diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 123 |
1 files changed, 70 insertions, 53 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6bf952734c..224c19cea3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Alex Kost <alezost@gmail.com> ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com> +;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -351,7 +352,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ("openblas" ,openblas) ("gfortran" ,gfortran) ("icu4c" ,icu4c) - ("libjpeg" ,libjpeg) + ("libjpeg" ,libjpeg-turbo) ("libpng" ,libpng) ("libtiff" ,libtiff) ("libxt" ,libxt) @@ -407,14 +408,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-24") + (version "1.3-25") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49")))) + "1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -428,14 +429,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-51.5") + (version "7.3-51.6") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26")))) + "1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -449,14 +450,14 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") (define-public r-class (package (name "r-class") - (version "7.3-16") + (version "7.3-17") (source (origin (method url-fetch) (uri (cran-uri "class" version)) (sha256 (base32 - "1jpdgj0lsi60q0mqbhfw809w8d66whix27y6wpdzll6775g3j3ll")))) + "04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -512,14 +513,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-78") + (version "0.8-79") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "01anirfbfa3ip5pyqv72cg4x7p0jsppmbvxrllw7bm28fl1hgiyq")))) + "1d5rk4k3khjrir1b4ciridd6vdpcgzi35r7p7ra4ky7vbaabcdmg")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -532,14 +533,14 @@ for reading and writing some dBase files.") (define-public r-kernsmooth (package (name "r-kernsmooth") - (version "2.23-16") + (version "2.23-17") (source (origin (method url-fetch) (uri (cran-uri "KernSmooth" version)) (sha256 (base32 - "1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq")))) + "11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b")))) (properties `((upstream-name . "KernSmooth"))) (build-system r-build-system) (native-inputs @@ -643,14 +644,14 @@ distributions beyond the exponential family.") (define-public r-nnet (package (name "r-nnet") - (version "7.3-13") + (version "7.3-14") (source (origin (method url-fetch) (uri (cran-uri "nnet" version)) (sha256 (base32 - "1z0rj5cm4ycw1y0gd5wwwg8c2298v90iybgqdqh17967jbi2125f")))) + "1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx")))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Feed-forward neural networks and multinomial log-linear models") @@ -681,14 +682,14 @@ classification, regression and survival trees.") (define-public r-spatial (package (name "r-spatial") - (version "7.3-11") + (version "7.3-12") (source (origin (method url-fetch) (uri (cran-uri "spatial" version)) (sha256 (base32 - "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32")))) + "0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn")))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Functions for kriging and point pattern analysis") @@ -1614,13 +1615,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "1a0h3dr519p3jj6aygbhwi9f2zwlan6d07f1gkh2db56y5vaq7yd")))) + "1jik4lywg4688dfi5fh8jbnmsxvq3382ii0nsw5armjzfq3v309s")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -2370,13 +2371,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.26.1") + (version "0.27.1") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk")))) + "1h1vfzym6hi1fqs9p5z5v0f4xldggr425frw8k6dsidah3qhg4h9")))) (build-system r-build-system) (inputs `(("libgit2" ,libgit2) @@ -2588,13 +2589,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.860.2.0") + (version "0.9.870.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1rg9ak0zbv8d9cyj10jq52nrcbk1pvfz28kbkhpx79mpjhrl7pb5")))) + "1r7iajxvbyvslsy16rqacc95azmjciw9lvcq31xl97fl09kmsq5v")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -3669,14 +3670,14 @@ more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "1bwwsljkg1bxh7xnqxv7n0n1s9y8x407i6lsv826vy1ss1k1fxpy")))) + "14rqx4dq574hilmdwrr34wyjg8rlw4rvndpsqd9plgxm3wwfsdg6")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -3684,6 +3685,8 @@ more complete @code{viridis} package.") ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/tidyselect") (synopsis "Select from a set of strings") (description @@ -3696,14 +3699,14 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "0safj8bcf8libwr0jx4059bmarngvhfddrcv8k5iw39m9lpxs0r4")))) + "18ypk63nifp5jj5d9880m49zdv7n4a18gac59wj5z5xk6qr7vfal")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3718,6 +3721,8 @@ selection.") ("r-stringi" ,r-stringi) ("r-tibble" ,r-tibble) ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/tidyr") (synopsis "Tidy data with `spread()` and `gather()` functions") (description @@ -4112,14 +4117,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-6") + (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "04fvjdab6vyyghyqy0abxvfbyr1myz6yib7ibwiyjw9yf7fjrcjp")))) + "12g6m8sf17q3qmm133nm4fa296w5n5d9ly3fvb2nvc0w4llkif3l")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -4241,18 +4246,20 @@ including: (define-public r-rocr (package (name "r-rocr") - (version "1.0-7") + (version "1.0-11") (source (origin (method url-fetch) (uri (cran-uri "ROCR" version)) (sha256 (base32 - "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7")))) + "0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p")))) (properties `((upstream-name . "ROCR"))) (build-system r-build-system) (propagated-inputs `(("r-gplots" ,r-gplots))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://rocr.bioinf.mpi-sb.mpg.de/") (synopsis "Visualizing the performance of scoring classifiers") (description @@ -4271,13 +4278,13 @@ mechanism.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-7") + (version "1.8-8") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "1w4542zs53bm261g95086a60576v334g1jrhnbgdqni4izf2s1wy")))) + "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -4957,16 +4964,16 @@ groupings.") (define-public r-vgam (package (name "r-vgam") - (version "1.1-2") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 - (base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq")))) + (base32 "1hwlrdx3nhdp83pvy1h23i16vbbhi4kizdhr58c8nvg7kqdzb7qc")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) - (inputs + (native-inputs `(("gfortran" ,gfortran))) (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM") (synopsis "Vector generalized linear and additive models") @@ -5280,14 +5287,14 @@ even in multithreaded code, typically using OpenMP.") (define-public r-mnormt (package (name "r-mnormt") - (version "1.5-6") + (version "1.5-7") (source (origin (method url-fetch) (uri (cran-uri "mnormt" version)) (sha256 (base32 - "0k8y08gj6z525yvc7y3dl2kzgnafbj3i7lvpamypsmqxf74zql99")))) + "1y0vlvh02wza2wvfd29wxjlw3jg9rnwnx3kph5qz4179kz87fgfg")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5786,42 +5793,51 @@ Java package that provides routines for various statistical distributions.") (define-public emacs-ess (package (name "emacs-ess") - (version "17.11") + (version "18.10.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/emacs-ess/ESS/archive/v" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-ess/ESS") + (commit (string-append "v" version)))) (sha256 (base32 - "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c")) - (file-name (string-append name "-" version ".tar.gz")) + "1yq41l2bicwjrc0b731iic20cpcnz6ppigri1jn621qv2qv22vy3")) + (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet '(begin ;; Stop ESS from trying to bundle an external julia-mode.el. (substitute* "lisp/Makefile" - (("^\tjulia-mode.elc\\\\\n") "") - (("^dist: all julia-mode.el") - "dist: all")) - ;; No need to build docs in so many formats. Also, skipping - ;; pdf lets us not pull in texlive. + (("^ess-julia.elc: julia-mode.elc") "") + (("^all: julia-mode.el") + "all:")) + ;; Include *.el files in install target. + (substitute* "lisp/Makefile" + (("\t\\$\\(INSTALL) \\$\\(ELC\\) \\$\\(LISPDIR\\)" elc) + (string-append "\t$(INSTALL) $(ELS) ess-autoloads.el " + "$(LISPDIR)\n" elc))) + ;; Only build docs in info format. (substitute* "doc/Makefile" - (("all : info text html pdf") + (("all : info text") "all : info") (("install: install-info install-other-docs") "install: install-info")) - ;; Test fails upstream + ;; Stop install-info from trying to update the info directory. + (substitute* "doc/Makefile" + ((".*\\$\\(INFODIR\\)/dir.*") "")) + ;; Fix roxygen preview test. (substitute* "test/ess-r-tests.el" - (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()") - "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed")) + (("Add together two numbers.\n") + "Add together two numbers. ") + (("##' add\\(10, 1\\)") "add(10, 1)")) #t)))) (build-system gnu-build-system) (arguments (let ((base-directory "/share/emacs/site-lisp")) `(#:make-flags (list (string-append "PREFIX=" %output) - (string-append "ETCDIR=" %output "/" + (string-append "ETCDIR=" %output ,base-directory "/etc") - (string-append "LISPDIR=" %output "/" + (string-append "LISPDIR=" %output ,base-directory)) #:phases (modify-phases %standard-phases @@ -5840,6 +5856,7 @@ Java package that provides routines for various statistical distributions.") ("r-minimal" ,r-minimal))) (native-inputs `(("perl" ,perl) + ("r-roxygen2" ,r-roxygen2) ("texinfo" ,texinfo))) (propagated-inputs `(("emacs-julia-mode" ,emacs-julia-mode))) |