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-rw-r--r--gnu/packages/statistics.scm385
1 files changed, 382 insertions, 3 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index ac7cb4677e..29cd34a4f3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -22,6 +22,7 @@
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
@@ -67,7 +68,11 @@
(add-before
'check 'set-timezone
;; Some tests require the timezone to be set.
- (lambda _ (setenv "TZ" "UTC") #t)))
+ (lambda _ (setenv "TZ" "UTC") #t))
+ (add-after 'build 'make-info
+ (lambda _ (zero? (system* "make" "info"))))
+ (add-after 'build 'install-info
+ (lambda _ (zero? (system* "make" "install-info")))))
#:configure-flags
'("--with-blas=openblas"
"--with-lapack"
@@ -83,11 +88,20 @@
"--with-system-pcre"
"--with-system-tre"
"--with-system-xz")))
+ ;; R has some support for Java. When the JDK is available at configure
+ ;; time environment variables pointing to the JDK will be recorded under
+ ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
+ ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
+ ;; the recorded environment variables in $R_HOME/etc. Refer to
+ ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
+ ;; for additional information.
+
+ ;; As the JDK is a rather large input with only very limited effects on R,
+ ;; we decided to drop it.
(native-inputs
`(("bzip2" ,bzip2)
("perl" ,perl)
("pkg-config" ,pkg-config)
- ("texlive" ,texlive) ; needed to make vignettes
("texinfo" ,texinfo) ; for building HTML manuals
("which" ,which) ; for tests/Examples/base-Ex.R
("xz" ,xz)))
@@ -96,7 +110,6 @@
("cairo" ,cairo)
("gfortran" ,gfortran)
("icu4c" ,icu4c)
- ("icedtea6" ,icedtea6 "jdk")
("lapack" ,lapack)
("libjpeg" ,libjpeg)
("libpng" ,libpng)
@@ -119,3 +132,369 @@ and clustering. It also provides robust support for producing
publication-quality data plots. A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
(license license:gpl3+)))
+
+(define-public r-colorspace
+ (package
+ (name "r-colorspace")
+ (version "1.2-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/colorspace_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/colorspace")
+ (synopsis "Color space manipulation")
+ (description
+ "This package carries out a mapping between assorted color spaces
+including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
+CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
+colors are provided.")
+ (license license:bsd-3)))
+
+(define-public r-dichromat
+ (package
+ (name "r-dichromat")
+ (version "2.0-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/dichromat_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/dichromat")
+ (synopsis "Color schemes for dichromats")
+ (description
+ "Dichromat collapses red-green or green-blue distinctions to simulate the
+effects of different types of color-blindness.")
+ (license license:gpl2+)))
+
+(define-public r-digest
+ (package
+ (name "r-digest")
+ (version "0.6.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/digest_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih"))))
+ (build-system r-build-system)
+ (home-page "http://dirk.eddelbuettel.com/code/digest.html")
+ (synopsis "Create cryptographic hash digests of R objects")
+ (description
+ "This package contains an implementation of a function 'digest()' for the
+creation of hash digests of arbitrary R objects (using the md5, sha-1,
+sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
+of R language objects, as well as a function 'hmac()' to create hash-based
+message authentication code.
+
+Please note that this package is not meant to be deployed for cryptographic
+purposes for which more comprehensive (and widely tested) libraries such as
+OpenSSL should be used.")
+ (license license:gpl2+)))
+
+(define-public r-gtable
+ (package
+ (name "r-gtable")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/gtable_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/gtable")
+ (synopsis "R library to arrange grobs in tables")
+ (description
+ "Gtable is a collection of tools to make it easier to work with
+\"tables\" of grobs.")
+ (license license:gpl2+)))
+
+(define-public r-labeling
+ (package
+ (name "r-labeling")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/labeling_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/labeling")
+ (synopsis "Axis labeling algorithms")
+ (description "The labeling package provides a range of axis labeling
+algorithms.")
+ (license license:expat)))
+
+(define-public r-magrittr
+ (package
+ (name "r-magrittr")
+ (version "1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/magrittr_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
+ (synopsis "A forward-pipe operator for R")
+ (description
+ "Magrittr provides a mechanism for chaining commands with a new
+forward-pipe operator, %>%. This operator will forward a value, or the result
+of an expression, into the next function call/expression. There is flexible
+support for the type of right-hand side expressions. For more information,
+see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
+ (license license:expat)))
+
+(define-public r-munsell
+ (package
+ (name "r-munsell")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/munsell_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-colorspace" ,r-colorspace)))
+ (home-page "http://cran.r-project.org/web/packages/munsell")
+ (synopsis "Munsell colour system")
+ (description
+ "The Munsell package contains Functions for exploring and using the
+Munsell colour system.")
+ (license license:expat)))
+
+(define-public r-rcpp
+ (package
+ (name "r-rcpp")
+ (version "0.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/Rcpp_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38"))))
+ (build-system r-build-system)
+ (home-page "http://www.rcpp.org")
+ (synopsis "Seamless R and C++ Integration")
+ (description
+ "The Rcpp package provides R functions as well as C++ classes which offer
+a seamless integration of R and C++. Many R data types and objects can be
+mapped back and forth to C++ equivalents which facilitates both writing of new
+code as well as easier integration of third-party libraries. Documentation
+about Rcpp is provided by several vignettes included in this package, via the
+'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
+and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
+'citation(\"Rcpp\")' for details on these last two.")
+ (license license:gpl2+)))
+
+(define-public r-plyr
+ (package
+ (name "r-plyr")
+ (version "1.8.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/plyr_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
+ (build-system r-build-system)
+ (native-inputs `(("r-rcpp" ,r-rcpp)))
+ (home-page "http://had.co.nz/plyr")
+ (synopsis "Tools for Splitting, Applying and Combining Data")
+ (description
+ "Plyr is a set of tools that solves a common set of problems: you need to
+break a big problem down into manageable pieces, operate on each piece and
+then put all the pieces back together. For example, you might want to fit a
+model to each spatial location or time point in your study, summarise data by
+panels or collapse high-dimensional arrays to simpler summary statistics.")
+ (license license:expat)))
+
+(define-public r-proto
+ (package
+ (name "r-proto")
+ (version "0.3-10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/proto_" version ".tar.gz"))
+ (sha256
+ (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
+ (build-system r-build-system)
+ (home-page "http://r-proto.googlecode.com")
+ (synopsis "Prototype object-based programming")
+ (description
+ "Proto is an object oriented system using object-based, also called
+prototype-based, rather than class-based object oriented ideas.")
+ (license license:gpl2+)))
+
+(define-public r-rcolorbrewer
+ (package
+ (name "r-rcolorbrewer")
+ (version "1.1-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/RColorBrewer_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
+ (synopsis "ColorBrewer palettes")
+ (description
+ "This package provides color schemes for maps (and other graphics)
+designed by Cynthia Brewer as described at http://colorbrewer2.org")
+ ;; Includes code licensed under bsd-4
+ (license license:asl2.0)))
+
+(define-public r-stringi
+ (package
+ (name "r-stringi")
+ (version "0.5-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://cran/src/contrib/stringi_"
+ version
+ ".tar.gz"))
+ (sha256
+ (base32
+ "183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw"))))
+ (build-system r-build-system)
+ (inputs `(("icu4c" ,icu4c)))
+ (native-inputs `(("pkg-config" ,pkg-config)))
+ (home-page "http://stringi.rexamine.com/")
+ (synopsis "Character string processing facilities")
+ (description
+ "This package allows for fast, correct, consistent, portable, as well as
+convenient character string/text processing in every locale and any native
+encoding. Owing to the use of the ICU library, the package provides R users
+with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
+programmers. Among available features there are: pattern searching
+ (e.g. via regular expressions), random string generation, string collation,
+transliteration, concatenation, date-time formatting and parsing, etc.")
+ (license license:bsd-3)))
+
+(define-public r-stringr
+ (package
+ (name "r-stringr")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/stringr_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-magrittr" ,r-magrittr)
+ ("r-stringi" ,r-stringi)))
+ (home-page "https://github.com/hadley/stringr")
+ (synopsis "Simple, consistent wrappers for common string operations")
+ (description
+ "Stringr is a consistent, simple and easy to use set of wrappers around
+the fantastic 'stringi' package. All function and argument names (and
+positions) are consistent, all functions deal with \"NA\"'s and zero length
+vectors in the same way, and the output from one function is easy to feed into
+the input of another.")
+ (license license:gpl2+)))
+
+(define-public r-reshape2
+ (package
+ (name "r-reshape2")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/reshape2_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-plyr" ,r-plyr)
+ ("r-rcpp" ,r-rcpp)
+ ("r-stringr" ,r-stringr)))
+ (home-page "https://github.com/hadley/reshape")
+ (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
+ (description
+ "Reshape2 is an R library to flexibly restructure and aggregate data
+using just two functions: melt and dcast (or acast).")
+ (license license:expat)))
+
+(define-public r-scales
+ (package
+ (name "r-scales")
+ (version "0.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/scales_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "12xrmn1vh64dl46bq7n7pa427aicb2ifjrby9in3m32nyvir0kac"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dichromat" ,r-dichromat)
+ ("r-labeling" ,r-labeling)
+ ("r-munsell" ,r-munsell)
+ ("r-plyr" ,r-plyr)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/hadley/scales")
+ (synopsis "Scale functions for visualization")
+ (description
+ "This package provides graphical scales that map data to aesthetics, and
+provides methods for automatically determining breaks and labels for axes and
+legends.")
+ (license license:expat)))
+
+(define-public r-ggplot2
+ (package
+ (name "r-ggplot2")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/ggplot2_"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0794kjqi3lrxb33lr1mykd58959hlgkhdn259vj8fxrh65mqw920"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-digest" ,r-digest)
+ ("r-gtable" ,r-gtable)
+ ("r-plyr" ,r-plyr)
+ ("r-proto" ,r-proto)
+ ("r-reshape2" ,r-reshape2)
+ ("r-scales" ,r-scales)))
+ (home-page "http://ggplot2.org")
+ (synopsis "An implementation of the grammar of graphics")
+ (description
+ "Ggplot2 is an implementation of the grammar of graphics in R. It
+combines the advantages of both base and lattice graphics: conditioning and
+shared axes are handled automatically, and you can still build up a plot step
+by step from multiple data sources. It also implements a sophisticated
+multidimensional conditioning system and a consistent interface to map data to
+aesthetic attributes.")
+ (license license:gpl2+)))