diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 186 |
1 files changed, 85 insertions, 101 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 64b7d820b4..9fae9575e8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31,7 +31,7 @@ ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net> ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com> -;;; Copyright © 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2020-2023, 2025 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com> ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> @@ -39,7 +39,7 @@ ;;; Copyright © 2022 Greg Hogan <code@greghogan.com> ;;; Copyright © 2023 Kyle Andrews <kyle@posteo.net> ;;; Copyright © 2024 Marco Baggio <guix@mawumag.com> -;;; Copyright © 2024, 2025 Spencer King <spencer.king@geneoscopy.com> +;;; Copyright © 2024, 2025 Spencer King <spencer.king@wustl.edu> ;;; Copyright © 2024-2025 Tor-björn Claesson <tclaesson@gmail.com> ;;; ;;; This file is part of GNU Guix. @@ -103,6 +103,7 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) #:use-module (gnu packages node) + #:use-module (gnu packages ocr) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) @@ -15563,6 +15564,30 @@ link (lines and ribbons), and text (gene) label. All functions require only R graphics packages that comes with the base installation.") (license license:gpl2+))) +(define-public r-circstats + (package + (name "r-circstats") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "CircStats" version)) + (sha256 + (base32 "07bg4zrs2iqh0pmi44pybi8hlvnxwcaa5zpg85rmf55kflxxkzlf")))) + (properties `((upstream-name . "CircStats"))) + (build-system r-build-system) + (arguments + (list + #:tests? #f)) + (propagated-inputs (list r-boot r-mass)) + (home-page "https://cran.r-project.org/package=CircStats") + (synopsis + "Circular Statistics, from \"Topics in Circular Statistics\" (2001)") + (description + "Circular Statistics, from \"Topics in Circular Statistics\" (2001) S. Rao +Jammalamadaka and A. @code{SenGupta}, World Scientific.") + (license license:gpl2))) + (define-public r-ctrdata (package (name "r-ctrdata") @@ -28722,7 +28747,7 @@ package works as intended.") `((upstream-name . "gitcreds") (updater-extra-native-inputs . ("r-mockery" "r-codetools")))) (build-system r-build-system) - (inputs (list git-minimal)) + (inputs (list git-minimal/pinned)) (native-inputs (list r-codetools r-knitr r-mockery r-testthat)) (home-page "https://github.com/r-lib/gitcreds") (synopsis "Query git credentials from R") @@ -28836,7 +28861,7 @@ terminals that do not support Unicode.") ;; This is necessary because git looks for $HOME/.gitconfig (setenv "HOME" "/tmp")))))) (inputs - (list git-minimal)) + (list git-minimal/pinned)) (propagated-inputs (list r-askpass r-curl r-jsonlite r-openssl r-sys)) (native-inputs @@ -38057,14 +38082,14 @@ offers access to an XPath \"interpreter\".") (define-public r-xml2 (package (name "r-xml2") - (version "1.3.8") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "01qhmlr5rhsn25ddb8cm3vl9vyqk5c5cgpc6c0krs9wccd1j4pbj")))) + "0qnw4id8bknm3anvd9dlpg344s18dnxzm8lhbyqkcpgqfya84bhc")))) (properties ;; Avoid dependency cycle. '((updater-ignored-native-inputs . ("r-httr")))) @@ -53413,21 +53438,40 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-stringfish (package (name "r-stringfish") - (version "0.16.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 - "14vrg6mkwwgw1klgpvjn7936yfxav55rainz71xjjih2j21vq21n")))) + "0x6nad21q7shsl7wjzldb6si7j09dyxksrpq29cxphh79d0ga2ly")))) (properties '((upstream-name . "stringfish") (updater-extra-inputs . ("pcre2")))) (build-system r-build-system) - ;; Tests require r-qs, which depends on this package. - (arguments (list #:tests? #false)) - (inputs (list pcre2)) + (arguments + (list + ;; Tests require r-qs, which depends on this package. + #:tests? #false + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-system-tbb + (lambda _ + (setenv "TBB_ROOT" #$(this-package-input "tbb")))) + (add-before 'install 'relax-gcc-14-strictness + (lambda _ + ;; XXX FIXME: $HOME/.R/Makevars seems to be the only way to + ;; set custom CFLAGS for R? + (setenv "HOME" (getcwd)) + (mkdir-p ".R") + (with-directory-excursion ".R" + (with-output-to-file "Makevars" + (lambda _ + (display (string-append + "CXXFLAGS=-g -O2" + " -Wno-error=changes-meaning\n")))))))))) + (inputs (list pcre2 tbb-2020)) (propagated-inputs (list r-rcpp r-rcppparallel)) (native-inputs @@ -53532,96 +53576,6 @@ functions to retrieve the directory of the latest run or latest several runs.") (license license:asl2.0))) -(define-public r-tfautograph - (package - (name "r-tfautograph") - (version "0.3.2") - (source - (origin - (method url-fetch) - (uri (cran-uri "tfautograph" version)) - (sha256 - (base32 - "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2")))) - (properties `((upstream-name . "tfautograph"))) - (build-system r-build-system) - (inputs (list tensorflow)) - (propagated-inputs - (list r-backports r-reticulate)) - (native-inputs (list r-testthat)) - (home-page "https://t-kalinowski.github.io/tfautograph/") - (synopsis "Autograph R for Tensorflow") - (description - "This package lets you translate R control flow expressions into -Tensorflow graphs.") - (license license:gpl3))) - -(define-public r-tensorflow - (package - (name "r-tensorflow") - (version "2.16.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "tensorflow" version)) - (sha256 - (base32 - "113ikbg2k56zigxwgxy242vxpikxkfkv150wn21zyfn9885wgbzm")))) - (properties `((upstream-name . "tensorflow"))) - (build-system r-build-system) - (propagated-inputs - (list r-config - r-lifecycle - r-processx - r-reticulate - r-rstudioapi - r-tfautograph - r-tfruns - r-yaml)) - (native-inputs (list r-testthat)) - (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 "2.15.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "keras" version)) - (sha256 - (base32 - "0xahkgww3dzp8vjz0456sn6ihz0w0q0dz1gnmx07r2vx81isirvc")))) - (properties `((upstream-name . "keras"))) - (build-system r-build-system) - (propagated-inputs - (list r-generics - r-glue - r-magrittr - r-r6 - r-reticulate - r-rlang - r-tensorflow - r-tfruns - r-zeallot)) - (native-inputs (list r-knitr r-testthat)) - (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))) - (define-public r-zzlite (package (name "r-zzlite") @@ -55480,6 +55434,36 @@ or animation) or multiple time series; methods for spatial and temporal matching or aggregation, retrieving coordinates, print, summary, etc.") (license license:gpl2+))) +(define-public r-tesseract + (package + (name "r-tesseract") + (version "5.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tesseract" version)) + (sha256 + (base32 "181fbv1qhqxljr67phkrxahbfgsxa73gzq30zq0wvi38gzbfbnv8")))) + (properties `((upstream-name . "tesseract"))) + (build-system r-build-system) + (inputs (list tesseract-ocr + zlib)) + (propagated-inputs (list r-curl + r-digest + r-pdftools + r-rappdirs + r-rcpp)) + (native-inputs (list pkg-config + r-knitr + r-spelling)) + (home-page "https://github.com/ropensci/tesseract") + (synopsis "Open Source OCR Engine") + (description + "Bindings to @code{tesseract}: an optical character recognition (OCR) engine +that supports over 100 languages. The engine is highly configurable in order +to tune the detection algorithms and obtain the best possible results.") + (license license:asl2.0))) + (define-public r-gstat (package (name "r-gstat") |