diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 302 |
1 files changed, 262 insertions, 40 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7231f9a94f..872d8d6f1a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -591,14 +591,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "17j8b46vn0kdpm7x6xyfqzz3la8mwzhjql6dbgyvqnrylbx4svyl")))) + "0m2wq9kqlxqxlzyx9fd0c4iw6qb7kpjrq7fqqa2kvwyj79vx6ahj")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -638,21 +638,19 @@ variables.") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "1vfzhpd4bqskq1sxh60dkab02m51g0dhj9i8mfqqbakhmkqggxa3")))) + "0ma0xcwjgj0sp9483s2y62ylv992dqjxqfgb3zl8f1pksypqdbac")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) - ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-ggpp" ,r-ggpp) - ("r-gridextra" ,r-gridextra) ("r-lubridate" ,r-lubridate) ("r-mass" ,r-mass) ("r-plyr" ,r-plyr) @@ -661,10 +659,7 @@ variables.") ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-splus2r" ,r-splus2r) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://www.r4photobiology.info/") @@ -2774,20 +2769,18 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "2.4.1") + (version "2.4.3") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "1san6dc7kg2wy6f1jr5p1br28zdrand8wwgg7p6xxnx45h773320")) + "0pr9jcdk1r9pi9iz0xm1g5yy5qyjk5r7hh9467abx4kpwx3hzdwm")) (modules '((guix build utils))) (snippet - '(begin - ;; unvendor readstat - (delete-file-recursively "src/readstat") - #t)))) + ;; unvendor readstat + '(delete-file-recursively "src/readstat")))) (build-system r-build-system) (arguments '(#:phases @@ -2796,8 +2789,7 @@ including functions for geolocation and routing.") (lambda _ ;; Not required, since we’re not building readstat. (substitute* "src/Makevars" - (("-lz") "-lreadstat")) - #t))))) + (("-lz") "-lreadstat"))))))) (inputs `(("readstat" ,readstat))) (native-inputs @@ -2812,10 +2804,10 @@ including functions for geolocation and routing.") ("r-tidyselect" ,r-tidyselect) ("r-vctrs" ,r-vctrs))) (home-page "https://haven.tidyverse.org") - (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") + (synopsis "Import and export SPSS, Stata and SAS files") (description - "This package lets you mport foreign statistical formats into R via the -embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") + "This package lets you import foreign statistical formats into R via the +@url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (license license:expat))) (define-public r-amap @@ -8427,14 +8419,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "16z79rvxkgdg0xq21f5aykikg6vjaiw1p9j9q42k2bz8qdswfd3b")))) + "0ks43z6vvdz0d0jv5d2qrm12yb4cwvi7p3kjk6byi4farhh368di")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -10296,24 +10288,24 @@ analysis.") (define-public r-tab (package (name "r-tab") - (version "4.1.1") + (version "5.1.1") (source (origin (method url-fetch) (uri (cran-uri "tab" version)) (sha256 (base32 - "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm")))) + "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv")))) (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) - ("r-gee" ,r-gee) + ("r-kableextra" ,r-kableextra) ("r-knitr" ,r-knitr) ("r-mass" ,r-mass) - ("r-survey" ,r-survey) - ("r-survival" ,r-survival) - ("r-xtable" ,r-xtable))) + ("r-survey" ,r-survey))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description @@ -11723,14 +11715,14 @@ address a bug.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.18") + (version "0.0.19") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4")))) + "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs @@ -16990,14 +16982,14 @@ package.") (define-public r-ggplotify (package (name "r-ggplotify") - (version "0.0.7") + (version "0.0.8") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 - "1vx2fg91ivssrxr4kzs9737hr8bsfs0q5pvd7lck7ffjpkjbclhh")))) + "08c9vxm8pg6l5g3r7wsfgzsq00xdrc6v4xnn7pd3qcyw7cc8s969")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -21003,14 +20995,14 @@ provided as well.") (define-public r-tuner (package (name "r-tuner") - (version "1.3.3") + (version "1.3.3.1") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 - "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx")))) + "12nixpqrc5gp7p2clr7ia6jwb0jq2i3brlxiwlp00ixmnm5g1jyd")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs `(("r-signal" ,r-signal))) @@ -25815,14 +25807,14 @@ simple interface for all functions.") (define-public r-iml (package (name "r-iml") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "iml" version)) (sha256 (base32 - "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7")))) + "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r")))) (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs @@ -25832,7 +25824,7 @@ simple interface for all functions.") ("r-future" ,r-future) ("r-future-apply" ,r-future-apply) ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) + ("r-keras" ,r-keras) ("r-metrics" ,r-metrics) ("r-prediction" ,r-prediction) ("r-r6" ,r-r6))) @@ -27716,16 +27708,18 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.19.3") + (version "1.20") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57")))) + "1h9i158czlzwbn5zakkqd2ggc9g90r73vdspmp6kgfcmy9frvwzz")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/MALDIquant") (synopsis "Quantitative analysis of mass spectrometry data") (description @@ -29957,3 +29951,231 @@ applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user stack based on Apache2.") (license license:asl2.0))) + +(define-public r-exactextractr + (package + (name "r-exactextractr") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "exactextractr" version)) + (sha256 + (base32 + "1xnccadbj03h7m81ix5qn0hx918xc9hbxnzgv5lr3hf8b26i9wni")))) + (properties `((upstream-name . "exactextractr"))) + (build-system r-build-system) + (inputs `(("geos" ,geos))) + (propagated-inputs + `(("r-raster" ,r-raster) + ("r-rcpp" ,r-rcpp) + ("r-sf" ,r-sf))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://isciences.gitlab.io/exactextractr/") + (synopsis "Fast extraction from raster datasets using polygons") + (description + "This package provides a replacement for the @code{extract} function from +the @code{raster} package that is suitable for extracting raster values using +@code{sf} polygons.") + (license license:asl2.0))) + +(define-public r-stringfish + (package + (name "r-stringfish") + (version "0.15.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "stringfish" version)) + (sha256 + (base32 + "0m8485p1gb5z2n2g5nyr38zixw4iv8xxm7bxspxlxvx6alhn03pn")))) + (properties `((upstream-name . "stringfish"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/traversc/stringfish") + (synopsis "Alternative string implementation") + (description + "This package provides an extendable, performant and multithreaded +@code{alt-string} implementation backed by C++ vectors and strings.") + (license license:gpl3))) + +(define-public r-rapiserialize + (package + (name "r-rapiserialize") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RApiSerialize" version)) + (sha256 + (base32 + "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j")))) + (properties `((upstream-name . "RApiSerialize"))) + (build-system r-build-system) + (home-page + "https://cran.r-project.org/package=RApiSerialize") + (synopsis "R API serialization") + (description + "This package provides other packages with access to the internal R +serialization code. Access to this code is provided at the C function level +by using the registration of native function mechanism. Client packages +simply include a single header file RApiSerializeAPI.h provided by this +package.") + (license license:gpl2+))) + +(define-public r-qs + (package + (name "r-qs") + (version "0.25.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "qs" version)) + (sha256 + (base32 + "0qzrhc5jsygj813k956b00h4b6haynz44rk6a4v34fv4ywq9ba7w")))) + (properties `((upstream-name . "qs"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-rapiserialize" ,r-rapiserialize) + ("r-rcpp" ,r-rcpp) + ("r-stringfish" ,r-stringfish))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/traversc/qs") + (synopsis "Quick serialization of R objects") + (description + "This package provides functions for quickly writing and reading any R +object to and from disk.") + (license license:gpl3))) + +(define-public r-rgeos + (package + (name "r-rgeos") + (version "0.5-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "rgeos" version)) + (sha256 + (base32 + "086l0qk3p4jq23bs91c4a65x4qz99z0hy0vsnvfqfvppdzz0vajb")))) + (properties `((upstream-name . "rgeos"))) + (build-system r-build-system) + (inputs + `(("geos" ,geos))) + (propagated-inputs + `(("r-sp" ,r-sp))) + (home-page "https://cran.r-project.org/package=rgeos") + (synopsis "Interface to Geometry Engine (GEOS)") + (description + "This package provides an R interface to Geometry Engine (GEOS) using the +C API for topology operations on geometries.") + (license license:gpl2+))) + +(define-public r-tfruns + (package + (name "r-tfruns") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tfruns" version)) + (sha256 + (base32 + "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9")))) + (properties `((upstream-name . "tfruns"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-config" ,r-config) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-reticulate" ,r-reticulate) + ("r-rlang" ,r-rlang) + ("r-rstudioapi" ,r-rstudioapi) + ("r-tidyselect" ,r-tidyselect) + ("r-whisker" ,r-whisker) + ("r-yaml" ,r-yaml))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/rstudio/tfruns") + (synopsis "Training run tools for TensorFlow") + (description + "Create and manage unique directories for each TensorFlow training run. +This package provides a unique, time stamped directory for each run along with +functions to retrieve the directory of the latest run or latest several +runs.") + (license license:asl2.0))) + +(define-public r-tensorflow + (package + (name "r-tensorflow") + (version "2.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tensorflow" version)) + (sha256 + (base32 + "00g9w4xmdyjl4578kmhng58k7afjkj2vwgcq2ik8rqwljkcz5pph")))) + (properties `((upstream-name . "tensorflow"))) + (build-system r-build-system) + (inputs `(("tensorflow" ,tensorflow))) + (propagated-inputs + `(("r-config" ,r-config) + ("r-jsonlite" ,r-jsonlite) + ("r-processx" ,r-processx) + ("r-reticulate" ,r-reticulate) + ("r-rstudioapi" ,r-rstudioapi) + ("r-tfruns" ,r-tfruns) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/rstudio/tensorflow") + (synopsis "R interface to TensorFlow") + (description + "R interface to TensorFlow a library for numerical computation using data +flow graphs. Nodes in the graph represent mathematical operations, while the +graph edges represent the multidimensional data arrays (tensors) communicated +between them.") + (license license:asl2.0))) + +(define-public r-keras + (package + (name "r-keras") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "keras" version)) + (sha256 + (base32 + "00bw5f5d81md8db1k6bf2a91by4k25xvlwxiwv188y4vw3bfc7md")))) + (properties `((upstream-name . "keras"))) + (build-system r-build-system) + (propagated-inputs + `(("r-generics" ,r-generics) + ("r-magrittr" ,r-magrittr) + ("r-r6" ,r-r6) + ("r-reticulate" ,r-reticulate) + ("r-rlang" ,r-rlang) + ("r-tensorflow" ,r-tensorflow) + ("r-tfruns" ,r-tfruns) + ("r-zeallot" ,r-zeallot))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://keras.rstudio.com") + (synopsis "R Interface to 'Keras'") + (description + "This package provides an interface to Keras, a high-level neural +networks API. Keras was developed with a focus on enabling fast +experimentation, supports both convolution based networks and recurrent +networks (as well as combinations of the two), and runs seamlessly on both CPU +and GPU devices.") + (license license:expat))) |