diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 385 |
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+))) |