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gnu: r: Rename to r-minimal.
* gnu/packages/statistics.scm (r): Rename to... (r-minimal): ...this new variable. (r-with-recommended-packages): Rename to... (r): ...this. * guix/build-system/r.scm (default-r): Reference r-minimal. * gnu/packages/emacs.scm (emacs-ess)[inputs], gnu/packages/machine-learning.scm (shogun)[inputs], gnu/packages/python.scm (python-rpy2)[inputs], gnu/packages/bioinformatics.scm (ribotaper)[inputs], (couger)[propagated-inputs], (roary)[inputs], (rsem)[inputs], (rcas-web)[inputs]: Change "r" to "r-minimal".
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6 changed files with 15 additions and 15 deletions
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@ -478,7 +478,7 @@ (define-public ribotaper
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(inputs
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`(("bedtools" ,bedtools-2.18)
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("samtools" ,samtools-0.1)
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("r" ,r)
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("r-minimal" ,r-minimal)
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("r-foreach" ,r-foreach)
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("r-xnomial" ,r-xnomial)
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("r-domc" ,r-domc)
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@ -1728,7 +1728,7 @@ (define-public couger
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("python2-scipy" ,python2-scipy)
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("python2-matplotlib" ,python2-matplotlib)))
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(propagated-inputs
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`(("r" ,r)
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`(("r-minimal" ,r-minimal)
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("libsvm" ,libsvm)
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("randomjungle" ,randomjungle)))
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(native-inputs
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@ -4004,7 +4004,7 @@ (define-public roary
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("grep" ,grep)
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("sed" ,sed)
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("gawk" ,gawk)
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("r" ,r)
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("r-minimal" ,r-minimal)
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("r-ggplot2" ,r-ggplot2)
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("coreutils" ,coreutils)))
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(home-page "http://sanger-pathogens.github.io/Roary")
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@ -4119,7 +4119,7 @@ (define-public rsem
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(inputs
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`(("boost" ,boost)
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("ncurses" ,ncurses)
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("r" ,r)
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("r-minimal" ,r-minimal)
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("perl" ,perl)
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("samtools" ,samtools-0.1)
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("zlib" ,zlib)))
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@ -7636,7 +7636,7 @@ (define-public rcas-web
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`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
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#t)))))
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(inputs
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`(("r" ,r)
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`(("r-minimal" ,r-minimal)
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("r-rcas" ,r-rcas)
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("guile-next" ,guile-next)
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("guile-json" ,guile2.2-json)
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@ -2924,7 +2924,7 @@ (define-public emacs-ess
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(string-append "SHELL = " (which "sh")))))))))
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(inputs
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`(("emacs" ,emacs-minimal)
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("r" ,r)))
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("r-minimal" ,r-minimal)))
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(native-inputs
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`(("perl" ,perl)
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("texinfo" ,texinfo)
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@ -402,7 +402,7 @@ (define (delete-ifdefs file)
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(inputs
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`(("python" ,python)
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("numpy" ,python-numpy)
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("r" ,r)
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("r-minimal" ,r-minimal)
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("octave" ,octave)
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("swig" ,swig)
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("hdf5" ,hdf5)
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@ -4085,7 +4085,7 @@ (define-public python-rpy2
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`(("readline" ,readline)
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("icu4c" ,icu4c)
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("pcre" ,pcre)
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("r" ,r)
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("r-minimal" ,r-minimal)
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("r-survival" ,r-survival)))
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(native-inputs
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`(("zlib" ,zlib)))
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@ -103,9 +103,9 @@ (define-public pspp
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;; Update this package together with the set of recommended packages: r-boot,
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;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
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;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
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(define-public r
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(define-public r-minimal
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(package
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(name "r")
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(name "r-minimal")
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(version "3.3.3")
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(source (origin
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(method url-fetch)
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@ -538,14 +538,14 @@ (define-public r-survival
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curves, Cox models, and parametric accelerated failure time models.")
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(license license:lgpl2.0+)))
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(define-public r-with-recommended-packages
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(package (inherit r)
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(name "r-with-recommended-packages")
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(define-public r
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(package (inherit r-minimal)
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(name "r")
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(source #f)
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(build-system trivial-build-system)
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(arguments '(#:builder (mkdir %output)))
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(propagated-inputs
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`(("r" ,r)
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`(("r-minimal" ,r-minimal)
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("r-boot" ,r-boot)
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("r-class" ,r-class)
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("r-cluster" ,r-cluster)
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@ -62,7 +62,7 @@ (define (default-r)
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"Return the default R package."
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;; Lazily resolve the binding to avoid a circular dependency.
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(let ((r-mod (resolve-interface '(gnu packages statistics))))
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(module-ref r-mod 'r)))
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(module-ref r-mod 'r-minimal)))
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(define* (lower name
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#:key source inputs native-inputs outputs system target
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