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Update R CRAN packages (#12019)

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* Update R CRAN packages

This PR update R CRAN packages. It also ensures that spack built
packages that correspond to R recommended packages are specified in the
dependency list. This is needed for #12015.

* Add more updates to packages

* Updated dependencies of CRAN R packages

Also, use cloud.r-project.org rather than cran.r-project.org to use
automatic redirection to mirrors. This minimizes the load on the cran
server.

* Update to latest versions of CRAN R packages

* Fix flake8 issues

Some blank lines at the end of a coupple of package files crept in.

* Adjust r-animation dependencies

The r-magick package depends on image-magick, so r-animation should as
well. Also, add in texlive for LaTeX support.

* New package: r-magick

* Adjust line spaces in r-magick

* Add swftools dependenct to r-animation

* New package: swftools

This is needed bt r-animation

* Add 'when' clause to some package dependencies

- r-animation
- r-coin
- r-dt
- r-openssl

* New package: r-ellipsis

* New package: r-vctrs

* New package: r-zeallot

* New package: r-generics

* New package: r-cardata

* Add r-progress dependency to r-readxl

* New package: r-askpass

* New package: r-openxlsx

* New package: r-rio

* New package: r-sys

* New package: r-zip

* Add more updated packages

These are updates that have happened while working on this PR as well as
catching the ones from the cran.rstudio.com URL that were missed before.

* New package: r-gower

* New package: r-recipes

* New package: r-squarem

* New package: r-libcoin

* New package: r-rcmdcheck

* New package: r-remotes

* New package: r-sessioninfo

* New package: r-xopen

* New package: r-rgexf

* New package: r-rook

* New package: r-later

* New package: r-promises

* New package: r-xfun

* New package: r-urca

* New package: r-ggsignif

* New package: r-polynom

* New package: r-ucminf

* New package: r-ordinal

* New package: r-inum

* New package: r-debugme

* New package: r-fs

* New package: r-shinyfiles

* New package: r-gsa

* New package: r-nmof

* New package: r-dosnow

* New package: r-rann

* New package: r-reticulate

* New package: r-future

* New package: r-globals

* New package: r-listenv

* New package: r-future-apply

* New package: r-rsvd

* New package: r-sctransform

* New package: r-mitools

* Remove a stray FIXME line

* Fix typo in dependency for r-rcmdcheck

* Remove the dependency on r-splines

The r-splines package never existed in spack, but it does not exist on
CRAN either. There is an archive version from 1999 but it does not have
the proper extension format for modern R packages. The latest version
does not depend on r-splines, and apparently previous versions at least
built without it. Also, bump the required R version.

* Fix typo in r-rcpp dependency

* Fix typos in dependencies

- r-diagrammer
- r-janitor
- r-seurat

Also, bump minimum R version for r-rngtools.

* New package: r-clisymbols

* New package: r-fitdistrplus

* New package: r-gbrd

* New package: r-gh

* New package: r-ini

* New package: r-metap

* New package: r-npsurv

* New package: r-rdpack

* New package: r-snakecase

* New package: r-tinytex

* New package: r-usethis

* Make recommended changes

Made the changes that were recommended in the initial review.

- change cran.rstudio.com to cloud.r-project.org
- change R-project to r-project
- for packages with no listed homepage use the canonical link to the
  package page
- for packages with a dependency constraint on R itself, specify the
  dependency type
- add `list_url` where missing from package

* New package: r-hdf5r

This is needed for some older versions of r-seurat.

* Set R versions in packages

If the R version is specified in the DESCRIPTION file then set it in the
respective spack package.py file.

* Update var/spack/repos/builtin/packages/r-aer/package.py

Change dependency version of r-car.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Set constraint of mlbench dependency of r-adabag

* Set constraint on r-rcpp dependency of r-ape

* Removed "suggested" r-testthat from r-bibtex

* Update var/spack/repos/builtin/packages/r-bindrcpp/package.py

Fix dependency spec of r-bindr in r-bindrcpp.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/r-blob/package.py

Add r-vctrs version constraint.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Remove r-base64enc dependency from r-callr

* Update var/spack/repos/builtin/packages/r-car/package.py

Set constraint on r-cardata dependency.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Remove unneeded dependencies from r-clipr

* Add gmake dependency to r-construct

* Set the proper homepage for r-crayon

* Add r-jsonlite as a dependency for r-crul

The jsonlite package moved from "suggests" to "imports" with 0.8.4.

* Remove accidental colon after package name

* Add version constraint to r-fpc dependency in r-dendextend

* Additional constraints for R version with r-digest

* Add r-jsonlite dependency for latest verion of r-dt

* Add r-htmltools dependency in r-dygraphs package

* Removed unneeded dependencies from r-fnn

* Remove unneeded dependencies from r-formatr

* Add version constraint for r-mvtnorm dependency in r-fpc

* Added gmake dependency to r-fs

* Add r-globals dependency in r-future-apply

* Add perl dependency to r-gdata

* Add openssl dependency for r-ggally

* Removed unneeded dependencies from r-globaloptions

* Update r-haven

- Add version constraint on r-forcats
- Add gmake build dependency

* Fixed gmake dependency

Gmake is a build only dependency.

* Apply suggestions from code review

Apply a batch of suggestions from Adam Stewart.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Remove unneeded dependencies from r-hoardr

* Fix r-htmlwidgets homepage

* Add gmake build dependency to r-httpuv

* Remove unneeded dependency from r-log4r

* Remove unneeded dependency from r-maldiquant

* Add gmake build dependency to r-minqa

* Remove unneeded dependency from r-mlbench

* Set constraint on R6 dependenvy of r-pbdzmq

* Set constraints on r-callr dependency of r-pkgbuild

* Remove unneeded dependency from r-nloptr

* Remove unneeded dependencies from r-pkgmaker

* Set R version constraint for r-raster

* Set version constraint on rcpp for r-rcppprorgess

* Added gmake build dependency

* Remove unneeded dependencies from r-rematch

* Remove unneeded dependency from r-plogr

* Add gmake build dependency for r-rcurl

* Apply suggestions from code review

Bring in more suggestions from Adam Stewart.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Remove cnpy dependency from r-rcppcnpy

The r-rcppcnpy package has its own modified copy of the cnpy source and
will build from that internal source. The cnpy dependency is therefore
unnecessary.

* Add comment to reconcile dependencies

The CRAN site lists Perl, Getopt::Long as a dependency. The Spack Perl
will have the Getopt::Long package installed so just depend on Perl.

* Add dependency on udunits2 with newer versions of r-units

* Set additional proj constraint for r-sf

Support for PROJ6 was added in r-sf-0.7-4.

* New package: pandoc

This package installs the pandoc and pandoc-citeproc binaries in order
to satisfy dependencies on pandoc until the Haskell framework is in
Spack.

* Add pandoc dependency to r-bookdown

* Add comment about MPI in r-ergm

* Add pandoc dependency for r-reprex

* Add proj constraints to r-rgdal dependencies

Support for PROJ6 was added in version 1.4-2.

* Modifications to r-rgl

- Rearranged the dependencies to be more consistent with other packages
- put the type last on the depends_on lines to be consistent with other
  packages
- Added version constraints for some dependencies
- Added pandoc build dependency

* Be more accurate with rjsonio constraint for r-rgooglemaps

* Remove unneeded dependencies from r-rhmmer

* Tweak constraints for r-rjava

- Set java version constraint
- add gmake build dependency

* Add pandoc dependency to r-markdown

* Remove unneeded dependencies from r-rrcov

* Tweak r-rstan package

- remove duplicate specifications
- remove unneeded when conditions
- add version constraints
- arrange to follow order on CRAN page more closely
- add gmake build dependency
- add pandoc build dependency

* Add pandoc build dependency for r-rstantools

* Remove unneeded dependency from r-runit

* Remove unneeded dependencies from r-selectr

* Remove example R code from description

The example would module loading to break, at least in the case of Lmod
using TCL module files. It could be during the TCL to Lua conversion but
the module fails due to interpreting ipart of the example as a command.

* Update r-seurat

New version of r-seurat with new dependencies.

* New package: r-dqrng

* New package: r-leiden

* New package: r-rcppannoy

* New package: r-rcppparallel

* New package: r-rspectra

* New package: r-sitmo

* New package: r-uwot

* Remove unneeded dependency from r-snow

* Remove unneeded dependency from r-sourcetools

* Added pandoc build dependency for r-stanheaders

* Remove unneeded dependencies from r-taxizedb

* Remove unneeded dependencies from r-tclust

* Add dependency constraints for r-threejs

The following are needed for version 0.2.2:
- r-matrix
- r-jsonlite

* Remove unneeded dependencies from r-vfs

* Remove unneeded dependencies from r-vgam

* Remove unneeded dependency from r-xlconnectjars

* Remove unneeded dependency from r-xlsxjars

* Remove unneeded dependency from r-xnomial

* Remove ~mpi from fftw dependency of swftools

* Apply suggestions from code review

Add latest round of suggestions from Adam Stewart.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Fix rjsonio spec for r-rgooglemaps

The r-rjsonio spec is a when conditional.

* Rename 3 R.* packages

- r-utils --> r-r-utils (R.utils)
- r-oo --> r-r-oo (R.oo)
- r-methodss3 --> r-r-methodss3 (R.methodsS3)

Also, renamed dependencies in packages that depend on these three.

* Loosen version constraint on mariadb for r-rmysql

Make the mariadb constraint on mariadb-5.5 rather than the more
specific, and limiting, mariadb-5.5.56. This will allow an external
mariadb, such as mariadb-5.5.60 on CentOS-7.5 to be used. It also allows
for r-rmysql to be built against newer versions of the mariadb-5.5
series that might be added to spack.
This commit is contained in:
Glenn Johnson
2019-08-30 18:22:13 -05:00
committed by Adam J. Stewart
parent 9c98323080
commit 661a894c85
579 changed files with 4618 additions and 1835 deletions
Download Patch File Download Diff File Expand all files Collapse all files

32
var/spack/repos/builtin/packages/pandoc/package.py Normal file
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@@ -0,0 +1,32 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import platform
class Pandoc(Package):
"""If you need to convert files from one markup format into another, pandoc
is your swiss-army knife."""
homepage = "https://pandoc.org"
# The following installs the binaries for pandoc and pandoc-cireproc. The
# reason for installing binaries is that pandoc is a Haskell package and
# the Haskell framework is not yet in Spack. See #1408 for a discussion of
# the challenges with Haskell. Until the Haskell framework is in Spack this
# package will meet the needs of packages that have a dependency on pandoc.
if platform.system() == "Linux":
url = "https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-linux.tar.gz"
version('2.7.3', sha256='eb775fd42ec50329004d00f0c9b13076e707cdd44745517c8ce2581fb8abdb75')
elif platform.system() == "Darwin":
url = "https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-macOS.zip"
version('2.7.3', sha256='fb93800c90f3fab05dbd418ee6180d086b619c9179b822ddfecb608874554ff0')
depends_on('texlive')
def install(self, spec, prefix):
install_tree('.', prefix)

9
var/spack/repos/builtin/packages/r-abind/package.py
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@@ -12,8 +12,11 @@ class RAbind(RPackage):
higher-dimensional arrays. Also provides functions 'adrop', 'asub', and
'afill' for manipulating, extracting and replacing data in arrays."""
homepage = "https://cran.r-project.org/"
url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/abind"
homepage = "https://cloud.r-project.org/package=abind"
url = "https://cloud.r-project.org/src/contrib/abind_1.4-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/abind"
version('1.4-5', sha256='3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c')
version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5')
depends_on('r@1.5.0:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-acepack/package.py
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@@ -9,8 +9,8 @@
class RAcepack(RPackage):
"""ACE and AVAS for Selecting Multiple Regression Transformations."""
homepage = "https://CRAN.R-project.org/package=acepack"
url = "https://cran.rstudio.com/src/contrib/acepack_1.4.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/acepack"
homepage = "https://cloud.r-project.org/package=acepack"
url = "https://cloud.r-project.org/src/contrib/acepack_1.4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/acepack"
version('1.4.1', 'a35354655e5260afa0e1860fcc68d871')

7
var/spack/repos/builtin/packages/r-ada/package.py
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@@ -10,10 +10,11 @@ class RAda(RPackage):
"""Performs discrete, real, and gentle boost under both exponential
and logistic loss on a given data set."""
homepage = "https://cran.r-project.org/web/packages/ada/index.html"
url = "https://cran.r-project.org/src/contrib/ada_2.0-5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ada"
homepage = "https://cloud.r-project.org/package=ada"
url = "https://cloud.r-project.org/src/contrib/ada_2.0-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ada"
version('2.0-5', '25ac0dc2650fba9e19f3d15c7c6721c1')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-rpart', type=('build', 'run'))

11
var/spack/repos/builtin/packages/r-adabag/package.py
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@@ -9,12 +9,15 @@
class RAdabag(RPackage):
"""Applies Multiclass AdaBoost.M1, SAMME and Bagging."""
homepage = "https://cran.r-project.org/package=adabag"
url = "https://cran.r-project.org/src/contrib/adabag_4.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/adabag"
homepage = "https://cloud.r-project.org/package=adabag"
url = "https://cloud.r-project.org/src/contrib/adabag_4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/adabag"
version('4.2', sha256='47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81')
version('4.1', '2e019f053d49f62ebb3b1697bbb50afa')
depends_on('r-rpart', type=('build', 'run'))
depends_on('r-mlbench', type=('build', 'run'))
depends_on('r-mlbench', when='@:4.1', type=('build', 'run'))
depends_on('r-caret', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-doparallel', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-ade4/package.py
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@@ -11,9 +11,12 @@ class RAde4(RPackage):
Environmental Sciences"""
homepage = "http://pbil.univ-lyon1.fr/ADE-4"
url = "https://cran.r-project.org/src/contrib/ade4_1.7-6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ade4"
url = "https://cloud.r-project.org/src/contrib/ade4_1.7-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ade4"
version('1.7-13', sha256='f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b')
version('1.7-11', sha256='4ccd799ae99bd625840b866a697c4a48adb751660470bf0d6cf9207b1927a572')
version('1.7-6', '63401ca369677538c96c3d7b75b3f4a1')
depends_on('r@2.10:')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-adegenet/package.py
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@@ -18,13 +18,16 @@ class RAdegenet(RPackage):
to illustrate various methods."""
homepage = "https://github.com/thibautjombart/adegenet/wiki"
url = "https://cran.r-project.org/src/contrib/adegenet_2.0.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/adegenet"
url = "https://cloud.r-project.org/src/contrib/adegenet_2.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/adegenet"
version('2.1.1', sha256='3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a')
version('2.1.0', sha256='7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a')
version('2.0.1', 'ecb1220ce7c9affaba2987bc7f38adda')
depends_on('r@2.14:')
depends_on('r@2.14:', type=('build', 'run'))
depends_on('r-ade4', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-igraph', type=('build', 'run'))
depends_on('r-ape', type=('build', 'run'))
depends_on('r-shiny', type=('build', 'run'))
@@ -34,3 +37,4 @@ class RAdegenet(RPackage):
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-dplyr@0.4.1:', type=('build', 'run'))
depends_on('r-vegan', type=('build', 'run'))
depends_on('r-boot', type=('build', 'run'))

16
var/spack/repos/builtin/packages/r-aer/package.py
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@@ -12,16 +12,18 @@ class RAer(RPackage):
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2."""
homepage = "https://cran.r-project.org/web/packages/AER/index.html"
url = "https://cran.r-project.org/src/contrib/AER_1.2-5.tar.gz"
list_url = "https://cran.rstudio.com/src/contrib/Archive/AER"
homepage = "https://cloud.r-project.org/package=AER"
url = "https://cloud.r-project.org/src/contrib/AER_1.2-5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/AER"
version('1.2-7', sha256='3aee5c606313710c2dca6c1e9b2c20a145aa33f2a3ecc5cfcec66c8e91838a93')
version('1.2-6', sha256='653c3a2d253819e0ce8c2cf12cff2ab222bf3d19dbf382b7c4b4c3d762469474')
version('1.2-5', '419df9dc8ee6e5edd79678fee06719ae')
depends_on('r@2.13.0:', type=('build', 'run'))
depends_on('r-car@2.10-19:', type=('build', 'run'))
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-car@2.0-19:', type=('build', 'run'))
depends_on('r-lmtest', type=('build', 'run'))
depends_on('r-sandwich', type=('build', 'run'))
depends_on('r-sandwich@2.4-0:', type=('build', 'run'))
depends_on('r-survival@2.37-5:', type=('build', 'run'))
depends_on('r-zoo', type=('build', 'run'))
depends_on('r-formula', type=('build', 'run'))
depends_on('r-formula@0.2-0:', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-als/package.py
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@@ -15,11 +15,12 @@ class RAls(RPackage):
decomposed simultaneously by assuming that one of the two matrices
in the bilinear decomposition is shared between datasets."""
homepage = "https://cran.r-project.org/package=ALS"
url = "https://cran.rstudio.com/src/contrib/ALS_0.0.6.tar.gz"
list_url = "https://cran.rstudio.com/src/contrib/Archive/ALS"
homepage = "https://cloud.r-project.org/package=ALS"
url = "https://cloud.r-project.org/src/contrib/ALS_0.0.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ALS"
version('0.0.6', 'b72d97911e8ab7e4f8aed1a710b3d62d')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-iso', type=('build', 'run'))
depends_on('r-nnls', type=('build', 'run'))
depends_on('r-nnls@1.1:', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-amap/package.py
View File

@@ -11,9 +11,11 @@ class RAmap(RPackage):
(With robust methods, and parallelized functions)."""
homepage = "http://mulcyber.toulouse.inra.fr/projects/amap/"
url = "https://cran.rstudio.com/src/contrib/amap_0.8-16.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/amap/"
url = "https://cloud.r-project.org/src/contrib/amap_0.8-16.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/amap/"
version('0.8-17', sha256='6b8473d1d35a9cbc611661882c8f681162e8f913f911ccd51629200ae72289c6')
version('0.8-16', sha256='d3775ad7f660581f7d2f070e426be95ae0d6743622943e6f5491988e5217d4e2')
depends_on('r@2.10.0:', type=('build', 'run'))
depends_on('r@2.10.0:', when='@:0.8-16', type=('build', 'run'))
depends_on('r@3.6.0:', when='@0.8-17:', type=('build', 'run'))

15
var/spack/repos/builtin/packages/r-animation/package.py
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@@ -13,11 +13,16 @@ class RAnimation(RPackage):
computational statistics, data mining and machine learning.
These functions maybe helpful in teaching statistics and data analysis."""
homepage = "https://cran.r-project.org/package=animation"
url = "https://cran.r-project.org/src/contrib/animation_2.5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/animation"
homepage = "https://cloud.r-project.org/package=animation"
url = "https://cloud.r-project.org/src/contrib/animation_2.5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/animation"
version('2.6', sha256='90293638920ac436e7e4de76ebfd92e1643ccdb0259b62128f16dd0b13245b0a')
version('2.5', sha256='b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f')
extends('r')
depends_on('r', type=('build', 'run'))
depends_on('r@2.14:', type=('build', 'run'))
depends_on('r-magick', when='@2.6:', type=('build', 'run'))
depends_on('image-magick')
depends_on('ffmpeg')
depends_on('swftools')
depends_on('texlive')

7
var/spack/repos/builtin/packages/r-ape/package.py
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@@ -24,9 +24,10 @@ class RApe(RPackage):
whose results are returned into R."""
homepage = "http://ape-package.ird.fr/"
url = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
url = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ape"
version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23')
version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415')
version('5.1', sha256='b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e')
version('5.0', sha256='c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960')
@@ -35,4 +36,4 @@ class RApe(RPackage):
depends_on('r@3.2:', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-rcpp@0.12.0:', type=('build', 'run'))

10
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@@ -12,12 +12,14 @@ class RArgparse(RPackage):
arguments and automatically generate usage."""
homepage = "https://github.com/trevorld/argparse"
url = "https://cran.r-project.org/src/contrib/argparse_1.1.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/argparse"
url = "https://cloud.r-project.org/src/contrib/argparse_1.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/argparse"
version('2.0.1', sha256='949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab')
version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b')
depends_on('r-proto@1:', type=('build', 'run'))
depends_on('r-proto@1:', when='@1.0.0:1.9.9', type=('build', 'run'))
depends_on('r-getopt', when='@1.0.0:1.9.9', type=('build', 'run'))
depends_on('r-r6', when='@2.0.0:', type=('build', 'run'))
depends_on('r-findpython', type=('build', 'run'))
depends_on('r-getopt', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))

25
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@@ -0,0 +1,25 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAskpass(RPackage):
"""Cross-platform utilities for prompting the user for credentials or a
passphrase, for example to authenticate with a server or read a protected
key. Includes native programs for MacOS and Windows, hence no 'tcltk' is
required. Password entry can be invoked in two different ways: directly
from R via the askpass() function, or indirectly as password-entry back-end
for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS
environment variables. Thereby the user can be prompted for credentials or
a passphrase if needed when R calls out to git or ssh."""
homepage = "https://github.com/jeroen/askpass#readme"
url = "https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/askpass"
version('1.1', sha256='db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f')
depends_on('r-sys@2.1:', type=('build', 'run'))

8
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@@ -12,8 +12,10 @@ class RAssertthat(RPackage):
producing friendly error messages so that your users know what they've done
wrong."""
homepage = "https://cran.r-project.org/package=assertthat"
url = "https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/assertthat"
homepage = "https://cloud.r-project.org/package=assertthat"
url = "https://cloud.r-project.org/src/contrib/assertthat_0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/assertthat"
version('0.2.1', sha256='85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f')
version('0.2.0', '8134f0072c6a84fd738d3bfc5e7f68ef')
version('0.1', '59f9d7f7c00077ea54d763b78eeb5798')

10
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@@ -15,9 +15,13 @@ class RBackports(RPackage):
can make use of the new functions without worrying about the
minimum required R version."""
homepage = "https://cran.r-project.org/package=backports"
url = "https://cran.r-project.org/src/contrib/backports_1.1.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/backports"
homepage = "https://cloud.r-project.org/package=backports"
url = "https://cloud.r-project.org/src/contrib/backports_1.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/backports"
version('1.1.4', sha256='ee4b5efef22fa7ef27d7983ffcd31db52f81e1fbb7189c6e89ee09b69349ff03')
version('1.1.3', sha256='e41bd146824ec921994f1b176d0e4cca0b36dd3db32ca7a954d872a5ba214cc1')
version('1.1.1', '969543a0af32dc23bba9bb37ec82008c')
version('1.1.0', 'b97a71b026fd7ede0e449be93d160c17')
depends_on('r@3.0.0:', type=('build', 'run'))

6
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@@ -11,9 +11,9 @@ class RBase64(RPackage):
Francois. New applications should use the 'openssl' or 'base64enc'
package instead."""
homepage = "https://cran.r-project.org/package=base64"
url = "https://cran.rstudio.com/src/contrib/base64_2.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/base64"
homepage = "https://cloud.r-project.org/package=base64"
url = "https://cloud.r-project.org/src/contrib/base64_2.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/base64"
version('2.0', 'f5a653842f75ad717ef6a00969868ae5')

6
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@@ -11,7 +11,9 @@ class RBase64enc(RPackage):
flexible than the orphaned base64 package."""
homepage = "http://www.rforge.net/base64enc"
url = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc"
url = "https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/base64enc"
version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190')
depends_on('r@2.9.0:', type=('build', 'run'))

9
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@@ -9,10 +9,13 @@
class RBayesm(RPackage):
"""Bayesian Inference for Marketing/Micro-Econometrics"""
homepage = "https://cran.r-project.org/web/packages/bayesm/index.html"
url = "https://cran.r-project.org/src/contrib/bayesm_3.1-0.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bayesm"
homepage = "https://cloud.r-project.org/package=bayesm"
url = "https://cloud.r-project.org/src/contrib/bayesm_3.1-0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bayesm"
version('3.1-3', sha256='51e4827eca8cd4cf3626f3c2282543df7c392b3ffb843f4bfb386fe104642a10')
version('3.1-2', sha256='a332f16e998ab10b17a2b1b9838d61660c36e914fe4d2e388a59f031d52ad736')
version('3.1-1', sha256='4854517dec30ab7c994de862aae1998c2d0c5e71265fd9eb7ed36891d4676078')
version('3.1-0.1', '34998382cafd3e7972d8a03245eac768')
depends_on('r@3.2.0:', type=('build', 'run'))

4
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@@ -11,8 +11,8 @@ class RBbmisc(RPackage):
guys, mainly for package development."""
homepage = "https://github.com/berndbischl/BBmisc"
url = "https://cran.r-project.org/src/contrib/BBmisc_1.11.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/BBmisc"
url = "https://cloud.r-project.org/src/contrib/BBmisc_1.11.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BBmisc"
version('1.11', '681642628037406beb6088d5f773473d')

6
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@@ -10,8 +10,8 @@ class RBeanplot(RPackage):
"""Plots univariate comparison graphs, an alternative to
boxplot/stripchart/violin plot."""
homepage = "https://cran.r-project.org/web/packages/beanplot/index.html"
url = "https://cran.rstudio.com/src/contrib/beanplot_1.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/beanplot"
homepage = "https://cloud.r-project.org/package=beanplot"
url = "https://cloud.r-project.org/src/contrib/beanplot_1.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/beanplot"
version('1.2', 'b24943208a4e61ee9ee0dc152634d5da')

6
var/spack/repos/builtin/packages/r-bfast/package.py
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@@ -9,9 +9,9 @@
class RBfast(RPackage):
"""bfast: Breaks For Additive Season and Trend (BFAST)"""
homepage = "https://cran.r-project.org/package=bfast"
url = "https://cran.r-project.org/src/contrib/bfast_1.5.7.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bfast"
homepage = "https://cloud.r-project.org/package=bfast"
url = "https://cloud.r-project.org/src/contrib/bfast_1.5.7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bfast"
version('1.5.7', sha256='01585fe8944d05ebdb13795214077bc1365f0c0372e2a1f7edb914356dace558')

6
var/spack/repos/builtin/packages/r-bglr/package.py
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@@ -9,9 +9,9 @@
class RBglr(RPackage):
"""BGLR: Bayesian Generalized Linear Regression"""
homepage = "https://cran.r-project.org/package=BGLR"
url = "https://cran.r-project.org/src/contrib/BGLR_1.0.8.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/BGLR"
homepage = "https://cloud.r-project.org/package=BGLR"
url = "https://cloud.r-project.org/src/contrib/BGLR_1.0.8.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BGLR"
version('1.0.8', sha256='5e969590d80b2f272c02a43b487ab1ffa13af386e0342993e6ac484fc82c9b95')

6
var/spack/repos/builtin/packages/r-bh/package.py
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@@ -22,9 +22,9 @@ class RBh(RPackage):
'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit'
'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'."""
homepage = "https://cran.r-project.org/web/packages/BH/index.html"
url = "https://cran.r-project.org/src/contrib/BH_1.65.0-1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/BH"
homepage = "https://cloud.r-project.org/package=BH"
url = "https://cloud.r-project.org/src/contrib/BH_1.65.0-1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BH"
version('1.69.0-1', sha256='a0fd4364b7e368f09c56dec030823f52c16da0787580af7e4615eddeb99baca2')
version('1.65.0-1', '7d0402188e4af59f4103f36616d6ee55')

4
var/spack/repos/builtin/packages/r-biasedurn/package.py
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@@ -15,7 +15,7 @@ class RBiasedurn(RPackage):
explanation of these distributions."""
homepage = "http://www.agner.org/random/"
url = "https://cran.rstudio.com/src/contrib/BiasedUrn_1.07.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/BiasedUrn/"
url = "https://cloud.r-project.org/src/contrib/BiasedUrn_1.07.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BiasedUrn/"
version('1.07', sha256='2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e')

7
var/spack/repos/builtin/packages/r-bibtex/package.py
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@@ -11,12 +11,11 @@ class RBibtex(RPackage):
Utility to parse a bibtex file."""
homepage = "https://cran.r-project.org/package=bibtex"
url = "https://cran.r-project.org/src/contrib/bibtex_0.4.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bibtex/"
homepage = "https://cloud.r-project.org/package=bibtex"
url = "https://cloud.r-project.org/src/contrib/bibtex_0.4.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bibtex/"
version('0.4.2', sha256='1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372')
depends_on('r@3.0.2:', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-testthat', type=('build', 'run'))

4
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@@ -11,8 +11,8 @@ class RBindr(RPackage):
bound function accepts additional arguments."""
homepage = "https://github.com/krlmlr/bindr"
url = "https://cran.r-project.org/src/contrib/bindr_0.1.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bindr"
url = "https://cloud.r-project.org/src/contrib/bindr_0.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bindr"
version('0.1.1', 'cfa02c563196a79bf8bb4db2e66585fd')
version('0.1', 'f3897a70cbad2d2981272772fa30bb59')

8
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@@ -11,12 +11,12 @@ class RBindrcpp(RPackage):
call a C++ function."""
homepage = "https://github.com/krlmlr/bindrcpp"
url = "https://cran.r-project.org/src/contrib/bindrcpp_0.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bindrcpp"
url = "https://cloud.r-project.org/src/contrib/bindrcpp_0.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bindrcpp"
version('0.2.2', '48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467')
version('0.2', '2ed7f19fd9a12587f882d90060e7a343')
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-bindr', type=('build', 'run'))
depends_on('r-rcpp@0.12.16:', type=('build', 'run'))
depends_on('r-bindr@0.1.1:', type=('build', 'run'))
depends_on('r-plogr', type=('build', 'run'))

4
var/spack/repos/builtin/packages/r-biom-utils/package.py
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@@ -12,8 +12,8 @@ class RBiomUtils(RPackage):
"""
homepage = "https://github.com/braithwaite/BIOM.utils/"
url = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/biom/"
url = "https://cloud.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/biom/"
version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375')

10
var/spack/repos/builtin/packages/r-bit/package.py
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@@ -9,7 +9,11 @@
class RBit(RPackage):
""" A class for vectors of 1-bit booleans."""
homepage = "https://cran.rstudio.com/web/packages/bit/index.html"
url = "https://cran.rstudio.com/src/contrib/bit_1.1-12.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bit"
homepage = "https://cloud.r-project.org/package=bit"
url = "https://cloud.r-project.org/src/contrib/bit_1.1-12.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bit"
version('1.1-14', sha256='5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254')
version('1.1-12', 'c4473017beb93f151a8e672e4d5747af')
depends_on('r@2.9.2:', type=('build', 'run'))

10
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@@ -20,9 +20,11 @@ class RBit64(RPackage):
inter- active data exploration
and manipulation and optionally leverage caching."""
homepage = "https://cran.rstudio.com/web/packages/bit64/index.html"
url = "https://cran.rstudio.com/src/contrib/bit64_0.9-7.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bit64"
homepage = "https://cloud.r-project.org/package=bit64"
url = "https://cloud.r-project.org/src/contrib/bit64_0.9-7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bit64"
version('0.9-7', 'ac4bc39827338c552d329d3d4d2339c2')
depends_on('r-bit', type=('build', 'run'))
depends_on('r@3.0.1:', type=('build', 'run'))
depends_on('r-bit@1.1-12:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-bitops/package.py
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@@ -10,8 +10,8 @@
class RBitops(RPackage):
"""Functions for bitwise operations on integer vectors."""
homepage = "https://cran.r-project.org/package=bitops"
url = "https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/bitops"
homepage = "https://cloud.r-project.org/package=bitops"
url = "https://cloud.r-project.org/src/contrib/bitops_1.0-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bitops"
version('1.0-6', 'fba16485a51b1ccd354abde5816b6bdd')

13
var/spack/repos/builtin/packages/r-blob/package.py
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@@ -12,9 +12,14 @@ class RBlob(RPackage):
package provides the blob object, a list of raw vectors, suitable
for use as a column in data frame."""
homepage = "https://cran.rstudio.com/web/packages/blob/index.html"
url = "https://cran.rstudio.com/src/contrib/blob_1.1.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/blob"
homepage = "https://cloud.r-project.org/package=blob"
url = "https://cloud.r-project.org/src/contrib/blob_1.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/blob"
version('1.2.0', sha256='1af1cfa28607bc0e2f1f01598a00a7d5d1385ef160a9e79e568f30f56538e023')
version('1.1.0', '1c729aca36fd5193d81b1cd5ed9d8a00')
depends_on('r-tibble', type=('build', 'run'))
depends_on('r-tibble', when='@:1.1.0', type=('build', 'run'))
depends_on('r-prettyunits', when='@1.2.0:', type=('build', 'run'))
depends_on('r-rlang', when='@1.2.0:', type=('build', 'run'))
depends_on('r-vctrs@0.2.0:', when='@1.2.0:', type=('build', 'run'))

7
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@@ -10,10 +10,11 @@ class RBlockmodeling(RPackage):
"""blockmodeling: Generalized and Classical
Blockmodeling of Valued Networks"""
homepage = "https://cran.r-project.org/package=blockmodeling"
url = "https://cran.rstudio.com/src/contrib/blockmodeling_0.3.1.tar.gz"
list_url = "https://cran.rstudio.com/src/contrib/Archive/blockmodeling/"
homepage = "https://cloud.r-project.org/package=blockmodeling"
url = "https://cloud.r-project.org/src/contrib/blockmodeling_0.3.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/blockmodeling/"
version('0.3.4', sha256='a269c83669dd5294cff0adddab36bc023db6a276a06b74b1fa94b7e407486987')
version('0.3.1', sha256='39e8360400cec6baa920d5589d4e779568bdf2954f7331be0e3cadf22a217d31')
depends_on('r-matrix', type=('build', 'run'))

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@@ -10,13 +10,17 @@ class RBookdown(RPackage):
"""Output formats and utilities for authoring books and technical
documents with R Markdown."""
homepage = "https://cran.r-project.org/package=bookdown"
url = "https://cran.rstudio.com/src/contrib/bookdown_0.5.tar.gz"
list_url = "https://cran.rstudio.com/src/contrib/Archive/bookdown"
homepage = "https://cloud.r-project.org/package=bookdown"
url = "https://cloud.r-project.org/src/contrib/bookdown_0.5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/bookdown"
version('0.12', sha256='38eb4c5b877ccd85b16cfe74a48c3bc53de2f276da98e5515f37e7a06e065bb0')
version('0.5', '7bad360948e2b22d28397870b9319f17')
depends_on('r-yaml@2.1.14:', type=('build', 'run'))
depends_on('r-rmarkdown@1.5:', type=('build', 'run'))
depends_on('r-knitr@1.16:', type=('build', 'run'))
depends_on('r-yaml@2.1.14:', when='@:0.10', type=('build', 'run'))
depends_on('r-rmarkdown@1.12:', type=('build', 'run'))
depends_on('r-knitr@1.22:', type=('build', 'run'))
depends_on('r-htmltools@0.3.6:', type=('build', 'run'))
depends_on('r-xfun@0.6:', when='@0.12:', type=('build', 'run'))
depends_on('r-tinytex@0.12:', when='@0.12:', type=('build', 'run'))
depends_on('pandoc@1.17.2:')

10
var/spack/repos/builtin/packages/r-boot/package.py
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@@ -11,9 +11,13 @@ class RBoot(RPackage):
Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997,
CUP), originally written by Angelo Canty for S."""
homepage = "https://cran.r-project.org/package=boot"
url = "https://cran.r-project.org/src/contrib/boot_1.3-18.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/boot"
homepage = "https://cloud.r-project.org/package=boot"
url = "https://cloud.r-project.org/src/contrib/boot_1.3-18.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/boot"
version('1.3-23', sha256='30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f')
version('1.3-22', sha256='cf1f0cb1e0a7a36dcb6ae038f5d0211a0e7a009c149bc9d21acb9c58c38b4dfc')
version('1.3-20', 'bb879fb4204a4f94ab82c98dd1ad5eca')
version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f')
depends_on('r@3.0.0:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-brew/package.py
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@@ -11,8 +11,8 @@ class RBrew(RPackage):
report generation. brew template syntax is similar to PHP, Ruby's erb
module, Java Server Pages, and Python's psp module."""
homepage = "https://cran.r-project.org/package=brew"
url = "https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/brew"
homepage = "https://cloud.r-project.org/package=brew"
url = "https://cloud.r-project.org/src/contrib/brew_1.0-6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/brew"
version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806')

16
var/spack/repos/builtin/packages/r-broom/package.py
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@@ -17,14 +17,22 @@ class RBroom(RPackage):
model-level statistics."""
homepage = "http://github.com/tidyverse/broom"
url = "https://cran.r-project.org/src/contrib/broom_0.4.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/broom"
url = "https://cloud.r-project.org/src/contrib/broom_0.4.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/broom"
version('0.5.2', sha256='16af7b446b24bc14461efbda9bea1521cf738c778c5e48fcc7bad45660a4ac62')
version('0.5.1', sha256='da9e6bf7cb8f960b83309cf107743976cc32b54524675f6471982abe3d1aae2e')
version('0.4.2', '6eabab1f2eaec10f93cf9aa56d6a61de')
depends_on('r-plyr', type=('build', 'run'))
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-plyr', when='@:0.4.2', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-psych', type=('build', 'run'))
depends_on('r-psych', when='@:0.4.2', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-backports', when='@0.5.0:', type=('build', 'run'))
depends_on('r-generics@0.0.2:', when='@0.5.1:', type=('build', 'run'))
depends_on('r-purrr', when='@0.5.0:', type=('build', 'run'))
depends_on('r-tibble', when='@0.5.0:', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-c50/package.py
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@@ -10,10 +10,14 @@
class RC50(RPackage):
"""C5.0 decision trees and rule-based models for pattern recognition."""
homepage = "https://cran.r-project.org/package=C50"
url = "https://cran.r-project.org/src/contrib/C50_0.1.0-24.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/C50"
homepage = "https://cloud.r-project.org/package=C50"
url = "https://cloud.r-project.org/src/contrib/C50_0.1.0-24.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/C50"
version('0.1.2', sha256='8f459856e0309274bee24462b7145db4eba1d71031c236db39000a5375bdfaba')
version('0.1.1', sha256='03bc1fc2f64bcd5c680568a24902deafab1965074a66f8802bc4cd0335bd01df')
version('0.1.0-24', '42631e65c5c579532cc6edf5ea175949')
depends_on('r@2.10.0:', type=('build', 'run'))
depends_on('r-partykit', type=('build', 'run'))
depends_on('r-cubist@0.2.1:', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-cairo/package.py
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@@ -11,10 +11,12 @@ class RCairo(RPackage):
bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display
(X11 and Win32) output"""
homepage = "https://cran.r-project.org/web/packages/Cairo/index.html"
url = "https://cran.r-project.org/src/contrib/Cairo_1.5-9.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/Cairo"
homepage = "https://cloud.r-project.org/package=Cairo"
url = "https://cloud.r-project.org/src/contrib/Cairo_1.5-9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/Cairo"
version('1.5-10', sha256='7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5')
version('1.5-9', '2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4')
depends_on('r@2.4.0:', type=('build', 'run'))
depends_on('cairo@1.2:')

12
var/spack/repos/builtin/packages/r-callr/package.py
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@@ -12,13 +12,13 @@ class RCallr(RPackage):
does exactly that."""
homepage = "https://github.com/MangoTheCat/callr"
url = "https://cran.r-project.org/src/contrib/callr_1.0.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/callr/"
url = "https://cloud.r-project.org/src/contrib/callr_1.0.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/callr/"
version('3.3.1', sha256='bf60da47357d3336aa395b0c9643235a621763c80d28bc9bb2257767d0a37967')
version('3.2.0', sha256='4bb47b1018e8eb5c683a86c05d0d9b8b25848db1f1b30e92cfebedc0ce14b0e8')
version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7')
version('1.0.0', 'd9af99bb95696310fa1e5d1cb7166c91')
depends_on('r-base64enc', type=('build', 'run'), when='@3.0.0:')
depends_on('r-processx@3.2.0:', type=('build', 'run'), when='@3.0.0')
depends_on('r-r6', type=('build', 'run'), when='@2.0.0')
depends_on('r-utils', type=('build', 'run'), when='@2.0.0')
depends_on('r-processx@3.4.0:', type=('build', 'run'), when='@3.0.0:')
depends_on('r-r6', type=('build', 'run'), when='@3.0.0:')

16
var/spack/repos/builtin/packages/r-car/package.py
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@@ -11,14 +11,24 @@ class RCar(RPackage):
Companion to Applied Regression, Second Edition, Sage, 2011."""
homepage = "https://r-forge.r-project.org/projects/car/"
url = "https://cran.r-project.org/src/contrib/car_2.1-4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/car"
url = "https://cloud.r-project.org/src/contrib/car_2.1-4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/car"
version('3.0-3', sha256='fa807cb12f6e7fb38ec534cac4eef54747945c2119a7d51155a2492ad778c36f')
version('3.0-2', sha256='df59a9ba8fed67eef5ddb8f92f2b41745df715d5695c71d562d7031513f37c50')
version('2.1-4', 'a66c307e8ccf0c336ed197c0f1799565')
version('2.1-2', '0f78ad74ef7130126d319acec23951a0')
depends_on('r@3.2.0:', when='@:3.0-2', type=('build', 'run'))
depends_on('r@3.5.0:', when='@3.0-3:', type=('build', 'run'))
depends_on('r-cardata@3.0-0:', when='@3.0:', type=('build', 'run'))
depends_on('r-abind', when='@3.0:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-mgcv', type=('build', 'run'))
depends_on('r-nnet', type=('build', 'run'))
depends_on('r-pbkrtest', type=('build', 'run'))
depends_on('r-pbkrtest@0.4-4:', type=('build', 'run'))
depends_on('r-quantreg', type=('build', 'run'))
depends_on('r-maptools', when='@3.0:', type=('build', 'run'))
depends_on('r-rio', when='@3.0:', type=('build', 'run'))
depends_on('r-lme4', when='@3.0:', type=('build', 'run'))
depends_on('r-nlme', when='@3.0:', type=('build', 'run'))

19
var/spack/repos/builtin/packages/r-cardata/package.py Normal file
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@@ -0,0 +1,19 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RCardata(RPackage):
"""Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied
Regression, Third Edition, Sage (forthcoming)."""
homepage = "https://r-forge.r-project.org/projects/car/"
url = "https://cloud.r-project.org/src/contrib/carData_3.0-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/carData"
version('3.0-2', sha256='3b5c4eff1cc1e456a5331084774503eaa06cf61fb7acf6b9e8a6bfabd5735494')
depends_on('r@3.0:', type=('build', 'run'))

14
var/spack/repos/builtin/packages/r-caret/package.py
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@@ -11,19 +11,23 @@ class RCaret(RPackage):
models."""
homepage = "https://github.com/topepo/caret/"
url = "https://cran.r-project.org/src/contrib/caret_6.0-73.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/caret"
url = "https://cloud.r-project.org/src/contrib/caret_6.0-73.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caret"
version('6.0-84', sha256='a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d')
version('6.0-83', sha256='9bde5e4da1f0b690bfe06c2439c0136504e851a8d360bf56b644f171fe20dcef')
version('6.0-73', 'ca869e3357b5358f028fb926eb62eb70')
version('6.0-70', '202d7abb6a679af716ea69fb2573f108')
depends_on('r@2.10:')
depends_on('r@2.10:', when='@:6.0-81', type=('build', 'run'))
depends_on('r@3.2.0:', when='@6.0-82:', type=('build', 'run'))
depends_on('r-lattice@0.20:', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-car', type=('build', 'run'))
depends_on('r-car', when='@:6.0-73', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-modelmetrics@1.1.0:', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-recipes@0.1.4:', when='@6.0-83:', type=('build', 'run'))
depends_on('r-withr@2.0.0:', when='@6.0-83:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-caroline/package.py
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@@ -10,9 +10,9 @@ class RCaroline(RPackage):
"""caroline: A Collection of Database, Data Structure, Visualization,
andUtility Functions for R"""
homepage = "https://cran.r-project.org/package=caroline"
url = "https://cran.r-project.org/src/contrib/caroline_0.7.6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/caroline"
homepage = "https://cloud.r-project.org/package=caroline"
url = "https://cloud.r-project.org/src/contrib/caroline_0.7.6.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caroline"
version('0.7.6', sha256='e7ba948f7d87f091b498dd0eec2ca4fdad7af4e2bbb67e0945c2f0d3f2eadda9')

9
var/spack/repos/builtin/packages/r-catools/package.py
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@@ -13,10 +13,13 @@ class RCatools(RPackage):
files, fast calculation of AUC, LogitBoost classifier, base64
encoder/decoder, round-off-error-free sum and cumsum, etc."""
homepage = "https://cran.r-project.org/package=caTools"
url = "https://cran.r-project.org/src/contrib/caTools_1.17.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/caTools"
homepage = "https://cloud.r-project.org/package=caTools"
url = "https://cloud.r-project.org/src/contrib/caTools_1.17.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/caTools"
version('1.17.1.2', sha256='69cc542fab5677462b1a768709d0c4a0a0790f5db53e1fe9ae7123787c18726b')
version('1.17.1.1', sha256='d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06')
version('1.17.1', '5c872bbc78b177b306f36709deb44498')
depends_on('r@2.2.0:', type=('build', 'run'))
depends_on('r-bitops', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-cdcfluview/package.py
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@@ -14,12 +14,14 @@ class RCdcfluview(RPackage):
to select and retrieve influenza data. Tools are provided to access the
data provided by the portal's underlying 'API'."""
homepage = "https://cran.r-project.org/package=cdcfluview"
url = "https://cran.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/cdcfluview"
homepage = "https://cloud.r-project.org/package=cdcfluview"
url = "https://cloud.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cdcfluview"
version('0.9.0', sha256='1b2064886858cbb1790ef808d88fbab75d3a9cf55e720638221a3377ff8dd244')
version('0.7.0', 'd592606fab3da3536f39a15c0fdbcd17')
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
@@ -29,4 +31,3 @@ class RCdcfluview(RPackage):
depends_on('r-readr', type=('build', 'run'))
depends_on('r-mmwrweek', type=('build', 'run'))
depends_on('r-units@0.4-6:', type=('build', 'run'))
depends_on('r@3.2.0:', type=('build', 'run'))

7
var/spack/repos/builtin/packages/r-cellranger/package.py
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@@ -10,11 +10,12 @@ class RCellranger(RPackage):
"""Helper functions to work with spreadsheets and the "A1:D10"
style of cell range specification."""
homepage = "https://cran.r-project.org/package=cellranger"
url = "https://cran.r-project.org/src/contrib/cellranger_1.1.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/cellranger"
homepage = "https://cloud.r-project.org/package=cellranger"
url = "https://cloud.r-project.org/src/contrib/cellranger_1.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cellranger"
version('1.1.0', '1abcfea6af5ab2e277cb99e86880456f')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-rematch', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-checkmate/package.py
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@@ -11,10 +11,12 @@ class RCheckmate(RPackage):
A substantial part of the package was written in C to
minimize any worries about execution time overhead."""
homepage = "https://cran.r-project.org/package=checkmate"
url = "https://cran.rstudio.com/src/contrib/checkmate_1.8.4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/checkmate"
homepage = "https://cloud.r-project.org/package=checkmate"
url = "https://cloud.r-project.org/src/contrib/checkmate_1.8.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/checkmate"
version('1.9.4', sha256='faa25754b757fe483b876f5d07b73f76f69a1baa971420892fadec4af4bbad21')
version('1.8.4', '00bd2c464386614da208f82c4b21910b')
depends_on('r-backports', type=('build', 'run'))
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-backports@1.1.0:', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-checkpoint/package.py
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@@ -12,11 +12,13 @@ class RCheckpoint(RPackage):
install packages as they existed on CRAN on a specific snapshot
date as if you had a CRAN time machine."""
homepage = "https://cran.r-project.org/package=checkpoint"
url = "https://cran.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/checkpoint"
homepage = "https://cloud.r-project.org/package=checkpoint"
url = "https://cloud.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint"
version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2')
version('0.4.3', sha256='c3e862f89f8838183d6028f7ed13683aec562e6dab77ad4b6a5e24ec653cfb64')
version('0.3.18', '021d7faeb72c36167951e103b2b065ea')
version('0.3.15', 'a4aa8320338f1434a330d984e97981ea')
depends_on('r@3.0.0:')
depends_on('r@3.0.0:', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-chemometrics/package.py
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@@ -10,9 +10,9 @@ class RChemometrics(RPackage):
"""R companion to the book "Introduction to Multivariate Statistical Analysis
in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)."""
homepage = "https://cran.r-project.org/web/packages/chemometrics/index.html"
url = "https://cran.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz"
list_url = "https://cran.rstudio.com/src/contrib/Archive/chemometrics"
homepage = "https://cloud.r-project.org/package=chemometrics"
url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/chemometrics"
version('1.4.2', '8137b0ca4004add9cc2ea81d2c54427f')
version('1.4.1', '1e5a89442bb4a61db0da884eedd74fc2')
@@ -29,3 +29,6 @@ class RChemometrics(RPackage):
depends_on('r-pls', type=('build', 'run'))
depends_on('r-som', type=('build', 'run'))
depends_on('r-pcapp', type=('build', 'run'))
depends_on('r-class', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-nnet', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-chron/package.py
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@@ -9,8 +9,12 @@
class RChron(RPackage):
"""Chronological objects which can handle dates and times."""
homepage = "https://cran.r-project.org/package=chron"
url = "https://cran.r-project.org/src/contrib/chron_2.3-47.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/chron"
homepage = "https://cloud.r-project.org/package=chron"
url = "https://cloud.r-project.org/src/contrib/chron_2.3-47.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/chron"
version('2.3-53', sha256='521814b46ba958eae28e29d8766aebd285da5e6fa16c5806603df3ae39f77309')
version('2.3-52', sha256='c47fcf4abb635babe6337604c876d4853d8a24639a98b71523746c56ce75b4a0')
version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f')
depends_on('r@2.12.0:', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-circlize/package.py
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@@ -18,13 +18,15 @@ class RCirclize(RPackage):
convenience and freedom to design figures for better understanding
complex patterns behind multiple dimensional data."""
homepage = "https://cran.r-project.org/package=circlize"
url = "https://cran.r-project.org/src/contrib/circlize_0.4.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/circlize"
homepage = "https://cloud.r-project.org/package=circlize"
url = "https://cloud.r-project.org/src/contrib/circlize_0.4.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/circlize"
version('0.4.6', sha256='cec88cfc5e512a111cc37177552c25698ccc0e9bbecb0d6e60657e7b115a56fa')
version('0.4.1', '6818830654f485abbdc8c74ec9087377')
version('0.4.0', '0dbf1b481930a759d6f413d17f8ae1c4')
depends_on('r-globaloptions', type=('build', 'run'))
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.0:', type=('build', 'run'))
depends_on('r-shape', type=('build', 'run'))
depends_on('r-colorspace', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-class/package.py
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@@ -11,9 +11,11 @@ class RClass(RPackage):
Learning Vector Quantization and Self-Organizing Maps."""
homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
url = "https://cran.r-project.org/src/contrib/class_7.3-14.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/class"
url = "https://cloud.r-project.org/src/contrib/class_7.3-14.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/class"
version('7.3-15', sha256='f6bf33d610c726d58622b6cea78a808c7d6a317d02409d27c17741dfd1c730f4')
version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))

11
var/spack/repos/builtin/packages/r-classint/package.py
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@@ -10,11 +10,16 @@ class RClassint(RPackage):
"""Selected commonly used methods for choosing univariate class intervals
for mapping or other graphics purposes."""
homepage = "https://cran.r-project.org/package=classInt"
url = "https://cran.r-project.org/src/contrib/classInt_0.1-24.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/classInt"
homepage = "https://cloud.r-project.org/package=classInt"
url = "https://cloud.r-project.org/src/contrib/classInt_0.1-24.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/classInt"
version('0.4-1', sha256='39c63f8e37b379033d73d57929b5b8ea41b0023626cc1cec648d66bade5d0103')
version('0.3-3', sha256='a93e685ef9c40d5977bb91d7116505a25303b229897a20544722a94ea1365f30')
version('0.3-1', sha256='e2e6f857b544dfecb482b99346aa3ecfdc27b4d401c3537ee8fbaf91caca92b9')
version('0.1-24', '45f1bde3ec7601ce17c99189be5c0fd5')
depends_on('r@2.2:', type=('build', 'run'))
depends_on('r-e1071', type=('build', 'run'))
depends_on('r-class', type=('build', 'run'))
depends_on('r-kernsmooth', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-cli/package.py
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@@ -12,11 +12,13 @@ class RCli(RPackage):
'Unicode' symbols with 'ASCII' alternatives."""
homepage = "https://github.com/r-lib/cli#readme"
url = "https://cran.r-project.org/src/contrib/cli_1.0.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/cli"
url = "https://cloud.r-project.org/src/contrib/cli_1.0.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cli"
version('1.1.0', sha256='4fc00fcdf4fdbdf9b5792faee8c7cf1ed5c4f45b1221d961332cda82dbe60d0a')
version('1.0.1', 'ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4')
version('1.0.0', 'e6c4169541d394d6d435c4b430b1dd77')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-assertthat', type=('build', 'run'))
depends_on('r-crayon', type=('build', 'run'))
depends_on('r-crayon@1.3.4:', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-clipr/package.py
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@@ -11,11 +11,11 @@ class RClipr(RPackage):
and X11 clipboards."""
homepage = "https://github.com/mdlincoln/clipr"
url = "https://cran.r-project.org/src/contrib/clipr_0.4.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/clipr"
url = "https://cloud.r-project.org/src/contrib/clipr_0.4.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/clipr"
version('0.7.0', sha256='03a4e4b72ec63bd08b53fe62673ffc19a004cc846957a335be2b30d046b8c2e2')
version('0.5.0', sha256='fd303f8b7f29badcdf490bb2d579acdfc4f4e1aa9c90ac77ab9d05ce3d053dbf')
version('0.4.0', '4012a31eb3b7a36bd3bac00f916e56a7')
depends_on('r-rstudioapi', type=('build', 'run'))
depends_on('r-testthat', type=('build', 'run'))
depends_on('xclip')

19
var/spack/repos/builtin/packages/r-clisymbols/package.py Normal file
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@@ -0,0 +1,19 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RClisymbols(RPackage):
"""A small subset of Unicode symbols, that are useful when building command
line applications. They fall back to alternatives on terminals that do not
support Unicode. Many symbols were taken from the 'figures' 'npm' package
(see <https://github.com/sindresorhus/figures>)."""
homepage = "https://github.com/gaborcsardi/clisymbols"
url = "https://cloud.r-project.org/src/contrib/clisymbols_1.2.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/clisymbols"
version('1.2.0', sha256='0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0')

11
var/spack/repos/builtin/packages/r-cluster/package.py
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@@ -11,10 +11,15 @@ class RCluster(RPackage):
Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw
(1990) "Finding Groups in Data"."""
homepage = "https://cran.r-project.org/web/packages/cluster/index.html"
url = "https://cran.rstudio.com/src/contrib/cluster_2.0.7-1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/cluster"
homepage = "https://cloud.r-project.org/package=cluster"
url = "https://cloud.r-project.org/src/contrib/cluster_2.0.7-1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cluster"
version('2.1.0', sha256='eaf955bef8f616ea563351ec7f597c445aec43e65991ca975e382ef1fd70aa14')
version('2.0.7-1', 'a37add21b91d3e4f3883d005331e0d45')
version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a')
version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59')
depends_on('r@3.0.1:', when='@:2.0.6', type=('build', 'run'))
depends_on('r@3.2.0:', when='@2.0.7:2.0.7-1', type=('build', 'run'))
depends_on('r@3.3.0:', when='@2.0.8:', type=('build', 'run'))

7
var/spack/repos/builtin/packages/r-clustergeneration/package.py
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@@ -9,10 +9,11 @@
class RClustergeneration(RPackage):
"""Random Cluster Generation (with Specified Degree of Separation)"""
homepage = "https://cran.r-project.org/package=clusterGeneration"
url = "https://cran.r-project.org/src/contrib/clusterGeneration_1.3.4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/clusterGeneration/"
homepage = "https://cloud.r-project.org/package=clusterGeneration"
url = "https://cloud.r-project.org/src/contrib/clusterGeneration_1.3.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/clusterGeneration/"
version('1.3.4', sha256='7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa')
depends_on('r@2.9.1:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))

2
var/spack/repos/builtin/packages/r-cner/package.py
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@@ -33,5 +33,5 @@ class RCner(RPackage):
depends_on('r-annotate@1.50.0:', type=('build', 'run'))
depends_on('r-go-db@3.3.0:', type=('build', 'run'))
depends_on('r-keggrest@1.14.0:', type=('build', 'run'))
depends_on('r-utils@2.3.0:', type=('build', 'run'))
depends_on('r-r-utils@2.3.0:', type=('build', 'run'))
depends_on('r@3.4.3:3.4.9', when='@1.14.0')

9
var/spack/repos/builtin/packages/r-coda/package.py
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@@ -12,10 +12,13 @@ class RCoda(RPackage):
diagnostic tests of convergence to the equilibrium distribution
of the Markov chain."""
homepage = "https://cran.r-project.org/web/packages/coda/index.html"
url = "https://cran.r-project.org/src/contrib/coda_0.19-1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/coda"
homepage = "https://cloud.r-project.org/package=coda"
url = "https://cloud.r-project.org/src/contrib/coda_0.19-1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/coda"
version('0.19-3', sha256='d3df1fc848bcf1af8fae13d61eeab60e99a3d4b4db384bec4326f909f502c5d6')
version('0.19-2', sha256='678a7e6a87a2723089daeb780ea37ac3d4319b37eabe26928ea3fa9c9b1eda0d')
version('0.19-1', '0d2aca6a5a3bdae9542708817c1ec001')
depends_on('r@2.14:', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-codetools/package.py
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@@ -9,9 +9,12 @@
class RCodetools(RPackage):
"""Code analysis tools for R."""
homepage = "https://cran.r-project.org/web/packages/codetools/index.html"
url = "https://cran.r-project.org/src/contrib/codetools_0.2-15.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/codetools"
homepage = "https://cloud.r-project.org/package=codetools"
url = "https://cloud.r-project.org/src/contrib/codetools_0.2-15.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/codetools"
version('0.2-16', sha256='f67a66175cb5d8882457d1e9b91ea2f16813d554fa74f80c1fd6e17cf1877501')
version('0.2-15', '37419cbc3de81984cf6d9b207d4f62d4')
version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d')
depends_on('r@2.1:', type=('build', 'run'))

14
var/spack/repos/builtin/packages/r-coin/package.py
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@@ -11,15 +11,19 @@ class RCoin(RPackage):
including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems."""
homepage = "https://cran.r-project.org/package=coin"
url = "https://cran.r-project.org/src/contrib/coin_1.1-3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/coin"
homepage = "https://cloud.r-project.org/package=coin"
url = "https://cloud.r-project.org/src/contrib/coin_1.1-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/coin"
version('1.3-0', sha256='adcebb37e0a7dfddbf8ec1e09c12a809bd76d90b5b8ff2b1048a75252ba11ef8')
version('1.2-2', sha256='d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb')
version('1.1-3', '97d3d21f1e4a5762e36dd718dd2d0661')
depends_on('r@2.14.0:')
depends_on('r@2.14.0:', when='@:1.2-2', type=('build', 'run'))
depends_on('r@3.4.0:', when='@1.3-0:', type=('build', 'run'))
depends_on('r-survival', type=('build', 'run'))
depends_on('r-modeltools@0.2-9:', type=('build', 'run'))
depends_on('r-mvtnorm@1.0-5:', type=('build', 'run'))
depends_on('r-multcomp', type=('build', 'run'))
depends_on('r-libcoin@1.0-0:', when='@1.3-0:', type=('build', 'run'))
depends_on('r-matrixstats@0.54.0:', when='@1.3-0:', type=('build', 'run'))

10
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@@ -12,9 +12,13 @@ class RColorspace(RPackage):
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided."""
homepage = "https://cran.r-project.org/web/packages/colorspace/index.html"
url = "https://cran.r-project.org/src/contrib/colorspace_1.3-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace"
homepage = "https://cloud.r-project.org/package=colorspace"
url = "https://cloud.r-project.org/src/contrib/colorspace_1.3-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/colorspace"
version('1.4-1', sha256='693d713a050f8bfecdb7322739f04b40d99b55aed168803686e43401d5f0d673')
version('1.4-0', sha256='ce003c5958dd704697959e9dc8a108c8cb568f8d78ece113235732afc5dff556')
version('1.3-2', '63000bab81d995ff167df76fb97b2984')
version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1')
depends_on('r@3.0.0:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-combinat/package.py
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@@ -9,8 +9,8 @@
class RCombinat(RPackage):
"""routines for combinatorics"""
homepage = "https://cran.r-project.org/package=combinat"
url = "https://cran.r-project.org/src/contrib/combinat_0.0-8.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/combinat/"
homepage = "https://cloud.r-project.org/package=combinat"
url = "https://cloud.r-project.org/src/contrib/combinat_0.0-8.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/combinat/"
version('0.0-8', sha256='1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1')

6
var/spack/repos/builtin/packages/r-commonmark/package.py
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@@ -9,8 +9,8 @@
class RCommonmark(RPackage):
"""commonmark: CommonMark and Github Markdown Rendering in R"""
homepage = "https://cran.r-project.org/package=commonmark"
url = "https://cran.r-project.org/src/contrib/commonmark_1.7.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/commonmark/"
homepage = "https://cloud.r-project.org/package=commonmark"
url = "https://cloud.r-project.org/src/contrib/commonmark_1.7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/commonmark/"
version('1.7', sha256='d14a767a3ea9778d6165f44f980dd257423ca6043926e3cd8f664f7171f89108')

6
var/spack/repos/builtin/packages/r-compositions/package.py
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@@ -9,9 +9,9 @@
class RCompositions(RPackage):
"""Compositional Data Analysis"""
homepage = "https://cran.r-project.org/web/packages/compositions/index.html"
url = "https://cran.r-project.org/src/contrib/compositions_1.40-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/compositions"
homepage = "https://cloud.r-project.org/package=compositions"
url = "https://cloud.r-project.org/src/contrib/compositions_1.40-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/compositions"
version('1.40-2', 'ad87efe2fb303d95472e73c8ca8d9a01')

7
var/spack/repos/builtin/packages/r-construct/package.py
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@@ -10,9 +10,9 @@ class RConstruct(RPackage):
"""conStruct: Models Spatially Continuous and Discrete Population
GeneticStructure"""
homepage = "https://cran.r-project.org/package=conStruct"
url = "https://cran.r-project.org/src/contrib/conStruct_1.0.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/conStruct"
homepage = "https://cloud.r-project.org/package=conStruct"
url = "https://cloud.r-project.org/src/contrib/conStruct_1.0.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/conStruct"
version('1.0.3', sha256='b449c133a944ad05a28f84f312ed4ccbc1574c4659aa09c678618d2ae9008310')
@@ -27,3 +27,4 @@ class RConstruct(RPackage):
depends_on('r-rstan@2.18.1:', type=('build', 'run'))
depends_on('r-rstantools@1.5.0:', type=('build', 'run'))
depends_on('r-stanheaders@2.18.0:', type=('build', 'run'))
depends_on('gmake', type='build')

7
var/spack/repos/builtin/packages/r-convevol/package.py
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@@ -9,12 +9,13 @@
class RConvevol(RPackage):
"""Quantifies and assesses the significance of convergent evolution"""
homepage = "https://cran.r-project.org/package=convevol"
url = "https://cran.r-project.org/src/contrib/convevol_1.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/convevol/"
homepage = "https://cloud.r-project.org/package=convevol"
url = "https://cloud.r-project.org/src/contrib/convevol_1.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/convevol/"
version('1.3', sha256='d6b24b9796a559f5280e277746189d141151ade4b14cc6b4c2d9d496d7f314ac')
depends_on('r@3.5.0:', type=('build', 'run'))
depends_on('r-ape', type=('build', 'run'))
depends_on('r-cluster', type=('build', 'run'))
depends_on('r-geiger', type=('build', 'run'))

6
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@@ -14,9 +14,9 @@ class RCorhmm(RPackage):
states in a Markov process and various other functions for evaluating
models of binary character evolution."""
homepage = "https://cran.r-project.org/package=corHMM"
url = "https://cran.r-project.org/src/contrib/corHMM_1.22.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/corHMM/"
homepage = "https://cloud.r-project.org/package=corHMM"
url = "https://cloud.r-project.org/src/contrib/corHMM_1.22.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/corHMM/"
version('1.22', sha256='d262fa1183eab32087afb70f1789fabae6fb49bec01d627974c54a088a48b10d')

8
var/spack/repos/builtin/packages/r-corpcor/package.py
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@@ -9,8 +9,10 @@
class RCorpcor(RPackage):
"""Efficient Estimation of Covariance and (Partial) Correlation"""
homepage = "https://cran.r-project.org/package=corpcor"
url = "https://cran.r-project.org/src/contrib/corpcor_1.6.9.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/corpcor"
homepage = "https://cloud.r-project.org/package=corpcor"
url = "https://cloud.r-project.org/src/contrib/corpcor_1.6.9.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/corpcor"
version('1.6.9', '7f447d9f389e5d7dedb5fe5baedca925')
depends_on('r@3.0.2:', type=('build', 'run'))

7
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@@ -10,8 +10,9 @@ class RCorrplot(RPackage):
"""A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering."""
homepage = "https://cran.r-project.org/package=corrplot"
url = "https://cran.r-project.org/src/contrib/corrplot_0.77.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/corrplot"
homepage = "https://cloud.r-project.org/package=corrplot"
url = "https://cloud.r-project.org/src/contrib/corrplot_0.77.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/corrplot"
version('0.84', sha256='0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc')
version('0.77', '2a5d54fd5c65618b9afba1a32f6b4542')

14
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@@ -16,14 +16,20 @@ class RCovr(RPackage):
or framework and tracks coverage of both R code and compiled
C/C++/FORTRAN code."""
homepage = "https://cran.r-project.org/package=covr"
url = "https://cran.r-project.org/src/contrib/covr_3.0.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/covr"
homepage = "https://cloud.r-project.org/package=covr"
url = "https://cloud.r-project.org/src/contrib/covr_3.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/covr"
version('3.3.0', sha256='c0aa0bd7b2dc05effdc2367c59d45294f46858930d1b14efb393b205021fc65a')
version('3.2.1', sha256='ea90daa48011e4ac4431ae47ee02fad98f54b529fc3900281cbeef7a2edef0a0')
version('3.2.0', sha256='b26135306b1d6b14dd4deb481359dd919a7ca1e802ca5479fed394dcf35f0ef9')
version('3.0.1', 'f88383f751fe5aa830a2b2e5c14aa66a')
depends_on('r@3.1.0:', type=('build', 'run'))
depends_on('r-digest', when='@3.2.0:', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-rex', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-crayon', type=('build', 'run'))
depends_on('r-withr', type=('build', 'run'))
depends_on('r-withr@1.0.2:', type=('build', 'run'))
depends_on('r-yaml', when='@3.3.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-cowplot/package.py
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@@ -15,18 +15,21 @@ class RCowplot(RPackage):
theme that is used in the Wilke lab, hence the package name,
which stands for Claus O. Wilke's plot package."""
homepage = "https://cran.r-project.org/package=cowplot"
url = "https://cran.rstudio.com/src/contrib/cowplot_0.8.0.tar.gz"
list_url = "https://cran.rstudio.com/src/contrib/Archive/cowplot"
homepage = "https://cloud.r-project.org/package=cowplot"
url = "https://cloud.r-project.org/src/contrib/cowplot_0.8.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cowplot"
version('1.0.0', sha256='70f9a7c46d10f409d1599f1afc9fd3c947051cf2b430f01d903c64ef1e6c98a5')
version('0.9.3', sha256='3e10475fd7506ea9297ed72eb1a3acf858c6fa99d26e46fc39654eba000c3dcb')
version('0.9.2', sha256='8b92ce7f92937fde06b0cfb86c7634a39b3b2101e362cc55c4bec6b3fde1d28f')
version('0.9.1', sha256='953fd9d6ff370472b9f5a9ee867a423bea3e26e406d08a2192ec1872a2e60047')
version('0.9.0', sha256='d5632f78294c3678c08d3eb090abe1eec5cc9cd15cb5d96f9c43794ead098cb5')
version('0.8.0', sha256='a617fde25030fe764f20967fb753a953d73b47745a2146c97c2565eb4d06700d')
depends_on('r@3.3.0:', type=('build', 'run'))
depends_on('r-ggplot2@2.1.0:', type=('build', 'run'))
depends_on('r-gtable@0.1.2:', type=('build', 'run'))
depends_on('r-plyr@1.8.2:', type=('build', 'run'))
depends_on('r@3.3.0:', when='@:0.9.4', type=('build', 'run'))
depends_on('r@3.5.0:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-ggplot2@2.1.1:', type=('build', 'run'))
depends_on('r-gtable', type=('build', 'run'))
depends_on('r-plyr@1.8.2:', when='@:0.9.9', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-rlang', when='@1.0.0:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-crayon/package.py
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@@ -13,9 +13,9 @@ class RCrayon(RPackage):
New styles can also be created easily. This package was inspired by the
'chalk' 'JavaScript' project."""
homepage = "https://cran.r-project.org/package=sourcetools"
url = "https://cran.rstudio.com/src/contrib/crayon_1.3.4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/crayon"
homepage = "https://github.com/r-lib/crayon#readme"
url = "https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/crayon"
version('1.3.4', '77c7c2906c59a3141306d86c89ffc7d3')
version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9')

10
var/spack/repos/builtin/packages/r-crosstalk/package.py
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@@ -10,13 +10,15 @@ class RCrosstalk(RPackage):
"""Provides building blocks for allowing HTML widgets to communicate with
each other, with Shiny or without (i.e. static .html files)."""
homepage = "https://cran.r-project.org/web/packages/crosstalk/index.html"
url = "https://cran.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz"
homepage = "https://cloud.r-project.org/package=crosstalk"
url = "https://cloud.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/crosstalk"
version('1.0.0', 'c13c21b81af2154be3f08870fd3a7077')
depends_on('r-htmltools', type=('build', 'run'))
depends_on('r-htmltools@0.3.5:', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-lazyeval', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-shiny', type=('build', 'run'))
depends_on('r-shiny@0.11:', type=('build', 'run'))
depends_on('r-r6', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-crul/package.py
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@@ -9,10 +9,11 @@
class RCrul(RPackage):
"""crul: HTTP Client"""
homepage = "https://cran.r-project.org/package=crul"
url = "https://cran.r-project.org/src/contrib/crul_0.7.4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/crul"
homepage = "https://cloud.r-project.org/package=crul"
url = "https://cloud.r-project.org/src/contrib/crul_0.7.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/crul"
version('0.8.4', sha256='dbd950ad3b68402e5a5955615b1abcb5c9bdc846c93aa25f96a7a58913d04c8b')
version('0.7.4', sha256='c963dd666ae3fc89b661ce19fce2fa19a16fc3825e1502105cae98ceb92c6014')
depends_on('r-curl@3.3:', type=('build', 'run'))
@@ -20,3 +21,4 @@ class RCrul(RPackage):
depends_on('r-mime', type=('build', 'run'))
depends_on('r-r6@2.2.0:', type=('build', 'run'))
depends_on('r-urltools@1.6.0:', type=('build', 'run'))
depends_on('r-jsonlite', when='@0.8.4:', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-cubature/package.py
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@@ -9,8 +9,12 @@
class RCubature(RPackage):
"""Adaptive multivariate integration over hypercubes"""
homepage = "https://cran.r-project.org/package=cubature"
url = "https://cran.r-project.org/src/contrib/cubature_1.1-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/cubature"
homepage = "https://cloud.r-project.org/package=cubature"
url = "https://cloud.r-project.org/src/contrib/cubature_1.1-2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/cubature"
version('2.0.3', sha256='79bf03ebdb64b0de1ef19d24051b9d922df9310254bee459bb47764522407a73')
version('2.0.2', sha256='641165c665ff490c523bccc05c42bb6851e42676b6b366b55fc442a51a8fbe8c')
version('1.1-2', '5617e1d82baa803a3814d92461da45c9')
depends_on('r-rcpp', when='@2.0.3:', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-cubist/package.py
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@@ -9,10 +9,12 @@
class RCubist(RPackage):
"""Regression modeling using rules with added instance-based corrections"""
homepage = "https://cran.r-project.org/package=Cubist"
url = "https://cran.r-project.org/src/contrib/Cubist_0.0.19.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/Cubist"
homepage = "https://cloud.r-project.org/package=Cubist"
url = "https://cloud.r-project.org/src/contrib/Cubist_0.0.19.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/Cubist"
version('0.2.2', sha256='cd3e152cc72ab33f720a8fb6b8b6787171e1c037cfda48f1735ab692ed6d85d4')
version('0.2.1', sha256='b310c3f166f15fa3e16f8d110d39931b0bb1b0aa8d0c9ac2af5a9a45081588a3')
version('0.0.19', 'bf9364f655536ec03717fd2ad6223a47')
depends_on('r-lattice', type=('build', 'run'))

7
var/spack/repos/builtin/packages/r-curl/package.py
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@@ -18,14 +18,15 @@ class RCurl(RPackage):
package with http specific tools and logic."""
homepage = "https://github.com/jeroenooms/curl"
url = "https://cran.r-project.org/src/contrib/curl_2.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/curl"
url = "https://cloud.r-project.org/src/contrib/curl_2.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/curl"
version('4.0', sha256='09a99c9c86666449188fbb211cb1e9fbdb5108ab56f0d09322cd0ae50e926171')
version('3.3', sha256='0cb0b9a9280edc42ebed94708541ec86b4f48779e722171e45227eab8a88a5bd')
version('3.0', '741202626eacd1f9c022b0a4d7be6d6a')
version('2.3', '7250ee8caed98ba76906ab4d32da60f8')
version('1.0', '93d34926d6071e1fba7e728b482f0dd9')
version('0.9.7', 'a101f7de948cb828fef571c730f39217')
depends_on('r@3.0.0:')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('curl')

6
var/spack/repos/builtin/packages/r-data-table/package.py
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@@ -13,9 +13,11 @@ class RDataTable(RPackage):
syntax, for faster development."""
homepage = "https://github.com/Rdatatable/data.table/wiki"
url = "https://cran.r-project.org/src/contrib/data.table_1.10.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/data.table"
url = "https://cloud.r-project.org/src/contrib/data.table_1.10.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/data.table"
version('1.12.2', sha256='db55c18f0d703a8bc1c806dd1f7551bb405cb867717f52ef9dd64405394d22f5')
version('1.12.0', sha256='611b112123dbd4ebd5200770fcdfaaeaab622adeb2b290d36018d3092742e3f7')
version('1.11.8', sha256='dc427465599cadd848b28a78e2fce3362867847b44148252054385999fe566d9')
version('1.11.6', sha256='ac6783c18e94d1bc05702ddec9fd87c542c744f640132f5ffc373348be84d9e9')
version('1.11.4', sha256='fdccf1dec3f38bb344163163decf3ffa0c0f8e2c70daa1bec8aac422716e81d5')

8
var/spack/repos/builtin/packages/r-dbi/package.py
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@@ -12,7 +12,11 @@ class RDbi(RPackage):
virtual and need to be extended by the various R/DBMS implementations."""
homepage = "http://rstats-db.github.io/DBI"
url = "https://cran.rstudio.com/src/contrib/DBI_0.7.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/DBI"
url = "https://cloud.r-project.org/src/contrib/DBI_0.7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/DBI"
version('1.0.0', sha256='ff16f118eb3f759183441835e932b87358dd80ab9800ce576a8f3df1b6f01cf5')
version('0.4-1', 'c7ee8f1c5037c2284e99c62698d0f087')
version('0.7', '66065dd687d758b72d638adb6a8cab2e')
depends_on('r@3.0.0:', type=('build', 'run'))

20
var/spack/repos/builtin/packages/r-dbplyr/package.py
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@@ -14,21 +14,23 @@ class RDbplyr(RPackage):
author."""
homepage = "https://github.com/tidyverse/dbplyr"
url = "https://cran.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/dbplyr"
url = "https://cloud.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/dbplyr"
version('1.4.2', sha256='b783f0da2c09a1e63f41168b02c0715b08820f02a351f7ab0aaa688432754de0')
version('1.4.1', sha256='cfe829f56acdc785c5af21bf3927cf08327504d78c4ae1477c405c81b131da95')
version('1.2.2', sha256='9d410bb0055fffe10f1f8da55a5b24d98322c7b571d74df61427d5888332bc48')
version('1.2.1', sha256='b348e7a02623f037632c85fb11be16c40c01755ae6ca02c8c189cdc192a699db')
version('1.2.0', sha256='02a5fa8dcf8a81c061fdaefa74f17896bee913720418b44dbd226a0d6b30799d')
version('1.1.0', sha256='7b1e456a2d1056fa6284582cd82d2df66d06b3eea92e9995f5a91a45f246f69d')
depends_on('r@3.2:', type=('build', 'run'))
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-assertthat@0.2.0:', type=('build', 'run'))
depends_on('r-dbi@0.7:', type=('build', 'run'))
depends_on('r-dplyr@0.7.4:', type=('build', 'run'))
depends_on('r-dbi@1.0.0:', type=('build', 'run'))
depends_on('r-dplyr@0.8.0:', type=('build', 'run'))
depends_on('r-glue@1.2.0:', type=('build', 'run'))
depends_on('r-purrr@0.2.4:', type=('build', 'run'))
depends_on('r-purrr@0.2.5:', type=('build', 'run'))
depends_on('r-r6@2.2.2:', type=('build', 'run'))
depends_on('r-rlang@0.1.6:', type=('build', 'run'))
depends_on('r-tibble@1.4.1:', type=('build', 'run'))
depends_on('r-tidyselect@0.2.2:', type=('build', 'run'))
depends_on('r-rlang@0.2.0:', type=('build', 'run'))
depends_on('r-tibble@1.4.2:', type=('build', 'run'))
depends_on('r-tidyselect@0.2.4:', type=('build', 'run'))

19
var/spack/repos/builtin/packages/r-debugme/package.py Normal file
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@@ -0,0 +1,19 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RDebugme(RPackage):
"""Specify debug messages as special string constants, and control
debugging of packages via environment variables."""
homepage = "https://github.com/r-lib/debugme#readme"
url = "https://cloud.r-project.org/src/contrib/debugme_1.1.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/debugme"
version('1.1.0', sha256='4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1')
depends_on('r-crayon', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-deldir/package.py
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@@ -13,10 +13,12 @@ class RDeldir(RPackage):
tessellations to sub-windows. Calculates perimeters of tessellations.
Summarises information about the tiles of the tessellation."""
homepage = "https://CRAN.R-project.org/package=deldir"
url = "https://cran.r-project.org/src/contrib/deldir_0.1-14.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/deldir"
homepage = "https://cloud.r-project.org/package=deldir"
url = "https://cloud.r-project.org/src/contrib/deldir_0.1-14.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/deldir"
version('0.1-23', sha256='e0112bce9fc94daf73596a0fff9b3958b80872e3bbb487be73e157b13a6f201d')
version('0.1-21', sha256='b9dabcc1813c7a0f8edaf720a94bdd611a83baf3d3e52e861d352369e815690c')
version('0.1-14', '6a22b13d962615cd9d51b6eae403409f')
depends_on('r@0.99:')
depends_on('r@0.99:', type=('build', 'run'))

14
var/spack/repos/builtin/packages/r-dendextend/package.py
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@@ -9,15 +9,17 @@
class RDendextend(RPackage):
"""dendextend: Extending 'Dendrogram' Functionality in R"""
homepage = "https://CRAN.R-project.org/package=dendextend"
url = "https://cran.r-project.org/src/contrib/dendextend_1.5.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/dendextend"
homepage = "https://cloud.r-project.org/package=dendextend"
url = "https://cloud.r-project.org/src/contrib/dendextend_1.5.2.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/dendextend"
version('1.12.0', sha256='b487fed8c1878a23b9e28394ee11f16a1831b76c90793eb486e6963c7162fa55')
version('1.10.0', sha256='88f0fb3362d69144daf4f35d0ea09f32c2df1adf614e040327a42552a8fd3224')
version('1.5.2', '1134869d94005727c63cf3037e2f1bbf')
depends_on('r@3.0.0:')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-magrittr@1.0.1:', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-fpc', type=('build', 'run'))
depends_on('r-whisker', type=('build', 'run'))
depends_on('r-fpc', when='@:1.10.0', type=('build', 'run'))
depends_on('r-whisker', when='@:1.5.2', type=('build', 'run'))
depends_on('r-viridis', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-deoptim/package.py
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@@ -11,8 +11,9 @@ class RDeoptim(RPackage):
"""Implements the differential evolution algorithm for global optimization
of a real-valued function of a real-valued parameter vector."""
homepage = "https://cran.r-project.org/package=DEoptim"
url = "https://cran.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptim"
homepage = "https://cloud.r-project.org/package=DEoptim"
url = "https://cloud.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptim"
version('2.2-4', sha256='0a547784090d1e9b93efc53768110621f35bed3692864f6ce5c0dda2ebd6d482')
version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326')

6
var/spack/repos/builtin/packages/r-deoptimr/package.py
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@@ -11,8 +11,8 @@ class RDeoptimr(RPackage):
Evolution stochastic algorithm for global optimization of
nonlinear programming problems."""
homepage = "https://cran.r-project.org/web/packages/DEoptimR/index.html"
url = "https://cran.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptimR"
homepage = "https://cloud.r-project.org/package=DEoptimR"
url = "https://cloud.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptimR"
version('1.0-8', 'c85836a504fbe4166e3c8eba0efe705d')

6
var/spack/repos/builtin/packages/r-desc/package.py
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@@ -9,9 +9,9 @@
class RDesc(RPackage):
"""desc: Manipulate DESCRIPTION Files"""
homepage = "https://cran.r-project.org/package=desc"
url = "https://cran.r-project.org/src/contrib/desc_1.2.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/desc/"
homepage = "https://cloud.r-project.org/package=desc"
url = "https://cloud.r-project.org/src/contrib/desc_1.2.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/desc/"
version('1.2.0', sha256='e66fb5d4fc7974bc558abcdc107a1f258c9177a29dcfcf9164bc6b33dd08dae8')

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var/spack/repos/builtin/packages/r-desolve/package.py
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@@ -12,8 +12,12 @@ class RDesolve(RPackage):
equations ('PDE'), of differential algebraic equations ('DAE'), and of
delay differential equations."""
homepage = "https://cran.r-project.org/package=deSolve"
url = "https://cran.r-project.org/src/contrib/deSolve_1.20.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/deSolve"
homepage = "https://cloud.r-project.org/package=deSolve"
url = "https://cloud.r-project.org/src/contrib/deSolve_1.20.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/deSolve"
version('1.24', sha256='3aa52c822abb0348a904d5bbe738fcea2b2ba858caab9f2831125d07f0d57b42')
version('1.21', sha256='45c372d458fe4c7c11943d4c409517849b1be6782dc05bd9a74b066e67250c63')
version('1.20', '85c6a2d8568944ae8eef27ac7c35fb25')
depends_on('r@2.15.0:', type=('build', 'run'))

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@@ -10,19 +10,30 @@ class RDevtools(RPackage):
"""Collection of package development tools."""
homepage = "https://github.com/hadley/devtools"
url = "https://cran.r-project.org/src/contrib/devtools_1.12.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/devtools"
url = "https://cloud.r-project.org/src/contrib/devtools_1.12.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/devtools"
version('2.1.0', sha256='c1f75346a90adf0669b5508fe68cc78bd3b114c1303fa7d22bf90991edd9230d')
version('2.0.2', sha256='99a2fa957068254b8ecdb3fc2d50e2950230910ea31c314fc0e7d934e4bd1709')
version('1.12.0', '73b46c446273566e5b21c9f5f72aeca3')
version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2')
depends_on('r@3.0.2:')
depends_on('r@3.0.2:', type=('build', 'run'))
depends_on('r-httr@0.4:', type=('build', 'run'))
depends_on('r-memoise@1.0.0:', type=('build', 'run'))
depends_on('r-whisker', type=('build', 'run'))
depends_on('r-whisker', when='@:1.9.9', type=('build', 'run'))
depends_on('r-digest', type=('build', 'run'))
depends_on('r-rstudioapi@0.2.0:', type=('build', 'run'))
depends_on('r-rstudioapi@0.7.0:', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-git2r@0.11.0:', type=('build', 'run'))
depends_on('r-git2r@0.23.0:', type=('build', 'run'))
depends_on('r-withr', type=('build', 'run'))
depends_on('r-usethis@1.5.0:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-callr', when='@2.0.0:', type=('build', 'run'))
depends_on('r-cli', when='@2.0.0:', type=('build', 'run'))
depends_on('r-pkgbuild@1.0.3:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-pkgload@1.0.2:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-rcmdcheck@1.3.3:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-remotes@2.1.0:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-roxygen2@6.1.1:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-sessioninfo@1.1.1:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-testthat@2.1.1:', when='@2.0.0:', type=('build', 'run'))

34
var/spack/repos/builtin/packages/r-diagrammer/package.py
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@@ -10,15 +10,31 @@ class RDiagrammer(RPackage):
"""Create graph diagrams and flowcharts using R."""
homepage = "https://github.com/rich-iannone/DiagrammeR"
url = "https://cran.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/DiagrammeR"
url = "https://cloud.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/DiagrammeR"
version('1.0.1', sha256='ccee8acf608fc909e73c6de4374cef5a570cb62e5f454ac55dda736f22f3f013')
version('1.0.0', sha256='2b186dae1b19018681b979e9444bf16559c42740d8382676fbaf3b0f8a44337e')
version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a')
depends_on('r-htmlwidgets', type=('build', 'run'))
depends_on('r-igraph', type=('build', 'run'))
depends_on('r-influencer', type=('build', 'run'))
depends_on('r-rstudioapi@0.6:', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-visnetwork', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r@3.2.0:', when='@0.9.2:', type=('build', 'run'))
depends_on('r-htmlwidgets@1.0:', type=('build', 'run'))
depends_on('r-igraph@1.1.2:', type=('build', 'run'))
depends_on('r-influencer@0.1.0:', type=('build', 'run'))
depends_on('r-rstudioapi@0.7:', type=('build', 'run'))
depends_on('r-stringr@1.3.0:', type=('build', 'run'))
depends_on('r-visnetwork@2.0.3:', type=('build', 'run'))
depends_on('r-scales@0.5.0:', type=('build', 'run'))
depends_on('r-dplyr@0.7.4:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-downloader@0.4:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-glue@1.2.0:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-htmltools@0.3.6:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-magrittr@1.5:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-purrr@0.2.4:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-rcolorbrewer@1.1-2:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-readr@1.1.1:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-rlang@0.2.0:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-rgexf@0.15.3:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-tibble@1.4.2:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-tidyr@0.8.0:', when='@1.0.0:', type=('build', 'run'))
depends_on('r-viridis@0.5.0:', when='@1.0.0:', type=('build', 'run'))

5
var/spack/repos/builtin/packages/r-dicekriging/package.py
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@@ -11,7 +11,8 @@ class RDicekriging(RPackage):
functions : km, print.km, plot.km, predict.km."""
homepage = "http://dice.emse.fr/"
url = "https://cran.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/DiceKriging"
url = "https://cloud.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/DiceKriging"
version('1.5.6', sha256='25466d2db9f17083d1c7b9545e5ec88f630be934f9373c2f7b36c38de4e64e92')
version('1.5.5', 'ee3e2d7a91d4a712467ef4f0b69c2844')

8
var/spack/repos/builtin/packages/r-dichromat/package.py
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@@ -10,8 +10,10 @@ class RDichromat(RPackage):
"""Collapse red-green or green-blue distinctions to simulate the effects of
different types of color-blindness."""
homepage = "https://cran.r-project.org/web/packages/dichromat/index.html"
url = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat"
homepage = "https://cloud.r-project.org/package=dichromat"
url = "https://cloud.r-project.org/src/contrib/dichromat_2.0-0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/dichromat"
version('2.0-0', '84e194ac95a69763d740947a7ee346a6')
depends_on('r@2.10:', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-diffusionmap/package.py
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@@ -11,16 +11,17 @@ class RDiffusionmap(RPackage):
computations taking place in c++ code, and support for interrupting those
computations even in multithreaded code, typically using OpenMP."""
homepage = "https://cran.r-project.org/web/packages/diffusionMap/index.html"
url = "https://cran.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz"
list_url = "https://cran.rstudio.com/src/contrib/Archive/diffusionMap"
homepage = "https://cloud.r-project.org/package=diffusionMap"
url = "https://cloud.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/diffusionMap"
version('1.1-0.1', sha256='b24cf841af2566ac36f4ede2885f2ff355a7905398444d6d89747315d99a8486')
version('1.1-0', 'cc7d728087ba08d9299ae3a64a8d8919')
version('1.0-0', 'bca462e6efe45c5eaa48d38621f0bd6f')
version('0.0-2', 'b599f47ebf30127e34ce2219dc3e43ae')
version('0.0-1', '20c2cc2fffb5237d5c0216207016c2a1')
depends_on('r@3.4.0:3.4.9')
depends_on('r@2.4.0:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-scatterplot3d', type=('build', 'run'))
depends_on('r-igraph', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-digest/package.py
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@@ -25,11 +25,14 @@ class RDigest(RPackage):
used."""
homepage = "http://dirk.eddelbuettel.com/code/digest.html"
url = "https://cran.r-project.org/src/contrib/digest_0.6.12.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/digest"
url = "https://cloud.r-project.org/src/contrib/digest_0.6.12.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/digest"
version('0.6.20', sha256='05674b0b5d888461ff770176c67b10a11be062b0fee5dbd9298f25a9a49830c7')
version('0.6.19', sha256='28d159bd589ecbd01b8da0826eaed417f5c1bf5a11b79e76bf67ce8d935cccf4')
version('0.6.12', '738efd4d9a37c5a4001ae66e954ce07e')
version('0.6.11', '52a864f55846b48b3cab0b5d0304a82a')
version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83')
depends_on('r@2.4.1:')
depends_on('r@2.4.1:', when='@:0.6.15', type=('build', 'run'))
depends_on('r@3.1.0:', when='@0.6.16:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-diptest/package.py
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@@ -9,8 +9,8 @@
class RDiptest(RPackage):
"""diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected"""
homepage = "https://CRAN.R-project.org/package=diptest"
url = "https://cran.r-project.org/src/contrib/diptest_0.75-7.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/diptest"
homepage = "https://cloud.r-project.org/package=diptest"
url = "https://cloud.r-project.org/src/contrib/diptest_0.75-7.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/diptest"
version('0.75-7', '1a4a958fda763f7c99cb485dbe5954ab')

5
var/spack/repos/builtin/packages/r-dismo/package.py
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@@ -11,8 +11,9 @@ class RDismo(RPackage):
entire geographic distributions form occurrences at a number of sites
and the environment at these sites."""
homepage = "https://cran.r-project.org/package=dismo"
url = "https://cran.r-project.org/src/contrib/dismo_1.1-4.tar.gz"
homepage = "https://cloud.r-project.org/package=dismo"
url = "https://cloud.r-project.org/src/contrib/dismo_1.1-4.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/dismo"
version('1.1-4', sha256='f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8')

3
var/spack/repos/builtin/packages/r-diversitree/package.py
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@@ -19,9 +19,10 @@ class RDiversitree(RPackage):
rate 'speciation' and extinction."""
homepage = "http://www.zoology.ubc.ca/prog/diversitree"
url = "https://cran.r-project.org/src/contrib/diversitree_0.9-10.tar.gz"
url = "https://cloud.r-project.org/src/contrib/diversitree_0.9-10.tar.gz"
list_url = "https://cron.r-project.org/src/contrib/Archive/diversitree"
version('0.9-11', sha256='4caa6a468f93de9f1c8c30e4457f34bb8346e1acdaf74f684005bfa86a950ecb')
version('0.9-10', sha256='e7df5910c8508a5c2c2d6d3deea53dd3f947bb762196901094c32a7033cb043e')
depends_on('r@2.1.0:', type=('build', 'run'))

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