spec): - """ - Checks that the version of R is appropriate for the Bioconductor - version. - """ - if spec.satisfies('@bioc-3.3'): - if not spec.satisfies('^R@3.3.0:3.3.9'): - raise InstallError('Must use R-3.3 for Bioconductor-3.3') - elif spec.satisfies('@bioc-3.2'): - if not spec.satisfies('^R@3.2.0:3.2.9'): - raise InstallError('Must use R-3.2 for Bioconductor-3.2') - - def install(self, spec, prefix): - self.validate(spec) - R('CMD', 'INSTALL', '--library=%s' % - self.module.r_lib_dir, '%s' % self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-R6/package.py b/var/spack/repos/builtin/packages/r-R6/package.py deleted file mode 100644 index 0b75888e79..0000000000 --- a/var/spack/repos/builtin/packages/r-R6/package.py +++ /dev/null @@ -1,46 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class RR6(Package): - """The R6 package allows the creation of classes with reference semantics, - similar to R's built-in reference classes. Compared to reference classes, - R6 classes are simpler and lighter-weight, and they are not built on S4 - classes so they do not require the methods package. These classes allow - public and private members, and they support inheritance, even when the - classes are defined in different packages.""" - - homepage = "https://github.com/wch/R6/" - url = "https://cran.r-project.org/src/contrib/R6_2.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R6" - - version('2.1.2', 'b6afb9430e48707be87638675390e457') - - extends('R') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index 96f623a096..f691ae13ea 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -37,7 +37,7 @@ class RAbind(Package): version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py index 4070b6fe8d..fe0c400aaa 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -36,7 +36,7 @@ class RAssertthat(Package): version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py index 4c5d14a90f..2289f40e4f 100644 --- a/var/spack/repos/builtin/packages/r-base64enc/package.py +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -35,7 +35,7 @@ class RBase64enc(Package): version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py index a0f30b779f..4b2b4ca11d 100644 --- a/var/spack/repos/builtin/packages/r-bh/package.py +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -47,7 +47,7 @@ class RBh(Package): version('1.60.0-2', 'b50fdc85285da05add4e9da664a2d551') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py new file mode 100644 index 0000000000..ce93356541 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py @@ -0,0 +1,56 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RBiocgenerics(Package): + """S4 generic functions needed by many Bioconductor packages.""" + + homepage = 'https://bioconductor.org/packages/BiocGenerics/' + version('bioc-3.3', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.3') + version('bioc-3.2', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.2') + + extends('r') + + def validate(self, spec): + """ + Checks that the version of R is appropriate for the Bioconductor + version. + """ + if spec.satisfies('@bioc-3.3'): + if not spec.satisfies('^R@3.3.0:3.3.9'): + raise InstallError('Must use R-3.3 for Bioconductor-3.3') + elif spec.satisfies('@bioc-3.2'): + if not spec.satisfies('^R@3.2.0:3.2.9'): + raise InstallError('Must use R-3.2 for Bioconductor-3.2') + + def install(self, spec, prefix): + self.validate(spec) + R('CMD', 'INSTALL', '--library=%s' % + self.module.r_lib_dir, '%s' % self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py index 6399202aba..7421ea4658 100644 --- a/var/spack/repos/builtin/packages/r-bitops/package.py +++ b/var/spack/repos/builtin/packages/r-bitops/package.py @@ -35,7 +35,7 @@ class RBitops(Package): version('1.0-6', 'fba16485a51b1ccd354abde5816b6bdd') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py index 1f2f541fec..0b78c202b8 100644 --- a/var/spack/repos/builtin/packages/r-boot/package.py +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -36,7 +36,7 @@ class RBoot(Package): version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py index 111606d576..10bbccf1de 100644 --- a/var/spack/repos/builtin/packages/r-brew/package.py +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -36,7 +36,7 @@ class RBrew(Package): version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py index e9b582b52f..6ce917521d 100644 --- a/var/spack/repos/builtin/packages/r-c50/package.py +++ b/var/spack/repos/builtin/packages/r-c50/package.py @@ -35,7 +35,7 @@ class RC50(Package): version('0.1.0-24', '42631e65c5c579532cc6edf5ea175949') - extends('R') + extends('r') depends_on('r-partykit', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index f4a3824983..fa2cc407b8 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -35,7 +35,7 @@ class RCar(Package): version('2.1-2', '0f78ad74ef7130126d319acec23951a0') - extends('R') + extends('r') depends_on('r-mass', type=nolink) depends_on('r-mgcv', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py index 460526c7d3..bfc2db5780 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -35,7 +35,7 @@ class RCaret(Package): version('6.0-70', '202d7abb6a679af716ea69fb2573f108') - extends('R') + extends('r') depends_on('r-lattice', type=nolink) depends_on('r-ggplot2', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py index adc64e269c..b2daa14c6b 100644 --- a/var/spack/repos/builtin/packages/r-catools/package.py +++ b/var/spack/repos/builtin/packages/r-catools/package.py @@ -38,7 +38,7 @@ class RCatools(Package): version('1.17.1', '5c872bbc78b177b306f36709deb44498') - extends('R') + extends('r') depends_on('r-bitops', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py index 9cd9d76e9e..9393ac416f 100644 --- a/var/spack/repos/builtin/packages/r-chron/package.py +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -34,7 +34,7 @@ class RChron(Package): version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index f541ea3611..627cce808c 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -35,7 +35,7 @@ class RClass(Package): version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') - extends('R') + extends('r') depends_on('r-mass', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index 0fdf2ce5de..2deb053322 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -36,7 +36,7 @@ class RCluster(Package): version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index bea2f78c82..206e4c09a5 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -34,7 +34,7 @@ class RCodetools(Package): version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index a7622cad95..48c50191ac 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -37,7 +37,7 @@ class RColorspace(Package): version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py index 1e0befbca9..f0578a7c81 100644 --- a/var/spack/repos/builtin/packages/r-crayon/package.py +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -38,7 +38,7 @@ class RCrayon(Package): version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py index 1d8f837922..4ae21947ae 100644 --- a/var/spack/repos/builtin/packages/r-cubature/package.py +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -34,7 +34,7 @@ class RCubature(Package): version('1.1-2', '5617e1d82baa803a3814d92461da45c9') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index 24c0eadb2d..71f28d4609 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -43,7 +43,7 @@ class RCurl(Package): version('1.0', '93d34926d6071e1fba7e728b482f0dd9') version('0.9.7', 'a101f7de948cb828fef571c730f39217') - extends('R') + extends('r') depends_on('curl') diff --git a/var/spack/repos/builtin/packages/r-datatable/package.py b/var/spack/repos/builtin/packages/r-datatable/package.py index fb0b2f1053..f0d2247d36 100644 --- a/var/spack/repos/builtin/packages/r-datatable/package.py +++ b/var/spack/repos/builtin/packages/r-datatable/package.py @@ -37,7 +37,7 @@ class RDatatable(Package): version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372') - extends('R') + extends('r') depends_on('r-chron', type='nolink') diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py index a1e06d5100..b0146ffb27 100644 --- a/var/spack/repos/builtin/packages/r-dbi/package.py +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -36,7 +36,7 @@ class RDbi(Package): version('0.4-1', 'c7ee8f1c5037c2284e99c62698d0f087') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py index 16aacccd0e..9f5302ce16 100644 --- a/var/spack/repos/builtin/packages/r-deoptim/package.py +++ b/var/spack/repos/builtin/packages/r-deoptim/package.py @@ -36,7 +36,7 @@ class RDeoptim(Package): version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 75506dd257..01adc6e327 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -34,7 +34,7 @@ class RDevtools(Package): version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') - extends('R') + extends('r') depends_on('r-httr', type=nolink) depends_on('r-memoise', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py index 7ff3b8548b..420e4d803a 100644 --- a/var/spack/repos/builtin/packages/r-diagrammer/package.py +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -34,7 +34,7 @@ class RDiagrammer(Package): version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a') - extends('R') + extends('r') depends_on('r-htmlwidgets', type=nolink) depends_on('r-igraph', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py index 663e5295af..240bfc3be7 100644 --- a/var/spack/repos/builtin/packages/r-dichromat/package.py +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -35,7 +35,7 @@ class RDichromat(Package): version('2.0-0', '84e194ac95a69763d740947a7ee346a6') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py index 1d11afb139..f573638b1b 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -49,7 +49,7 @@ class RDigest(Package): version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py index 7cebfd9e58..c78624d6d8 100644 --- a/var/spack/repos/builtin/packages/r-doparallel/package.py +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -35,7 +35,7 @@ class RDoparallel(Package): version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43') - extends('R') + extends('r') depends_on('r-foreach', type=nolink) depends_on('r-iterators', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index ded7651278..2e0f43b726 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -35,10 +35,10 @@ class RDplyr(Package): version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef') - extends('R') + extends('r') depends_on('r-assertthat', type=nolink) - depends_on('r-R6', type=nolink) + depends_on('r-r6', type=nolink) depends_on('r-rcpp', type=nolink) depends_on('r-tibble', type=nolink) depends_on('r-magrittr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py index f134ee8913..2612ce3a57 100644 --- a/var/spack/repos/builtin/packages/r-dt/package.py +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -36,7 +36,7 @@ class RDt(Package): version('0.1', '5c8df984921fa484784ec4b8a4fb6f3c') - extends('R') + extends('r') depends_on('r-htmltools', type=nolink) depends_on('r-htmlwidgets', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py index 9b01d7aa18..94441dd6d5 100644 --- a/var/spack/repos/builtin/packages/r-dygraphs/package.py +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -38,7 +38,7 @@ class RDygraphs(Package): version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833') - extends('R') + extends('r') depends_on('r-magrittr', type=nolink) depends_on('r-htmlwidgets', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py index c2e7166403..ef29cc3318 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -36,7 +36,7 @@ class RE1071(Package): version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') - extends('R') + extends('r') depends_on('r-class', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index 5583c0ed68..c9a980a2c5 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -37,7 +37,7 @@ class REvaluate(Package): version('0.9', '877d89ce8a9ef7f403b1089ca1021775') - extends('R') + extends('r') depends_on('r-stringr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index a09b458eaf..2b92013db8 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -42,7 +42,7 @@ class RFilehash(Package): version('2.3', '01fffafe09b148ccadc9814c103bdc2f') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py index 2a7324ae99..7f2b1e63a8 100644 --- a/var/spack/repos/builtin/packages/r-foreach/package.py +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -40,7 +40,7 @@ class RForeach(Package): version('1.4.3', 'ef45768126661b259f9b8994462c49a0') - extends('R') + extends('r') depends_on('r-codetools', type=nolink) depends_on('r-iterators', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py index df38fc5680..a248518f58 100644 --- a/var/spack/repos/builtin/packages/r-foreign/package.py +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -36,7 +36,7 @@ class RForeign(Package): version('0.8-66', 'ff12190f4631dca31e30ca786c2c8f62') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 4c92e1f34b..3935ee9000 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -39,7 +39,7 @@ class RFormatr(Package): version('1.4', '98b9b64b2785b35f9df403e1aab6c73c') - extends('R') + extends('r') depends_on('r-codetools', type=nolink) depends_on('r-shiny', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py index 3c4347ee50..cd5b0b41e9 100644 --- a/var/spack/repos/builtin/packages/r-formula/package.py +++ b/var/spack/repos/builtin/packages/r-formula/package.py @@ -36,7 +36,7 @@ class RFormula(Package): version('1.2-1', '2afb31e637cecd0c1106317aca1e4849') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py index 0a09a1145b..2897ad922d 100644 --- a/var/spack/repos/builtin/packages/r-gdata/package.py +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -50,7 +50,7 @@ class RGdata(Package): version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f') - extends('R') + extends('r') depends_on('r-gtools', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py index 21ae07fd41..dec9a3939e 100644 --- a/var/spack/repos/builtin/packages/r-geosphere/package.py +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -36,7 +36,7 @@ class RGeosphere(Package): version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e') - extends('R') + extends('r') depends_on('r-sp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py index 2dfca19b51..d6c6d53c21 100644 --- a/var/spack/repos/builtin/packages/r-ggmap/package.py +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -37,7 +37,7 @@ class RGgmap(Package): version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a') - extends('R') + extends('r') depends_on('r-ggplot2', type=nolink) depends_on('r-proto', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index a8cf21930f..c0c37d9164 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -40,7 +40,7 @@ class RGgplot2(Package): version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') - extends('R') + extends('r') depends_on('r-digest', type=nolink) depends_on('r-gtable', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 29b2069ae9..9c6720b4aa 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -36,7 +36,7 @@ class RGgvis(Package): version('0.4.2', '039f45e5c7f1e0652779163d7d99f922') - extends('R') + extends('r') depends_on('r-assertthat', type=nolink) depends_on('r-jsonlite', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py index 646299b97b..08910b0fe1 100644 --- a/var/spack/repos/builtin/packages/r-gistr/package.py +++ b/var/spack/repos/builtin/packages/r-gistr/package.py @@ -40,7 +40,7 @@ class RGistr(Package): version('0.3.6', '49d548cb3eca0e66711aece37757a2c0') - extends('R') + extends('r') depends_on('r-jsonlite', type=nolink) depends_on('r-httr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py index 1f08379d6e..1387581306 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -36,7 +36,7 @@ class RGit2r(Package): version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') - extends('R') + extends('r') depends_on('zlib') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py index af6e1d1b63..895c066e57 100644 --- a/var/spack/repos/builtin/packages/r-glmnet/package.py +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -39,7 +39,7 @@ class RGlmnet(Package): version('2.0-5', '049b18caa29529614cd684db3beaec2a') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) depends_on('r-foreach', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py index bcb7caa0fb..54e1d397a6 100644 --- a/var/spack/repos/builtin/packages/r-googlevis/package.py +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -38,7 +38,7 @@ class RGooglevis(Package): version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468') - extends('R') + extends('r') depends_on('r-jsonlite', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py index a2f55b4470..1afc1af3ac 100644 --- a/var/spack/repos/builtin/packages/r-gridbase/package.py +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -34,7 +34,7 @@ class RGridbase(Package): version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index 537426d42f..582cd39b85 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -35,7 +35,7 @@ class RGridextra(Package): version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2') - extends('R') + extends('r') depends_on('r-gtable', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py index 74dee0b3d5..a633e8273f 100644 --- a/var/spack/repos/builtin/packages/r-gtable/package.py +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -34,7 +34,7 @@ class RGtable(Package): version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py index 367bb30f87..6676ec1be3 100644 --- a/var/spack/repos/builtin/packages/r-gtools/package.py +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -53,7 +53,7 @@ class RGtools(Package): version('3.5.0', '45f8800c0336d35046641fbacc56bdbb') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index 5d2972ff96..b9a7e612c3 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -36,7 +36,7 @@ class RHexbin(Package): version('1.27.1', '7f380390c6511e97df10a810a3b3bb7c') - extends('R') + extends('r') depends_on('r-lattice', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py index f977a7302f..e9fb7c34d5 100644 --- a/var/spack/repos/builtin/packages/r-highr/package.py +++ b/var/spack/repos/builtin/packages/r-highr/package.py @@ -37,7 +37,7 @@ class RHighr(Package): version('0.6', 'bf47388c5f57dc61962362fb7e1d8b16') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 21cdbe9184..aa776f3929 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -34,7 +34,7 @@ class RHtmltools(Package): version('0.3.5', '5f001aff4a39e329f7342dcec5139724') - extends('R') + extends('r') depends_on('r-digest', type=nolink) depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py index 8090776f06..615936c585 100644 --- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -36,7 +36,7 @@ class RHtmlwidgets(Package): version('0.6', '7fa522d2eda97593978021bda9670c0e') - extends('R') + extends('r') depends_on('r-htmltools', type=nolink) depends_on('r-jsonlite', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index 57025d3a3c..c353dacc5f 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -40,7 +40,7 @@ class RHttpuv(Package): version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') - extends('R') + extends('r') depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index 227594fc0d..bf7ce4dccb 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -36,13 +36,13 @@ class RHttr(Package): version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') - extends('R') + extends('r') depends_on('r-jsonlite', type=nolink) depends_on('r-mime', type=nolink) depends_on('r-curl', type=nolink) depends_on('r-openssl', type=nolink) - depends_on('r-R6', type=nolink) + depends_on('r-r6', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py index 37925d4e02..8c1a6252ba 100644 --- a/var/spack/repos/builtin/packages/r-igraph/package.py +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -36,7 +36,7 @@ class RIgraph(Package): version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) depends_on('r-magrittr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py index dd525daf2b..8102954daa 100644 --- a/var/spack/repos/builtin/packages/r-influencer/package.py +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -40,7 +40,7 @@ class RInfluencer(Package): version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5') - extends('R') + extends('r') depends_on('r-igraph', type=nolink) depends_on('r-matrix', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py index 35eb8ca76f..0694af6d34 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -36,7 +36,7 @@ class RInline(Package): version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py index a3c49feb93..00de6b35ac 100644 --- a/var/spack/repos/builtin/packages/r-irdisplay/package.py +++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py @@ -36,7 +36,7 @@ class RIrdisplay(Package): version('0.4.4', '5be672fb82185b90f23bd99ac1e1cdb6') - extends('R') + extends('r') depends_on('r-repr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py index 34b5c3c363..4890d95b3e 100644 --- a/var/spack/repos/builtin/packages/r-irkernel/package.py +++ b/var/spack/repos/builtin/packages/r-irkernel/package.py @@ -35,7 +35,7 @@ class RIrkernel(Package): version('master', git='https://github.com/IRkernel/IRkernel.git', tag='0.7') - extends('R') + extends('r') depends_on('r-repr', type=nolink) depends_on('r-irdisplay', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py index 42cc142e8a..caae09930c 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -36,7 +36,7 @@ class RIrlba(Package): version('2.0.0', '557674cf8b68fea5b9f231058c324d26') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py index f5a3489e7d..7e6fb9890d 100644 --- a/var/spack/repos/builtin/packages/r-iterators/package.py +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -35,7 +35,7 @@ class RIterators(Package): version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py index ef940720f8..2ec11e744b 100644 --- a/var/spack/repos/builtin/packages/r-jpeg/package.py +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -36,7 +36,7 @@ class RJpeg(Package): version('0.1-8', '696007451d14395b1ed1d0e9af667a57') - extends('R') + extends('r') depends_on('jpeg') diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index d1cb4b52c1..d01caf1f95 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -44,7 +44,7 @@ class RJsonlite(Package): version('1.0', 'c8524e086de22ab39b8ac8000220cc87') version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index 4976e12b45..4ad22cf33f 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -37,7 +37,7 @@ class RKnitr(Package): version('1.14', 'ef0fbeaa9372f99ffbc57212a7781511') version('0.6' , 'c67d6db84cd55594a9e870c90651a3db') - extends('R') + extends('r') depends_on('r-evaluate', type=nolink) depends_on('r-digest', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py index 02e5da9d85..daf971bf44 100644 --- a/var/spack/repos/builtin/packages/r-labeling/package.py +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -34,7 +34,7 @@ class RLabeling(Package): version('0.3', 'ccd7082ec0b211aba8a89d85176bb534') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index a798b1ce65..9308a869a2 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -37,7 +37,7 @@ class RLattice(Package): version('0.20-34', 'c2a648b22d4206ae7526fb70b8e90fed') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py index f80fb4d272..138691759f 100644 --- a/var/spack/repos/builtin/packages/r-lazyeval/package.py +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -36,7 +36,7 @@ class RLazyeval(Package): version('0.2.0', 'df1daac908dcf02ae7e12f4335b1b13b') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py index 2a91100c34..ab7fd2c48a 100644 --- a/var/spack/repos/builtin/packages/r-leaflet/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -36,7 +36,7 @@ class RLeaflet(Package): version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df') - extends('R') + extends('r') depends_on('r-base64enc', type=nolink) depends_on('r-htmlwidgets', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index c52d9d0e27..2f9ee3e48f 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -37,7 +37,7 @@ class RLme4(Package): version('1.1-12', 'da8aaebb67477ecb5631851c46207804') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) depends_on('r-mass', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py index 31a36f1f7e..ff98eeadcf 100644 --- a/var/spack/repos/builtin/packages/r-lmtest/package.py +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -36,7 +36,7 @@ class RLmtest(Package): version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe') - extends('R') + extends('r') depends_on('r-zoo', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 2e5661fa4d..125762de1e 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -39,7 +39,7 @@ class RLubridate(Package): version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') - extends('R') + extends('r') depends_on('r-stringr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index 2b8f95351a..ff32903125 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -37,7 +37,7 @@ class RMagic(Package): version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') - extends('R') + extends('r') depends_on('r-abind', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py index 11476c3d1e..c41f4eff8f 100644 --- a/var/spack/repos/builtin/packages/r-magrittr/package.py +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -38,7 +38,7 @@ class RMagrittr(Package): version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py index 0f8bbe199b..bace22a125 100644 --- a/var/spack/repos/builtin/packages/r-mapproj/package.py +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -34,7 +34,7 @@ class RMapproj(Package): version('1.2-4', '10e22bde1c790e1540672f15ddcaee71') - extends('R') + extends('r') depends_on('r-maps', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py index 1e0bfd2d43..8cbb646643 100644 --- a/var/spack/repos/builtin/packages/r-maps/package.py +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -35,7 +35,7 @@ class RMaps(Package): version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py index 8d045a4ed4..df9254e187 100644 --- a/var/spack/repos/builtin/packages/r-maptools/package.py +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -38,7 +38,7 @@ class RMaptools(Package): version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836') - extends('R') + extends('r') depends_on('r-sp', type=nolink) depends_on('r-foreign', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py index c34727d2b0..9648412e50 100644 --- a/var/spack/repos/builtin/packages/r-markdown/package.py +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -38,7 +38,7 @@ class RMarkdown(Package): version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff') - extends('R') + extends('r') depends_on('r-mime', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index 1ab01d2256..eda7dccabf 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -35,7 +35,7 @@ class RMass(Package): version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index 1b45dc55ca..02f193dd9b 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -35,7 +35,7 @@ class RMatrix(Package): version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') - extends('R') + extends('r') depends_on('r-lattice', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py index 3cdce6fea6..62adab7f15 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -35,7 +35,7 @@ class RMatrixmodels(Package): version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index 81f3ff1dab..da93131554 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -35,7 +35,7 @@ class RMemoise(Package): version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac') - extends('R') + extends('r') depends_on('r-digest', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index 4c49462ba2..5b8f04a84c 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -37,7 +37,7 @@ class RMgcv(Package): version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') - extends('R') + extends('r') depends_on('r-nlme', type=nolink) depends_on('r-matrix', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index 5e78889a76..55d40c5663 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -36,7 +36,7 @@ class RMime(Package): version('0.5', '87e00b6d57b581465c19ae869a723c4d') version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py index 16cff20b41..a38f00f9ab 100644 --- a/var/spack/repos/builtin/packages/r-minqa/package.py +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -35,7 +35,7 @@ class RMinqa(Package): version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105') - extends('R') + extends('r') depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index 54416502d9..b32bea6249 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -38,7 +38,7 @@ class RMultcomp(Package): version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') - extends('R') + extends('r') depends_on('r-mvtnorm', type=nolink) depends_on('r-survival', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index b96b90f9c7..4250b00ec2 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -38,7 +38,7 @@ class RMunsell(Package): version('0.4.3', 'ebd205323dc37c948f499ee08be9c476') - extends('R') + extends('r') depends_on('r-colorspace', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index b3f7db60c6..956ae6bc44 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -35,7 +35,7 @@ class RMvtnorm(Package): version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index 11bf7abb38..3949967022 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -47,7 +47,7 @@ class RNcdf4(Package): version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a') - extends('R') + extends('r') depends_on('netcdf') diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py index 8884f7cf1b..2374b78d7b 100644 --- a/var/spack/repos/builtin/packages/r-networkd3/package.py +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -35,7 +35,7 @@ class RNetworkd3(Package): version('0.2.12', '356fe4be59698e6fb052644bd9659d84') - extends('R') + extends('r') depends_on('r-htmlwidgets', type=nolink) depends_on('r-igraph', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index 1b6bb114e1..02a0836fd8 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -34,7 +34,7 @@ class RNlme(Package): version('3.1-128', '3d75ae7380bf123761b95a073eb55008') - extends('R') + extends('r') depends_on('r-lattice', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py index 58cb585c49..8b5e947710 100644 --- a/var/spack/repos/builtin/packages/r-nloptr/package.py +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -40,7 +40,7 @@ class RNloptr(Package): version('1.0.4', '9af69a613349b236fd377d0a107f484c') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index c30a1ac101..e33a9364d4 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -39,7 +39,7 @@ class RNmf(Package): version('0.20.6', '81df07b3bf710a611db5af24730ff3d0') - extends('R') + extends('r') depends_on('r-pkgmaker', type=nolink) depends_on('r-registry', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py index be048f5ad0..6f5e7d6504 100644 --- a/var/spack/repos/builtin/packages/r-nnet/package.py +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -35,7 +35,7 @@ class RNnet(Package): version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py index bff7d0f195..1ee6105576 100644 --- a/var/spack/repos/builtin/packages/r-np/package.py +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -40,7 +40,7 @@ class RNp(Package): version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389') - extends('R') + extends('r') depends_on('r-boot', type=nolink) depends_on('r-cubature', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index 3e77923d76..f5442b102f 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -43,7 +43,7 @@ class ROpenssl(Package): version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') - extends('R') + extends('r') depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py index 9520952bd7..f978b9f779 100644 --- a/var/spack/repos/builtin/packages/r-packrat/package.py +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -35,7 +35,7 @@ class RPackrat(Package): version('0.4.7-1', '80c2413269b292ade163a70ba5053e84') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py index dff9099c07..ab994ce4d2 100644 --- a/var/spack/repos/builtin/packages/r-partykit/package.py +++ b/var/spack/repos/builtin/packages/r-partykit/package.py @@ -42,7 +42,7 @@ class RPartykit(Package): version('1.1-1', '8fcb31d73ec1b8cd3bcd9789639a9277') - extends('R') + extends('r') depends_on('r-survival', type=nolink) depends_on('r-formula', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index b5a9546124..e6c546e921 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -41,9 +41,9 @@ class RPbdzmq(Package): version('0.2-4', 'e5afb70199aa54d737ee7a0e26bde060') - extends('R') + extends('r') - depends_on('r-R6', type=nolink) + depends_on('r-r6', type=nolink) depends_on('zeromq') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index 40b6f96927..0bd749abe1 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -38,7 +38,7 @@ class RPbkrtest(Package): version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') - extends('R') + extends('r') depends_on('r-lme4', type=nolink) depends_on('r-matrix', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index 87daec5ad0..5c9e5496e7 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -40,7 +40,7 @@ class RPkgmaker(Package): version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4') - extends('R') + extends('r') depends_on('r-registry', type=nolink) depends_on('r-codetools', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index d1d61dbc4d..ec02193d40 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -34,7 +34,7 @@ class RPlotrix(Package): version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index fe4512347a..cc9c19b98a 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -40,7 +40,7 @@ class RPlyr(Package): version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b') - extends('R') + extends('r') depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py index d3a80a4e16..aa3d4f3c69 100644 --- a/var/spack/repos/builtin/packages/r-png/package.py +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -36,7 +36,7 @@ class RPng(Package): version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f') - extends('R') + extends('r') depends_on('libpng') diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py index 102d86d2fa..dba2289311 100644 --- a/var/spack/repos/builtin/packages/r-praise/package.py +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -34,7 +34,7 @@ class RPraise(Package): version('1.0.0', '9318724cec0454884b5f762bee2da6a1') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py index 07ace3ad29..109ea5fe4f 100644 --- a/var/spack/repos/builtin/packages/r-proto/package.py +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -35,7 +35,7 @@ class RProto(Package): version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py index acd502b536..e9cbab3878 100644 --- a/var/spack/repos/builtin/packages/r-pryr/package.py +++ b/var/spack/repos/builtin/packages/r-pryr/package.py @@ -36,7 +36,7 @@ class RPryr(Package): version('0.1.2', '66b597a762aa15a3b7037779522983b6') - extends('R') + extends('r') depends_on('r-stringr', type=nolink) depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py index ecfbf49055..bf27e1a41b 100644 --- a/var/spack/repos/builtin/packages/r-quantmod/package.py +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -35,7 +35,7 @@ class RQuantmod(Package): version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631') - extends('R') + extends('r') depends_on('r-xts', type=nolink) depends_on('r-zoo', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py index 89a26070ba..81aa242ee8 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -39,7 +39,7 @@ class RQuantreg(Package): version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') - extends('R') + extends('r') depends_on('r-sparsem', type=nolink) depends_on('r-matrix', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py new file mode 100644 index 0000000000..cb5593f6fc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RR6(Package): + """The R6 package allows the creation of classes with reference semantics, + similar to R's built-in reference classes. Compared to reference classes, + R6 classes are simpler and lighter-weight, and they are not built on S4 + classes so they do not require the methods package. These classes allow + public and private members, and they support inheritance, even when the + classes are defined in different packages.""" + + homepage = "https://github.com/wch/R6/" + url = "https://cran.r-project.org/src/contrib/R6_2.1.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/R6" + + version('2.1.2', 'b6afb9430e48707be87638675390e457') + + extends('r') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py index 1066c217f4..4d56210c99 100644 --- a/var/spack/repos/builtin/packages/r-randomforest/package.py +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -35,7 +35,7 @@ class RRandomforest(Package): version('4.6-12', '071c03af974198e861f1475c5bab9e7a') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py index 39f4256703..017838428c 100644 --- a/var/spack/repos/builtin/packages/r-raster/package.py +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -36,7 +36,7 @@ class RRaster(Package): version('2.5-8', '2a7db931c74d50516e82d04687c0a577') - extends('R') + extends('r') depends_on('r-sp', type=nolink) depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py index 074c545534..c410acaba2 100644 --- a/var/spack/repos/builtin/packages/r-rbokeh/package.py +++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py @@ -36,7 +36,7 @@ class RRbokeh(Package): version('0.5.0', '4e14778c3fbd9286460ca28c68f57d10') - extends('R') + extends('r') depends_on('r-htmlwidgets', type=nolink) depends_on('r-maps', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py index b81ec2561c..4734a1674f 100644 --- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -35,7 +35,7 @@ class RRcolorbrewer(Package): version('1.1-2', '66054d83eade4dff8a43ad4732691182') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 94580a8700..1637faca03 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -43,7 +43,7 @@ class RRcpp(Package): version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b') version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index ecf9256ab3..f0aebb54f0 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -46,7 +46,7 @@ class RRcppeigen(Package): version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py index 119a84718a..89402cfbff 100644 --- a/var/spack/repos/builtin/packages/r-registry/package.py +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -34,7 +34,7 @@ class RRegistry(Package): version('0.3', '85345b334ec81eb3da6edcbb27c5f421') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py index 2e1f6126f9..11d43cf7ea 100644 --- a/var/spack/repos/builtin/packages/r-repr/package.py +++ b/var/spack/repos/builtin/packages/r-repr/package.py @@ -36,7 +36,7 @@ class RRepr(Package): version('0.9', 'db5ff74893063b492f684e42283070bd') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index 769e82aff9..1fd8067bbe 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -35,7 +35,7 @@ class RReshape2(Package): version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') - extends('R') + extends('r') depends_on('r-plyr', type=nolink) depends_on('r-stringr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py index 0d28b68b94..0e0d94a3d3 100644 --- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -37,7 +37,7 @@ class RRgooglemaps(Package): version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5') - extends('R') + extends('r') depends_on('r-png', type=nolink) depends_on('r-rjsonio', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py index 41af3a4392..e18fc2499c 100644 --- a/var/spack/repos/builtin/packages/r-rinside/package.py +++ b/var/spack/repos/builtin/packages/r-rinside/package.py @@ -48,7 +48,7 @@ class RRinside(Package): version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88') - extends('R') + extends('r') depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index 47804bd7fc..e1de4b77ff 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -35,7 +35,7 @@ class RRjava(Package): version('0.9-8', '51ae0d690ceed056ebe7c4be71fc6c7a') - extends('R') + extends('r') depends_on('jdk') diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py index 94ca45f485..db25a92916 100644 --- a/var/spack/repos/builtin/packages/r-rjson/package.py +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -34,7 +34,7 @@ class RRjson(Package): version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py index b56dfbe21d..a62f17abf7 100644 --- a/var/spack/repos/builtin/packages/r-rjsonio/package.py +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -48,7 +48,7 @@ class RRjsonio(Package): version('1.3-0', '72c395622ba8d1435ec43849fd32c830') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py index c379388314..c65ff7df9b 100644 --- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py +++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py @@ -35,7 +35,7 @@ class RRmarkdown(Package): version('1.0', '264aa6a59e9680109e38df8270e14c58') - extends('R') + extends('r') depends_on('r-knitr', type=nolink) depends_on('r-yaml', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index bc42c51ca9..4164dd3721 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -34,7 +34,7 @@ class RRmysql(Package): version('0.10.9', '3628200a1864ac3005cfd55cc7cde17a') - extends('R') + extends('r') depends_on('r-dbi', type=nolink) depends_on('mariadb') diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index 2f33cd9f88..2c06306f31 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -38,7 +38,7 @@ class RRngtools(Package): version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') - extends('R') + extends('r') depends_on('r-pkgmaker', type=nolink) depends_on('r-stringr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index 11fe0ace56..af142c841a 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -34,7 +34,7 @@ class RRodbc(Package): version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e') - extends('R') + extends('r') depends_on('unixodbc') diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py index 4f4b8dcafa..1c017d7898 100644 --- a/var/spack/repos/builtin/packages/r-roxygen2/package.py +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -35,7 +35,7 @@ class RRoxygen2(Package): version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7') - extends('R') + extends('r') depends_on('r-stringr', type=nolink) depends_on('r-stringi', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 999fb4a1b9..3f7b64693f 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -42,7 +42,7 @@ class RRpostgresql(Package): version('0.4-1', 'e7b22e212afbb2cbb88bab937f93e55a') - extends('R') + extends('r') depends_on('r-dbi', type=nolink) depends_on('postgresql') diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py index 7684792ba1..fad75827d4 100644 --- a/var/spack/repos/builtin/packages/r-rsnns/package.py +++ b/var/spack/repos/builtin/packages/r-rsnns/package.py @@ -41,7 +41,7 @@ class RRsnns(Package): version('0.4-7', 'ade7736611c456effb5f72e0ce0a1e6f') - extends('R') + extends('r') depends_on('r-rcpp', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index c7d41f0fb3..a22421ed87 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -36,7 +36,7 @@ class RRsqlite(Package): version('1.0.0', 'e6cbe2709612b687c13a10d30c7bad45') - extends('R') + extends('r') depends_on('r-dbi', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 1d0052563b..4f580d7853 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -42,7 +42,7 @@ class RRstan(Package): version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a') - extends('R') + extends('r') depends_on('r-ggplot2', type=nolink) depends_on('r-stanheaders', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index bf9b35fe5b..1a20fc226b 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -36,7 +36,7 @@ class RRstudioapi(Package): version('0.6', 'fdb13bf46aab02421557e713fceab66b') version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index 472e706e72..d013c8889c 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -37,7 +37,7 @@ class RRzmq(Package): depends_on('zeromq') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index ffd62b1b14..a9d39d37f9 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -35,7 +35,7 @@ class RSandwich(Package): version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') - extends('R') + extends('r') depends_on('r-zoo', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index 44bd5a5a2a..0072de8f5f 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -35,7 +35,7 @@ class RScales(Package): version('0.4.0', '7b5602d9c55595901192248bca25c099') - extends('R') + extends('r') depends_on('r-rcolorbrewer', type=nolink) depends_on('r-dichromat', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index a80860f4a5..4617e8a0b2 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -37,7 +37,7 @@ class RShiny(Package): version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611') - extends('R') + extends('r') depends_on('r-httpuv', type=nolink) depends_on('r-mime', type=nolink) @@ -45,7 +45,7 @@ class RShiny(Package): depends_on('r-xtable', type=nolink) depends_on('r-digest', type=nolink) depends_on('r-htmltools', type=nolink) - depends_on('r-R6', type=nolink) + depends_on('r-r6', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py index bb7589d490..ecb75203bb 100644 --- a/var/spack/repos/builtin/packages/r-sp/package.py +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -37,7 +37,7 @@ class RSp(Package): version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1') - extends('R') + extends('r') depends_on('r-lattice', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index c4dabf5c15..1bd8835d5a 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -36,7 +36,7 @@ class RSparsem(Package): version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py index c77b5aa8b6..681969f18d 100644 --- a/var/spack/repos/builtin/packages/r-stanheaders/package.py +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -48,7 +48,7 @@ class RStanheaders(Package): version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index cc57caf8cd..5a5f4ee18a 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -42,7 +42,7 @@ class RStringi(Package): version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') - extends('R') + extends('r') depends_on('icu4c') diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index 08ded95833..43bae9bbf0 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -38,7 +38,7 @@ class RStringr(Package): version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') - extends('R') + extends('r') depends_on('r-stringi', type=nolink) depends_on('r-magrittr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py index 646793f7a4..619f22cb59 100644 --- a/var/spack/repos/builtin/packages/r-survey/package.py +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -40,7 +40,7 @@ class RSurvey(Package): version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py index cfba9298fe..71652c2bcc 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -36,7 +36,7 @@ class RSurvival(Package): version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py index a85aa8baef..a6b5fbddd3 100644 --- a/var/spack/repos/builtin/packages/r-tarifx/package.py +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -34,7 +34,7 @@ class RTarifx(Package): version('1.0.6', '7e782e04bd69d929b29f91553382e6a2') - extends('R') + extends('r') depends_on('r-reshape2', type=nolink) depends_on('r-plyr', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py index a10b55d66c..2f2b0f3c4f 100644 --- a/var/spack/repos/builtin/packages/r-testit/package.py +++ b/var/spack/repos/builtin/packages/r-testit/package.py @@ -36,7 +36,7 @@ class RTestit(Package): version('0.5', 'f206d3cbdc5174e353d2d05ba6a12e59') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py index 60dfd2afcd..8d4d174128 100644 --- a/var/spack/repos/builtin/packages/r-testthat/package.py +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -35,13 +35,13 @@ class RTestthat(Package): version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc') - extends('R') + extends('r') depends_on('r-digest', type=nolink) depends_on('r-crayon', type=nolink) depends_on('r-praise', type=nolink) depends_on('r-magrittr', type=nolink) - depends_on('r-R6', type=nolink) + depends_on('r-r6', type=nolink) def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-thdata/package.py b/var/spack/repos/builtin/packages/r-thdata/package.py index e1cf050181..a389da3045 100644 --- a/var/spack/repos/builtin/packages/r-thdata/package.py +++ b/var/spack/repos/builtin/packages/r-thdata/package.py @@ -34,7 +34,7 @@ class RThdata(Package): version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') - extends('R') + extends('r') depends_on('r-survival', type=nolink) depends_on('r-mass', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py index 89ecce8bfc..e3aa271b3e 100644 --- a/var/spack/repos/builtin/packages/r-threejs/package.py +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -35,7 +35,7 @@ class RThreejs(Package): version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b') - extends('R') + extends('r') depends_on('r-htmlwidgets', type=nolink) depends_on('r-base64enc', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index c601de3c88..6d59a40147 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -35,7 +35,7 @@ class RTibble(Package): version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') - extends('R') + extends('r') depends_on('r-assertthat', type=nolink) depends_on('r-lazyeval', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index d82ae278fe..c83d75b6fd 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -36,7 +36,7 @@ class RTidyr(Package): version('0.5.1', '3cadc869510c054ed93d374ab44120bd') - extends('R') + extends('r') depends_on('r-tibble', type=nolink) depends_on('r-dplyr', type=nolink) depends_on('r-stringi', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py index c9b40a8262..355ba6ca3c 100644 --- a/var/spack/repos/builtin/packages/r-ttr/package.py +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -34,7 +34,7 @@ class RTtr(Package): version('0.23-1', '35f693ac0d97e8ec742ebea2da222986') - extends('R') + extends('r') depends_on('r-xts', type=nolink) depends_on('r-zoo', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py index 97541bc3b8..9a2455017b 100644 --- a/var/spack/repos/builtin/packages/r-uuid/package.py +++ b/var/spack/repos/builtin/packages/r-uuid/package.py @@ -36,7 +36,7 @@ class RUuid(Package): version('0.1-2', 'f97d000c0b16bca455fb5bf2cd668ddf') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py index 06e609b1ef..f7c0b25369 100644 --- a/var/spack/repos/builtin/packages/r-vcd/package.py +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -39,7 +39,7 @@ class RVcd(Package): version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02') - extends('R') + extends('r') depends_on('r-mass', type=nolink) depends_on('r-colorspace', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py index 90d55bbb2f..6cce369325 100644 --- a/var/spack/repos/builtin/packages/r-visnetwork/package.py +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -35,7 +35,7 @@ class RVisnetwork(Package): version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7') - extends('R') + extends('r') depends_on('r-htmlwidgets', type=nolink) depends_on('r-htmltools', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py index f338d150f1..8edea7e840 100644 --- a/var/spack/repos/builtin/packages/r-whisker/package.py +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -35,7 +35,7 @@ class RWhisker(Package): version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index 5ce7437c84..92b941b32f 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -37,7 +37,7 @@ class RWithr(Package): version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py index 458045ff74..586a99f76f 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -42,7 +42,7 @@ class RXgboost(Package): version('0.4-4', 'c24d3076058101a71de4b8af8806697c') - extends('R') + extends('r') depends_on('r-matrix', type=nolink) depends_on('r-datatable', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 332c80fb92..64b95f84e0 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -36,7 +36,7 @@ class RXlconnect(Package): version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') version('0.2-11', '9d1769a103cda05665df399cc335017d') - extends('R') + extends('r') depends_on('r-xlconnectjars', type=nolink) depends_on('r-rjava', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index 26e822d2b7..37dbed2783 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -35,7 +35,7 @@ class RXlconnectjars(Package): version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') - extends('R') + extends('r') depends_on('r-rjava', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index 6fed09296d..4c7b8ee15d 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -35,7 +35,7 @@ class RXlsx(Package): version('0.5.7', '36b1b16f29c54b6089b1dae923180dd5') - extends('R') + extends('r') depends_on('r-rjava', type=nolink) depends_on('r-xlsxjars', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index 19f0006ce9..22bda6e83f 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -35,7 +35,7 @@ class RXlsxjars(Package): version('0.6.1', '5a1721d5733cb42f3a29e3f353e39166') - extends('R') + extends('r') depends_on('r-rjava', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py index 5affe7f08a..416491cbe6 100644 --- a/var/spack/repos/builtin/packages/r-xml/package.py +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -37,7 +37,7 @@ class RXml(Package): version('3.98-1.5', 'd1cfcd56f7aec96a84ffca91aea507ee') version('3.98-1.4', '1a7f3ce6f264eeb109bfa57bedb26c14') - extends('R') + extends('r') depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py index 46434b4842..8c675e1b3b 100644 --- a/var/spack/repos/builtin/packages/r-xtable/package.py +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -34,7 +34,7 @@ class RXtable(Package): version('1.8-2', '239e4825cd046156a67efae3aac01d86') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py index d8a4b62d27..678a9f4bf4 100644 --- a/var/spack/repos/builtin/packages/r-xts/package.py +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -37,7 +37,7 @@ class RXts(Package): version('0.9-7', 'a232e94aebfa654653a7d88a0503537b') - extends('R') + extends('r') depends_on('r-zoo', type=nolink) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py index b68f26e9b8..d8a3c9bacc 100644 --- a/var/spack/repos/builtin/packages/r-yaml/package.py +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -35,7 +35,7 @@ class RYaml(Package): version('2.1.13', 'f2203ea395adaff6bd09134666191d9a') - extends('R') + extends('r') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index d889cacbee..27295c7afc 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -38,7 +38,7 @@ class RZoo(Package): version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') - extends('R') + extends('r') depends_on('r-lattice', type=nolink) diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py new file mode 100644 index 0000000000..a60fa8122c --- /dev/null +++ b/var/spack/repos/builtin/packages/r/package.py @@ -0,0 +1,184 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +from spack.util.environment import * +import shutil + + +class R(Package): + """R is 'GNU S', a freely available language and environment for + statistical computing and graphics which provides a wide variety of + statistical and graphical techniques: linear and nonlinear modelling, + statistical tests, time series analysis, classification, clustering, etc. + Please consult the R project homepage for further information.""" + + homepage = "https://www.r-project.org" + url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz" + + extendable = True + + version('3.3.1', 'f50a659738b73036e2f5635adbd229c5') + version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') + version('3.2.3', '1ba3dac113efab69e706902810cc2970') + version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') + version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3') + version('3.2.0', '66fa17ad457d7e618191aa0f52fc402e') + version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4') + version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74') + + variant('external-lapack', default=False, + description='Links to externally installed BLAS/LAPACK') + variant('X', default=False, + description='Enable X11 support (call configure --with-x)') + + # Virtual dependencies + depends_on('blas', when='+external-lapack') + depends_on('lapack', when='+external-lapack') + + # Concrete dependencies + depends_on('readline') + depends_on('ncurses') + depends_on('icu4c') + depends_on('glib') + depends_on('zlib') + depends_on('zlib@:1.2.8', when='@:3.3.1') + depends_on('bzip2') + depends_on('libtiff') + depends_on('jpeg') + depends_on('cairo') + depends_on('cairo+X', when='+X') + depends_on('cairo~X', when='~X') + depends_on('pango') + depends_on('freetype') + depends_on('tcl') + depends_on('tk') + depends_on('tk+X', when='+X') + depends_on('tk~X', when='~X') + depends_on('libx11', when='+X') + depends_on('libxt', when='+X') + depends_on('curl') + depends_on('pcre') + depends_on('jdk') + + @property + def etcdir(self): + return join_path(prefix, 'rlib', 'R', 'etc') + + def install(self, spec, prefix): + rlibdir = join_path(prefix, 'rlib') + configure_args = ['--prefix=%s' % prefix, + '--libdir=%s' % rlibdir, + '--enable-R-shlib', + '--enable-BLAS-shlib', + '--enable-R-framework=no'] + if '+external-lapack' in spec: + configure_args.extend(['--with-blas', '--with-lapack']) + + configure(*configure_args) + make() + make('install') + + # Make a copy of Makeconf because it will be needed to properly build R + # dependencies in Spack. + src_makeconf = join_path(self.etcdir, 'Makeconf') + dst_makeconf = join_path(self.etcdir, 'Makeconf.spack') + shutil.copy(src_makeconf, dst_makeconf) + + self.filter_compilers(spec, prefix) + + def filter_compilers(self, spec, prefix): + """Run after install to tell the configuration files and Makefiles + to use the compilers that Spack built the package with. + + If this isn't done, they'll have CC and CXX set to Spack's generic + cc and c++. We want them to be bound to whatever compiler + they were built with.""" + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + + filter_file(env['CC'], self.compiler.cc, + join_path(self.etcdir, 'Makeconf'), **kwargs) + filter_file(env['CXX'], self.compiler.cxx, + join_path(self.etcdir, 'Makeconf'), **kwargs) + filter_file(env['F77'], self.compiler.f77, + join_path(self.etcdir, 'Makeconf'), **kwargs) + filter_file(env['FC'], self.compiler.fc, + join_path(self.etcdir, 'Makeconf'), **kwargs) + + # ======================================================================== + # Set up environment to make install easy for R extensions. + # ======================================================================== + + @property + def r_lib_dir(self): + return join_path('rlib', 'R', 'library') + + def setup_dependent_environment(self, spack_env, run_env, extension_spec): + # Set R_LIBS to include the library dir for the + # extension and any other R extensions it depends on. + r_libs_path = [] + for d in extension_spec.traverse(deptype=nolink, deptype_query='run'): + if d.package.extends(self.spec): + r_libs_path.append(join_path(d.prefix, self.r_lib_dir)) + + r_libs_path = ':'.join(r_libs_path) + spack_env.set('R_LIBS', r_libs_path) + spack_env.set('R_MAKEVARS_SITE', + join_path(self.etcdir, 'Makeconf.spack')) + + # Use the number of make_jobs set in spack. The make program will + # determine how many jobs can actually be started. + spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs)) + + # For run time environment set only the path for extension_spec and + # prepend it to R_LIBS + if extension_spec.package.extends(self.spec): + run_env.prepend_path('R_LIBS', join_path( + extension_spec.prefix, self.r_lib_dir)) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('LIBRARY_PATH', + join_path(self.prefix, 'rlib', 'R', 'lib')) + run_env.prepend_path('LD_LIBRARY_PATH', + join_path(self.prefix, 'rlib', 'R', 'lib')) + run_env.prepend_path('CPATH', + join_path(self.prefix, 'rlib', 'R', 'include')) + + def setup_dependent_package(self, module, ext_spec): + """Called before R modules' install() methods. In most cases, + extensions will only need to have one line: + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path)""" + + # R extension builds can have a global R executable function + module.R = Executable(join_path(self.spec.prefix.bin, 'R')) + + # Add variable for library directry + module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir) + + # Make the site packages directory for extensions, if it does not exist + # already. + if ext_spec.package.is_extension: + mkdirp(module.r_lib_dir) diff --git a/var/spack/repos/builtin/packages/samrai/no-tool-build.patch b/var/spack/repos/builtin/packages/samrai/no-tool-build.patch new file mode 100644 index 0000000000..1adf0cf721 --- /dev/null +++ b/var/spack/repos/builtin/packages/samrai/no-tool-build.patch @@ -0,0 +1,20 @@ +--- SAMRAI/Makefile.in 2013-05-31 11:04:32.000000000 -0700 ++++ SAMRAI/Makefile.in.notools 2014-05-30 10:31:15.135979900 -0700 +@@ -8,7 +8,7 @@ + ## + ######################################################################### + +-default: library tools ++default: library + + SAMRAI = @top_srcdir@ + SUBDIR = . +@@ -135,7 +135,7 @@ + done + $(MAKE) archive_remove_obj_names + +-install: library tools ++install: library + $(INSTALL) -d -m 755 $(INSTDIR)/config + $(INSTALL) -d -m 755 $(INSTDIR)/lib + $(INSTALL) -d -m 755 $(INSTDIR)/bin diff --git a/var/spack/repos/builtin/packages/samrai/package.py b/var/spack/repos/builtin/packages/samrai/package.py new file mode 100644 index 0000000000..e0648290d6 --- /dev/null +++ b/var/spack/repos/builtin/packages/samrai/package.py @@ -0,0 +1,77 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Samrai(Package): + """SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) + is an object-oriented C++ software library enables exploration of + numerical, algorithmic, parallel computing, and software issues + associated with applying structured adaptive mesh refinement + (SAMR) technology in large-scale parallel application development. + + """ + homepage = "https://computation.llnl.gov/project/SAMRAI/" + url = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz" + list_url = homepage + + version('3.9.1', '232d04d0c995f5abf20d94350befd0b2') + version('3.8.0', 'c18fcffa706346bfa5828b36787ce5fe') + version('3.7.3', '12d574eacadf8c9a70f1bb4cd1a69df6') + version('3.7.2', 'f6a716f171c9fdbf3cb12f71fa6e2737') + version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce') + version('3.5.2-beta', 'd072d9d681eeb9ada15ce91bea784274') + version('3.5.0-beta', '1ad18a319fc573e12e2b1fbb6f6b0a19') + version('3.4.1-beta', '00814cbee2cb76bf8302aff56bbb385b') + version('3.3.3-beta', '1db3241d3e1cab913dc310d736c34388') + version('3.3.2-beta', 'e598a085dab979498fcb6c110c4dd26c') + version('2.4.4', '04fb048ed0efe7c531ac10c81cc5f6ac') + + depends_on("mpi") + depends_on("zlib") + depends_on("hdf5+mpi") + depends_on("boost") + + # don't build tools with gcc + patch('no-tool-build.patch', when='%gcc') + + # TODO: currently hard-coded to use openmpi - be careful! + def install(self, spec, prefix): + configure( + "--prefix=%s" % prefix, + "--with-CXX=%s" % spec['mpi'].prefix.bin + "/mpic++", + "--with-CC=%s" % spec['mpi'].prefix.bin + "/mpicc", + "--with-hdf5=%s" % spec['hdf5'].prefix, + "--with-boost=%s" % spec['boost'].prefix, + "--with-zlib=%s" % spec['zlib'].prefix, + "--without-blas", + "--without-lapack", + "--with-hypre=no", + "--with-petsc=no", + "--enable-opt", + "--disable-debug") + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/sdl2-image/package.py b/var/spack/repos/builtin/packages/sdl2-image/package.py new file mode 100644 index 0000000000..5df207ac55 --- /dev/null +++ b/var/spack/repos/builtin/packages/sdl2-image/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Sdl2Image(Package): + """SDL is designed to provide the bare bones of creating a graphical + program. """ + + homepage = "http://sdl.beuc.net/sdl.wiki/SDL_image" + url = "https://www.libsdl.org/projects/SDL_image/release/SDL2_image-2.0.1.tar.gz" + + version('2.0.1', 'd94b94555ba022fa249a53a021dc3606') + + depends_on('sdl2') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/sdl2_image/package.py b/var/spack/repos/builtin/packages/sdl2_image/package.py deleted file mode 100644 index 5df207ac55..0000000000 --- a/var/spack/repos/builtin/packages/sdl2_image/package.py +++ /dev/null @@ -1,43 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class Sdl2Image(Package): - """SDL is designed to provide the bare bones of creating a graphical - program. """ - - homepage = "http://sdl.beuc.net/sdl.wiki/SDL_image" - url = "https://www.libsdl.org/projects/SDL_image/release/SDL2_image-2.0.1.tar.gz" - - version('2.0.1', 'd94b94555ba022fa249a53a021dc3606') - - depends_on('sdl2') - - def install(self, spec, prefix): - configure('--prefix={0}'.format(prefix)) - - make() - make('install') diff --git a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py new file mode 100644 index 0000000000..eeddf194ea --- /dev/null +++ b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +import os +import shutil + + +class ThePlatinumSearcher(Package): + """Fast parallel recursive grep alternative""" + homepage = "https://github.com/monochromegane/the_platinum_searcher" + url = "https://github.com/monochromegane/the_platinum_searcher" + + package = 'github.com/monochromegane/the_platinum_searcher/...' + + version('head', go=package) + + extends("go", deptypes='build') + + def install(self, spec, prefix): + env = os.environ + env['GOPATH'] = self.stage.source_path + ':' + env['GOPATH'] + go('install', self.package, env=env) + shutil.copytree('bin', os.path.join(prefix, 'bin')) diff --git a/var/spack/repos/builtin/packages/the-silver-searcher/package.py b/var/spack/repos/builtin/packages/the-silver-searcher/package.py new file mode 100644 index 0000000000..c98e964efa --- /dev/null +++ b/var/spack/repos/builtin/packages/the-silver-searcher/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class TheSilverSearcher(Package): + """Fast recursive grep alternative""" + homepage = "http://geoff.greer.fm/ag/" + url = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz" + + version('0.32.0', '3fdfd5836924246073d5344257a06823') + version('0.30.0', '95e2e7859fab1156c835aff7413481db') + + depends_on('pcre') + depends_on('xz') + depends_on('pkg-config', type='build') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/the_platinum_searcher/package.py b/var/spack/repos/builtin/packages/the_platinum_searcher/package.py deleted file mode 100644 index eeddf194ea..0000000000 --- a/var/spack/repos/builtin/packages/the_platinum_searcher/package.py +++ /dev/null @@ -1,45 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * -import os -import shutil - - -class ThePlatinumSearcher(Package): - """Fast parallel recursive grep alternative""" - homepage = "https://github.com/monochromegane/the_platinum_searcher" - url = "https://github.com/monochromegane/the_platinum_searcher" - - package = 'github.com/monochromegane/the_platinum_searcher/...' - - version('head', go=package) - - extends("go", deptypes='build') - - def install(self, spec, prefix): - env = os.environ - env['GOPATH'] = self.stage.source_path + ':' + env['GOPATH'] - go('install', self.package, env=env) - shutil.copytree('bin', os.path.join(prefix, 'bin')) diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py deleted file mode 100644 index c98e964efa..0000000000 --- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py +++ /dev/null @@ -1,44 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - - -class TheSilverSearcher(Package): - """Fast recursive grep alternative""" - homepage = "http://geoff.greer.fm/ag/" - url = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz" - - version('0.32.0', '3fdfd5836924246073d5344257a06823') - version('0.30.0', '95e2e7859fab1156c835aff7413481db') - - depends_on('pcre') - depends_on('xz') - depends_on('pkg-config', type='build') - - def install(self, spec, prefix): - configure("--prefix=%s" % prefix) - - make() - make("install") diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py index b1b7dada6f..b0c6c8a42f 100644 --- a/var/spack/repos/builtin/packages/uberftp/package.py +++ b/var/spack/repos/builtin/packages/uberftp/package.py @@ -35,7 +35,7 @@ class Uberftp(Package): version('2_7', 'faaea2d6e1958c1105cfc9147824e03c') version('2_6', '784210976f259f9d19c0798c19778d34') - depends_on('globus_toolkit') + depends_on('globus-toolkit') def install(self, spec, prefix): configure('--prefix={0}'.format(prefix)) -- cgit v1.2.3-60-g2f50