diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 343 |
1 files changed, 309 insertions, 34 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 040c2ead4a..8277026c32 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> @@ -15,7 +15,7 @@ ;;; Copyright © 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> -;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net> +;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> ;;; @@ -62,6 +62,7 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages javascript) + #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -2361,21 +2362,44 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and ;; Any version of the LGPL. (license license:lgpl3+))) +(define-public r-bdsmatrix + (package + (name "r-bdsmatrix") + (version "1.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "bdsmatrix" version)) + (sha256 + (base32 + "17ddvz4gnih7rx0lr1gzk280xyh6x796cf2x794dvplpiiq83skh")))) + (properties `((upstream-name . "bdsmatrix"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/bdsmatrix/") + (synopsis "Routines for block diagonal symmetric matrices") + (description + "This package provides procedures to work with block diagonal symmetric +matrices, a special case of sparse matrices.") + (license license:lgpl2.0))) + (define-public r-bbmle (package (name "r-bbmle") - (version "1.0.20") + (version "1.0.22") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 - "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc")))) + "1idn55w5f3iw4r0ydyww8xyinninw07sxlwfqb565vmdrs87dwl4")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) + `(("r-bdsmatrix" ,r-bdsmatrix) + ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mvtnorm" ,r-mvtnorm) ("r-numderiv" ,r-numderiv))) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") @@ -2991,14 +3015,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "1.8.12") + (version "1.9.12") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf")))) + "13r7fyjsl93m121awnwfhya8a0lw0l2byn60yqdbf9gp3lmb9ny0")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -3080,14 +3104,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98")))) + "1n32qc2a3n9cykm8dv9qcr77kdhqfsjiqf6kgfk9s0lnpx2zaldm")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -4047,14 +4071,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv")))) + "0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -4086,14 +4110,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms")))) + "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -5721,18 +5745,19 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.13") + (version "1.14") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd")))) + "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) + `(("r-rappdirs" ,r-rappdirs) + ("r-jsonlite" ,r-jsonlite) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstudio/reticulate") @@ -5747,14 +5772,14 @@ Python to R they are converted back to R types.") (define-public r-bibtex (package (name "r-bibtex") - (version "0.4.2") + (version "0.4.2.1") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 - "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz")))) + "1ks1w59ldwmfd1sj8ap7smyhf8dhykv7xnwrl8z9xzkcfpv1rbc0")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) (home-page "https://github.com/romainfrancois/bibtex") @@ -6871,14 +6896,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (define-public r-rootsolve (package (name "r-rootsolve") - (version "1.8.1") + (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 - "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx")))) + "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6929,13 +6954,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-46") + (version "0.1-47") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b")))) + (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -12550,6 +12575,12 @@ running IRkernel session.") "--name" "ir" "--prefix" out (string-append out "/site-library/IRkernel/kernelspec")) + ;; Record the absolute file name of the 'R' executable in + ;; 'kernel.json'. + (substitute* (string-append out "/share/jupyter" + "/kernels/ir/kernel.json") + (("\\[\"R\",") + (string-append "[\"" (which "R") "\","))) #t)))))) (inputs `(("jupyter" ,jupyter))) @@ -12559,6 +12590,8 @@ running IRkernel session.") ("r-evaluate" ,r-evaluate) ("r-irdisplay" ,r-irdisplay) ("r-jsonlite" ,r-jsonlite) + ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) + ("r-minimal" ,r-minimal) ("r-pbdzmq" ,r-pbdzmq) ("r-repr" ,r-repr) ("r-uuid" ,r-uuid))) @@ -14885,18 +14918,17 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (define-public r-sctransform (package (name "r-sctransform") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 - "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p")))) + "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn")))) (build-system r-build-system) (propagated-inputs - `(("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) + `(("r-future-apply" ,r-future-apply) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-mass" ,r-mass) @@ -15172,14 +15204,14 @@ annotated biological functions.") (define-public r-plot3d (package (name "r-plot3d") - (version "1.1.1") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 - "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn")))) + "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs `(("r-misc3d" ,r-misc3d))) @@ -15904,19 +15936,18 @@ PROJ.4 library.") (define-public r-insol (package (name "r-insol") - (version "1.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "insol" version)) (sha256 (base32 - "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5")))) + "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1")))) (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rgdal" ,r-rgdal))) + `(("r-raster" ,r-raster))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://meteoexploration.com/R/insol/index.html") @@ -16007,13 +16038,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.25") + (version "1.27") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp")))) + (base32 "1qhjq4vxlxd9qmhf6i26x1k7bzhldlxzbby1zgcplicdvlqk951d")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs @@ -18966,3 +18997,247 @@ algorithm to identify key players, and Valente's bridging metric. The betweenness, Key Players, and bridging implementations are parallelized with OpenMP.") (license license:gpl2))) + +(define-public r-emplik + (package + (name "r-emplik") + (version "1.0-4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "emplik" version)) + (sha256 + (base32 + "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c")))) + (properties `((upstream-name . "emplik"))) + (build-system r-build-system) + (propagated-inputs + `(("r-quantreg" ,r-quantreg))) + (home-page "http://www.ms.uky.edu/~mai/EmpLik.html") + (synopsis "Empirical likelihood ratio for censored/truncated data") + (description + "This package provides empirical likelihood ratio tests for +means/quantiles/hazards from possibly censored and/or truncated data. It also +does regression.") + (license license:gpl2+))) + +(define-public r-imputeyn + (package + (name "r-imputeyn") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "imputeYn" version)) + (sha256 + (base32 + "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs")))) + (properties `((upstream-name . "imputeYn"))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-emplik" ,r-emplik) + ("r-mvtnorm" ,r-mvtnorm) + ("r-quadprog" ,r-quadprog) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/imputeYn/") + (synopsis "Impute last largest censored observation under weighted least squares") + (description + "This package allows for the imputation of the last largest censored +observantions. This method brings less bias and more efficient estimates for +AFT models.") + (license license:gpl2))) + +(define-public r-adapenetclass + (package + (name "r-adapenetclass") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "AdapEnetClass" version)) + (sha256 + (base32 + "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc")))) + (properties `((upstream-name . "AdapEnetClass"))) + (build-system r-build-system) + (propagated-inputs + `(("r-glmnet" ,r-glmnet) + ("r-imputeyn" ,r-imputeyn) + ("r-lars" ,r-lars) + ("r-quadprog" ,r-quadprog))) + (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/") + (synopsis "Class of adaptive elastic net methods for censored data") + (description + "This package provides methods for variable selection for AFT models.") + (license license:gpl2))) + +(define-public r-flock + (package + (name "r-flock") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "flock" version)) + (sha256 + (base32 + "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7")))) + (properties `((upstream-name . "flock"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/flock/") + (synopsis "Process synchronization using file locks") + (description + "This package implements synchronization between R processes (spawned by +using the @code{parallel} package for instance) using file locks. It supports +both exclusive and shared locking.") + (license license:asl2.0))) + +(define-public r-archivist + (package + (name "r-archivist") + (version "2.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "archivist" version)) + (sha256 + (base32 + "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7")))) + (properties `((upstream-name . "archivist"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dbi" ,r-dbi) + ("r-digest" ,r-digest) + ("r-flock" ,r-flock) + ("r-httr" ,r-httr) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite))) + (home-page "https://pbiecek.github.io/archivist/") + (synopsis "Tools for storing, restoring and searching for R objects") + (description + "Data exploration and modelling is a process in which a lot of data +artifacts are produced. Artifacts like: subsets, data aggregates, plots, +statistical models, different versions of data sets and different versions of +results. Archivist helps to store and manage artifacts created in R. It +allows you to store selected artifacts as binary files together with their +metadata and relations. Archivist allows sharing artifacts with others. It +can look for already created artifacts by using its class, name, date of the +creation or other properties. It also makes it easy to restore such +artifacts.") + (license license:gpl2))) + +(define-public r-versions + (package + (name "r-versions") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "versions" version)) + (sha256 + (base32 + "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd")))) + (properties `((upstream-name . "versions"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/versions/") + (synopsis "Query and install specific versions of CRAN packages") + (description + "This package allows you to install specified versions of R packages +hosted on CRAN and provides functions to list available versions and the +versions of currently installed packages.") + (license license:bsd-3))) + +(define-public r-adapr + (package + (name "r-adapr") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "adapr" version)) + (sha256 + (base32 + "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw")))) + (properties `((upstream-name . "adapr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-archivist" ,r-archivist) + ("r-devtools" ,r-devtools) + ("r-digest" ,r-digest) + ("r-doparallel" ,r-doparallel) + ("r-gdata" ,r-gdata) + ("r-ggplot2" ,r-ggplot2) + ("r-git2r" ,r-git2r) + ("r-igraph" ,r-igraph) + ("r-knitr" ,r-knitr) + ("r-plotly" ,r-plotly) + ("r-plyr" ,r-plyr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard) + ("r-versions" ,r-versions))) + (home-page "https://cran.r-project.org/web/packages/adapr/") + (synopsis "Implementation of an accountable data analysis process") + (description + "This package tracks reading and writing within R scripts that are +organized into a directed acyclic graph. It contains an interactive Shiny +application @code{adaprApp()}. It uses Git and file hashes to track version +histories of inputs and outputs.") + (license license:lgpl2.0))) + +(define-public r-adapsamp + (package + (name "r-adapsamp") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AdapSamp" version)) + (sha256 + (base32 + "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis")))) + (properties `((upstream-name . "AdapSamp"))) + (build-system r-build-system) + (propagated-inputs `(("r-pracma" ,r-pracma))) + (home-page "https://cran.r-project.org/web/packages/AdapSamp/") + (synopsis "Adaptive sampling algorithms") + (description + "For distributions whose probability density functions are log-concave, +the adaptive rejection sampling algorithm can be used to build envelope +functions for sampling. For others, the modified adaptive rejection sampling +algorithm, the concave-convex adaptive rejection sampling algorithm, and the +adaptive slice sampling algorithm can be used. This R package mainly includes +these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and +@code{rASS()}. These functions can realize sampling based on the algorithms +above.") + (license license:gpl2))) + +(define-public r-adaptalint + (package + (name "r-adaptalint") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "adaptalint" version)) + (sha256 + (base32 + "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf")))) + (properties `((upstream-name . "adaptalint"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-lintr" ,r-lintr) + ("r-purrr" ,r-purrr))) + (home-page "https://cran.r-project.org/web/packages/adaptalint/") + (synopsis "Check R code style") + (description + "This package provides tools to infer the code style (which style rules +are followed and which ones are not) from one package and use it to check +another. This makes it easier to find and correct the most important problems +first.") + (license license:gpl3))) |