diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 353 |
1 files changed, 311 insertions, 42 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0ac35a909b..bc95fd2aa4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35,6 +35,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) @@ -113,16 +114,18 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.") (define-public r-selectr (package (name "r-selectr") - (version "0.3-2") + (version "0.4-1") (source (origin (method url-fetch) (uri (cran-uri "selectr" version)) (sha256 (base32 - "0kdrj64rqg4z6hg92y9r2h602a2i73r5rnlpg23ys33d5d32n8jy")))) + "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b")))) (build-system r-build-system) - (propagated-inputs `(("r-stringr" ,r-stringr))) + (propagated-inputs + `(("r-stringr" ,r-stringr) + ("r-r6" ,r-r6))) (home-page "https://sjp.co.nz/projects/selectr/") (synopsis "Translate CSS selectors to XPath expressions") (description @@ -190,14 +193,14 @@ that.") (define-public r-readxl (package (name "r-readxl") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 - "1bf7gxw9r11m4llyymplxiaa4gzgyj4bwmwad5in756pzq3jzmpv")))) + "05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) @@ -404,14 +407,14 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-plogr (package (name "r-plogr") - (version "0.1-1") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "plogr" version)) (sha256 (base32 - "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) + "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/plogr") (synopsis "R bindings for the plog C++ logging library") @@ -424,13 +427,13 @@ error stream.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.15") + (version "0.12.16") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1pnv6sl4vdn69ygmgrb1b3gsigfdcfb56wnzikic93l8gkvdsvxv")))) + (base32 "1rm8hcy72p1jvxikvmkwg20pjqmvmfvqb45lfghmddp2adp67qfl")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -448,14 +451,14 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see (define-public r-bindr (package (name "r-bindr") - (version "0.1") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "bindr" version)) (sha256 (base32 - "0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc")))) + "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/bindr") (synopsis "Parametrized active bindings") @@ -467,14 +470,14 @@ where the bound function accepts additional arguments.") (define-public r-bindrcpp (package (name "r-bindrcpp") - (version "0.2") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "bindrcpp" version)) (sha256 (base32 - "0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh")))) + "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) (build-system r-build-system) (propagated-inputs `(("r-bindr" ,r-bindr) @@ -554,14 +557,14 @@ ellipses, circles, cylinders, arrows, ...") (define-public r-globaloptions (package (name "r-globaloptions") - (version "0.0.12") + (version "0.0.13") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 - "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0")))) + "04jvha0mafslqz5nr99xjylg9n2x31gj9v4mgyg7qcmfwpqyw3ch")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (home-page "https://github.com/jokergoo/GlobalOptions") @@ -936,19 +939,21 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-6") + (version "0.6-7") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "0fm6z049aaq2c9xagm8n64d9560hg9d8hyb0m359fii672nhkz6q")))) + "1b62gs7w1xqadqd7ir41jnxlcf14gcqfxd0915kn9ckdlsdrh0sw")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\""))) (inputs `(("openmpi" ,openmpi))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") (synopsis "R interface to message-passing interface (MPI)") (description @@ -1364,14 +1369,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "02xf5d968raz9gnq5ywy04wz29xpdyca1hm79vbbg1mcxvzdl1dz")))) + "11k9npmzp3nk2qx0h1dwwfc37j4ddd9y54bppxby0ffnb8qlpw1k")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -1411,14 +1416,14 @@ regression using Kernel Ridge Regression.") (define-public r-prodlim (package (name "r-prodlim") - (version "1.6.1") + (version "2018.04.18") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 - "0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz")))) + "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb")))) (build-system r-build-system) (propagated-inputs `(("r-kernsmooth" ,r-kernsmooth) @@ -1476,21 +1481,75 @@ Engineering and Computational Finance\" and for managing chronological and calendar objects.") (license license:gpl2+))) +(define-public r-magic + (package + (name "r-magic") + (version "1.5-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "magic" version)) + (sha256 + (base32 + "083cgpp3v03li0h8597b3g21pd9lkbmn9pyssblnhc800mpc52vz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind))) + (home-page "https://github.com/RobinHankin/magic.git") + (synopsis "Create and investigate magic squares") + (description + "This package provides a collection of efficient, vectorized algorithms +for the creation and investigation of magic squares and hypercubes, including +a variety of functions for the manipulation and analysis of arbitrarily +dimensioned arrays.") + (license license:gpl2))) + +(define-public r-geometry + (package + (name "r-geometry") + (version "0.3-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "geometry" version)) + (sha256 + (base32 + "0s09vi0rr0smys3an83mz6fk41bplxyz4myrbiinf4qpk6n33qib")))) + (build-system r-build-system) + (propagated-inputs `(("r-magic" ,r-magic))) + (home-page "http://geometry.r-forge.r-project.org/") + (synopsis "Mesh generation and surface tesselation") + (description + "This package makes the qhull library available in R, in a similar manner +as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace +intersections about a point, Voronoi diagrams, furthest-site Delaunay +triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, +and higher dimensions. It implements the Quickhull algorithm for computing +the convex hull. Qhull does not support constrained Delaunay triangulations, +or mesh generation of non-convex objects, but the package does include some R +functions that allow for this. Currently the package only gives access to +Delaunay triangulation and convex hull computation.") + ;; The Qhull sources are included and are distributed under a custom + ;; non-copyleft license. The R sources are released under GPL version 2. + (license (list license:gpl2 + (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) + (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.1.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "13w8ir5rd80rka4mq343zd4wn93vfw870lzfqrd3cxgwb1bwcw7y")))) + "1i2zcz20zy9xd42kdz09njbkq07mj2pp6f07z6dnwi5hrmvhbh9r")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-class" ,r-class) + ("r-geometry" ,r-geometry) ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-robustbase" ,r-robustbase) @@ -1761,14 +1820,14 @@ color labels, layout, etc.") (define-public r-stringdist (package (name "r-stringdist") - (version "0.9.4.6") + (version "0.9.4.7") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 - "0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci")))) + "1qg80wmcrpkba9njvgjdg15bgw7ddks40kkfh5x61as9lhchy4i4")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") @@ -1986,14 +2045,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.10-1") + (version "0.10-2") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "1j9ddh9v9081zrqlpylsk13fldilhjdyaw6r6pa726fhgnrsf8a2")))) + "1i11fczks4lh8rpi6xbm9bm7f3jpcp6xw03kv178g3n3361qhmc1")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (native-inputs `(("gfortran" ,gfortran))) @@ -2172,19 +2231,20 @@ plotting. a three dimensional point cloud.") (define-public r-ggridges (package (name "r-ggridges") - (version "0.4.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 - "0kfa3icqdalqdg1klxjrhfl7if35d3wnsiyl86bprw5dyqyh3lh3")))) + "1znvsbl3px8dddpjgdrygnpz4s685wizi0jnjvx2hrz58i0chjqj")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales))) + ("r-scales" ,r-scales) + ("r-withr" ,r-withr))) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description @@ -2511,14 +2571,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1ryd7m570y6q3w71wd5dz042b3d0dv24g2rbkw1kdx0n6jj9gsbd")))) + "1kmqvny3rw4p5kgxz6mhqfpp7j3nnpp22dfai4kjrr2cfmj6wvb7")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2555,14 +2615,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.3") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0mhxlr4709mca9jshnah5i7yjyy6k12s933619p7p9c8nbqj39cn")))) + "1pg4jfyvandjwz3lmr38pbqi9d045iwkk3xklhsfhhxq6aviq9p7")))) (build-system r-build-system) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") @@ -2577,14 +2637,14 @@ automatically.") (define-public r-metap (package (name "r-metap") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "06ny9zkilawdy0s8yiwhnygs3yppw89bbyf76zgdavykbzscz5lh")))) + "03vg0mb6q7j2z0pkxykbak0hcp6dcak7zxs1lw9hswz9kqrq5jhz")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -2775,14 +2835,14 @@ Cambridge University Press, 1993.") (define-public r-quantmod (package (name "r-quantmod") - (version "0.4-12") + (version "0.4-13") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 - "0y7gh0k1s10vdsfch8777avbhf99mc9crikvx7ahqrw0j631vmhq")))) + "16aldg96z7amp5mr90nb8127yy04gxsihfr26km5p3cx3j117yv0")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -3323,14 +3383,14 @@ It also includes interpolation functions.") (define-public r-psych (package (name "r-psych") - (version "1.7.8") + (version "1.8.3.3") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k")))) + "1zhp8j81nkzd65168zdw9ylypb9n07ajan21x0wqcn8jdbg970sg")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -3354,14 +3414,14 @@ serve as a useful front end for structural equation modeling.") (define-public r-gsubfn (package (name "r-gsubfn") - (version "0.6-6") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "gsubfn" version)) (sha256 (base32 - "196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv")))) + "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) (propagated-inputs `(("r-proto" ,r-proto))) (home-page "http://gsubfn.googlecode.com") @@ -3704,3 +3764,212 @@ selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.") (license license:gpl3+))) + +(define-public r-openxlsx + (package + (name "r-openxlsx") + (version "4.0.17") + (source + (origin + (method url-fetch) + (uri (cran-uri "openxlsx" version)) + (sha256 + (base32 + "1mq4lasp12kc30sxcsmz9gskd114l8s7z7wd6svv2nm8qllrhsqi")))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/awalker89/openxlsx") + (synopsis "Read, write and edit XLSX files") + (description + "This package simplifies the creation of Excel @code{.xlsx} files by +providing a high level interface to writing, styling and editing worksheets. +Through the use of Rcpp, read/write times are comparable to the @code{xlsx} +and @code{XLConnect} packages with the added benefit of removing the +dependency on Java.") + (license license:gpl3))) + +(define-public r-rio + (package + (name "r-rio") + (version "0.5.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "rio" version)) + (sha256 + (base32 + "158xg3vj0glk3fslwi6fywwmfym2b6kn3fdmjligdfy5lf68khix")))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-data-table" ,r-data-table) + ("r-foreign" ,r-foreign) + ("r-haven" ,r-haven) + ("r-openxlsx" ,r-openxlsx) + ("r-readxl" ,r-readxl) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/leeper/rio") + (synopsis "Swiss-army knife for data I/O") + (description + "This package provides streamlined data import and export infrastructure +by making assumptions that the user is probably willing to make: @code{import} +and @code{export} determine the data structure from the file extension, +reasonable defaults are used for data import and export (e.g., +@code{stringsAsFactors=FALSE}), web-based import is natively +supported (including from SSL/HTTPS), compressed files can be read directly +without explicit decompression, and fast import packages are used where +appropriate. An additional convenience function, @code{convert}, provides a +simple method for converting between file types.") + (license license:gpl2))) + +(define-public r-maptools + (package + (name "r-maptools") + (version "0.9-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "maptools" version)) + (sha256 + (base32 + "075lmb3b62171cw2dg8fv1vwmvfzg39r1ji7jwb8s5k9dz88ry1v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreign" ,r-foreign) + ("r-lattice" ,r-lattice) + ("r-sp" ,r-sp))) + (home-page "http://r-forge.r-project.org/projects/maptools/") + (synopsis "Tools for reading and handling spatial objects") + (description + "This package provides a set of tools for manipulating and reading +geographic data, in particular ESRI Shapefiles. It includes binary access to +GSHHG shoreline files. The package also provides interface wrappers for +exchanging spatial objects with other R packages.") + ;; The C source files from shapelib are released under the Expat license. + ;; The R code is released under GPL version 2 or later. + (license (list license:gpl2+ + license:expat)))) + +(define-public r-later + (package + (name "r-later") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "later" version)) + (sha256 + (base32 + "0z9jymmclkq9zcg1fd8p6gsnm5z1sn3n9pfz3bs03qjrkbizgrvz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang))) + (home-page "https://github.com/r-lib/later") + (synopsis "Utilities for delaying function execution") + (description + "This package provides tools to execute arbitrary R or C functions some +time after the current time, after the R execution stack has emptied.") + (license license:gpl2+))) + +(define-public r-promises + (package + (name "r-promises") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "promises" version)) + (sha256 + (base32 + "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-later" ,r-later) + ("r-magrittr" ,r-magrittr) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang))) + (home-page "https://rstudio.github.io/promises") + (synopsis "Abstractions for promise-based asynchronous programming") + (description + "This package provides fundamental abstractions for doing asynchronous +programming in R using promises. Asynchronous programming is useful for +allowing a single R process to orchestrate multiple tasks in the background +while also attending to something else. Semantics are similar to JavaScript +promises, but with a syntax that is idiomatic R.") + (license license:expat))) + +(define-public r-dosnow + (package + (name "r-dosnow") + (version "1.0.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "doSNOW" version)) + (sha256 + (base32 + "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n")))) + (properties `((upstream-name . "doSNOW"))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-snow" ,r-snow))) + (home-page "https://cran.r-project.org/web/packages/doSNOW") + (synopsis "Foreach parallel adaptor for the snow package") + (description + "This package provides a parallel backend for the @code{%dopar%} function +using the @code{snow} package.") + (license license:gpl2))) + +(define-public r-snowfall + (package + (name "r-snowfall") + (version "1.84-6.1") + (source (origin + (method url-fetch) + (uri (cran-uri "snowfall" version)) + (sha256 + (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) + (build-system r-build-system) + (propagated-inputs + `(("r-snow" ,r-snow))) + (home-page "http://cran.r-project.org/web/packages/snowfall/") + (synopsis "Easier cluster computing") + (description "This package is a usability wrapper around snow for easier +development of parallel R programs. This package offers e.g. extended error +checks, and additional functions. All functions work in sequential mode, too, +if no cluster is present or wished. The package is also designed as connector +to the cluster management tool @code{sfCluster}, but can also used without +it.") + (license license:gpl2+))) + +(define-public r-codedepends + (package + (name "r-codedepends") + (version "0.5-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "CodeDepends" version)) + (sha256 + (base32 + "03p82s0abca2jimzqvxdzykfzca7c7fhm5xsjxybcksr4gggr5sc")))) + (properties `((upstream-name . "CodeDepends"))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-xml" ,r-xml))) + (home-page "http://cran.r-project.org/web/packages/CodeDepends") + (synopsis "Analysis of R code for reproducible research and code comprehension") + (description + "This package provides tools for analyzing R expressions or blocks of +code and determining the dependencies between them. It focuses on R scripts, +but can be used on the bodies of functions. There are many facilities +including the ability to summarize or get a high-level view of code, +determining dependencies between variables, code improvement suggestions.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) |