diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 670 |
1 files changed, 369 insertions, 301 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3a66e611e4..d17061205f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015-2023 Ricardo Wurmus <[email protected]> +;;; Copyright © 2015-2024 Ricardo Wurmus <[email protected]> ;;; Copyright © 2015 Vicente Vera Parra <[email protected]> ;;; Copyright © 2016 Andreas Enge <[email protected]> ;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner <[email protected]> @@ -18,6 +18,7 @@ ;;; Copyright © 2021 Frank Pursel <[email protected]> ;;; Copyright © 2022 Simon Tournier <[email protected]> ;;; Copyright © 2023 gemmaro <[email protected]> +;;; Copyright © 2023 Felix Gruber <[email protected]> ;;; Copyright © 2023 Troy Figiel <[email protected]> ;;; ;;; This file is part of GNU Guix. @@ -114,7 +115,7 @@ (define-public pspp (package (name "pspp") - (version "1.4.1") + (version "2.0.0") (source (origin (method url-fetch) @@ -122,11 +123,16 @@ version ".tar.gz")) (sha256 (base32 - "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan")))) + "1pyqlab9kw65wxc8pilcwb64l18w37xxdg3r6n287c7mda4cpxm8")))) (build-system gnu-build-system) (arguments (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'patch-test-suite + (lambda _ + (substitute* "tests/output/tex.at" + (("AT_CHECK\\(\\[LC_ALL=C.UTF-8 pspp") + "AT_CHECK([LC_ALL=en_US.UTF-8 pspp")))) (add-before 'check 'prepare-tests ;; Prevent irrelevant errors that cause test output mismatches: ;; ‘Fontconfig error: No writable cache directories’ @@ -148,7 +154,7 @@ `(,glib "bin") ;for glib-genmarshal perl pkg-config - python-2 ;for tests + python-3 ;for tests texinfo)) (home-page "https://www.gnu.org/software/pspp/") (synopsis "Statistical analysis") @@ -228,157 +234,162 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") "0aj51j34q2b28y28xvlf0dwdj8vpnhjwpvqf7xm05s7fq857dxdk")))) (build-system gnu-build-system) (arguments - `(#:disallowed-references (,tzdata-for-tests) - #:make-flags - (list (string-append "LDFLAGS=-Wl,-rpath=" - (assoc-ref %outputs "out") - "/lib/R/lib") - ;; This affects the embedded timestamp of only the core packages. - "PKG_BUILT_STAMP=1970-01-01") - #:phases - (modify-phases %standard-phases - (add-before 'configure 'do-not-compress-serialized-files - (lambda* (#:key inputs #:allow-other-keys) - ;; This ensures that Guix can detect embedded store references; - ;; see bug #28157 for details. - (substitute* "src/library/base/makebasedb.R" - (("compress = TRUE") "compress = FALSE")))) - (add-before 'configure 'patch-coreutils-paths - (lambda* (#:key inputs #:allow-other-keys) - (let ((uname-bin (search-input-file inputs "/bin/uname")) - (rm-bin (search-input-file inputs "/bin/rm"))) - (substitute* "src/scripts/R.sh.in" - (("uname") uname-bin)) - (substitute* "src/unix/sys-std.c" - (("rm -Rf ") (string-append rm-bin " -Rf "))) - (substitute* "src/library/parallel/R/detectCores.R" - (("'grep") - (string-append "'" - (search-input-file inputs "/bin/grep"))) - (("\\| wc -l") - (string-append "| " - (search-input-file inputs "/bin/wc") - " -l")))))) - (add-after 'unpack 'patch-tests - (lambda _ - ;; This is needed because R is run during the check phase and - ;; /bin/sh doesn't exist in the build container. - (substitute* "src/unix/sys-unix.c" - (("\"/bin/sh\"") - (string-append "\"" (which "sh") "\""))) - ;; This test fails because line numbers are off by two. - (substitute* "tests/reg-packages.R" - (("8 <= print" m) (string-append "## " m))))) - (add-after 'unpack 'build-reproducibly - (lambda _ - ;; The documentation contains time stamps to demonstrate - ;; documentation generation in different phases. - (substitute* "src/library/tools/man/Rd2HTML.Rd" - (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S") - "(removed for reproducibility)")) - - ;; Remove timestamp from tracing environment. This fixes - ;; reproducibility of "methods.rd{b,x}". - (substitute* "src/library/methods/R/trace.R" - (("dateCreated = Sys.time\\(\\)") - "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")")) - - ;; Ensure that gzipped files are reproducible. - (substitute* '("src/library/grDevices/Makefile.in" - "doc/manual/Makefile.in") - (("R_GZIPCMD\\)" line) - (string-append line " -n"))) - - ;; The "srcfile" procedure in "src/library/base/R/srcfile.R" - ;; queries the mtime of a given file and records it in an object. - ;; This is acceptable at runtime to detect stale source files, - ;; but it destroys reproducibility at build time. - - ;; Similarly, the "srcfilecopy" procedure records the current - ;; time. We change both of them to respect SOURCE_DATE_EPOCH. - (substitute* "src/library/base/R/srcfile.R" - (("timestamp <- (timestamp.*|file.mtime.*)" _ time) - (string-append "timestamp <- \ + (list + #:disallowed-references `(,tzdata-for-tests) + #:make-flags + #~(list (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib/R/lib") + ;; This affects the embedded timestamp of only the core packages. + "PKG_BUILT_STAMP=1970-01-01") + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'do-not-compress-serialized-files + (lambda _ + ;; This ensures that Guix can detect embedded store references; + ;; see bug #28157 for details. + (substitute* "src/library/base/makebasedb.R" + (("compress = TRUE") "compress = FALSE")) + (substitute* '("src/library/tools/Makefile.in" + "share/make/basepkg.mk" + "share/make/lazycomp.mk") + (("makeLazyLoading\\(") + "makeLazyLoading(compress=FALSE,")))) + (add-before 'configure 'patch-coreutils-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ((uname-bin (search-input-file inputs "/bin/uname")) + (rm-bin (search-input-file inputs "/bin/rm"))) + (substitute* "src/scripts/R.sh.in" + (("uname") uname-bin)) + (substitute* "src/unix/sys-std.c" + (("rm -Rf ") (string-append rm-bin " -Rf "))) + (substitute* "src/library/parallel/R/detectCores.R" + (("'grep") + (string-append "'" + (search-input-file inputs "/bin/grep"))) + (("\\| wc -l") + (string-append "| " + (search-input-file inputs "/bin/wc") + " -l")))))) + (add-after 'unpack 'patch-tests + (lambda _ + ;; This is needed because R is run during the check phase and + ;; /bin/sh doesn't exist in the build container. + (substitute* "src/unix/sys-unix.c" + (("\"/bin/sh\"") + (string-append "\"" (which "sh") "\""))) + ;; This test fails because line numbers are off by two. + (substitute* "tests/reg-packages.R" + (("8 <= print" m) (string-append "## " m))))) + (add-after 'unpack 'build-reproducibly + (lambda _ + ;; The documentation contains time stamps to demonstrate + ;; documentation generation in different phases. + (substitute* "src/library/tools/man/Rd2HTML.Rd" + (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S") + "(removed for reproducibility)")) + + ;; Remove timestamp from tracing environment. This fixes + ;; reproducibility of "methods.rd{b,x}". + (substitute* "src/library/methods/R/trace.R" + (("dateCreated = Sys.time\\(\\)") + "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")")) + + ;; Ensure that gzipped files are reproducible. + (substitute* '("src/library/grDevices/Makefile.in" + "doc/manual/Makefile.in") + (("R_GZIPCMD\\)" line) + (string-append line " -n"))) + + ;; The "srcfile" procedure in "src/library/base/R/srcfile.R" + ;; queries the mtime of a given file and records it in an object. + ;; This is acceptable at runtime to detect stale source files, + ;; but it destroys reproducibility at build time. + + ;; Similarly, the "srcfilecopy" procedure records the current + ;; time. We change both of them to respect SOURCE_DATE_EPOCH. + (substitute* "src/library/base/R/srcfile.R" + (("timestamp <- (timestamp.*|file.mtime.*)" _ time) + (string-append "timestamp <- \ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\ } else { " time "}, origin=\"1970-01-01\")\n"))) - ;; This library is installed using "install_package_description", - ;; so we need to pass the "builtStamp" argument. - (substitute* "src/library/tools/Makefile.in" - (("(install_package_description\\(.*\"')\\)\"" line prefix) - (string-append prefix ", builtStamp='1970-01-01')\""))) - - (substitute* "src/library/Recommended/Makefile.in" - (("INSTALL_OPTS =" m) - (string-append m " --built-timestamp=1970-01-01" m))) - - ;; R bundles an older version of help2man, which does not respect - ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man, - ;; because that breaks a test. - (with-fluids ((%default-port-encoding "ISO-8859-1")) - (substitute* "tools/help2man.pl" - (("my \\$date = strftime \"%B %Y\", localtime" line) - (string-append line " 1")))) - - ;; The "References" section of this file when converted to - ;; package.rds is sometimes stored with a newline, sometimes with - ;; a space. We avoid this problem by removing the line break - ;; that is suspected to be the culprit. - (substitute* "src/library/methods/DESCRIPTION.in" - (("\\(2008\\)\n") "(2008) ") - ((" ``Software") "``Software") - (("Data Analysis:.") "Data Analysis:\n") - (("Programming with R") " Programming with R")) - (substitute* "src/library/tools/DESCRIPTION.in" - (("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr") - "codetools, methods, xml2, curl, commonmark, + ;; This library is installed using "install_package_description", + ;; so we need to pass the "builtStamp" argument. + (substitute* "src/library/tools/Makefile.in" + (("(install_package_description\\(.*\"')\\)\"" line prefix) + (string-append prefix ", builtStamp='1970-01-01')\""))) + + (substitute* "src/library/Recommended/Makefile.in" + (("INSTALL_OPTS =" m) + (string-append m " --built-timestamp=1970-01-01" m))) + + ;; R bundles an older version of help2man, which does not respect + ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man, + ;; because that breaks a test. + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* "tools/help2man.pl" + (("my \\$date = strftime \"%B %Y\", localtime" line) + (string-append line " 1")))) + + ;; The "References" section of this file when converted to + ;; package.rds is sometimes stored with a newline, sometimes with + ;; a space. We avoid this problem by removing the line break + ;; that is suspected to be the culprit. + (substitute* "src/library/methods/DESCRIPTION.in" + (("\\(2008\\)\n") "(2008) ") + ((" ``Software") "``Software") + (("Data Analysis:.") "Data Analysis:\n") + (("Programming with R") " Programming with R")) + (substitute* "src/library/tools/DESCRIPTION.in" + (("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr") + "codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr")))) - (add-before 'build 'set-locales - (lambda _ - (setlocale LC_ALL "C") - (setenv "LC_ALL" "C"))) - (add-before 'configure 'set-default-pager - ;; Set default pager to "cat", because otherwise it is "false", - ;; making "help()" print nothing at all. - (lambda _ (setenv "PAGER" "cat"))) - (add-before 'configure 'set-timezone - ;; Some tests require the timezone to be set. However, the - ;; timezone may not just be "UTC", or else a brittle regression - ;; test in reg-tests-1d will fail. - ;; We also need TZ during the configure step. - (lambda* (#:key inputs #:allow-other-keys) - (setenv "TZ" "UTC+1") - (setenv "TZDIR" - (search-input-directory inputs - "share/zoneinfo")))) - (add-before 'check 'set-home - ;; Some tests require that HOME be set. - (lambda _ (setenv "HOME" "/tmp"))) - (add-after 'build 'make-info - (lambda _ (invoke "make" "info"))) - (add-after 'build 'install-info - (lambda _ (invoke "make" "install-info")))) + (add-before 'build 'set-locales + (lambda _ + (setlocale LC_ALL "C") + (setenv "LC_ALL" "C"))) + (add-before 'configure 'set-default-pager + ;; Set default pager to "cat", because otherwise it is "false", + ;; making "help()" print nothing at all. + (lambda _ (setenv "PAGER" "cat"))) + (add-before 'configure 'set-timezone + ;; Some tests require the timezone to be set. However, the + ;; timezone may not just be "UTC", or else a brittle regression + ;; test in reg-tests-1d will fail. + ;; We also need TZ during the configure step. + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo")))) + (add-before 'check 'set-home + ;; Some tests require that HOME be set. + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'build 'make-info + (lambda _ (invoke "make" "info"))) + (add-after 'build 'install-info + (lambda _ (invoke "make" "install-info")))) #:configure-flags - `(;; We build the recommended packages here, because they are needed in - ;; order to run the test suite. We disable them in the r-minimal - ;; package. - "--with-cairo" - "--with-blas=-lopenblas" - "--with-libpng" - "--with-jpeglib" - "--with-libtiff" - "--with-ICU" - "--with-tcltk" - ,(string-append "--with-tcl-config=" - (assoc-ref %build-inputs "tcl") + #~(list + ;; We build the recommended packages here, because they are needed in + ;; order to run the test suite. We disable them in the r-minimal + ;; package. + "--with-cairo" + "--with-blas=-lopenblas" + "--with-libpng" + "--with-jpeglib" + "--with-libtiff" + "--with-ICU" + "--with-tcltk" + (string-append "--with-tcl-config=" + #$(this-package-input "tcl") "/lib/tclConfig.sh") - ,(string-append "--with-tk-config=" - (assoc-ref %build-inputs "tk") + (string-append "--with-tk-config=" + #$(this-package-input "tk") "/lib/tkConfig.sh") - "--enable-R-shlib" - "--enable-BLAS-shlib" - "--with-system-tre"))) + "--enable-R-shlib" + "--enable-BLAS-shlib" + "--with-system-tre"))) ;; R has some support for Java. When the JDK is available at configure ;; time environment variables pointing to the JDK will be recorded under ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R @@ -443,45 +454,44 @@ available, greatly increasing its breadth and scope.") (package (inherit r-with-tests) (name "r-minimal") (arguments - `(#:tests? #f - ,@(substitute-keyword-arguments (package-arguments r-with-tests) - ((#:disallowed-references refs '()) - (cons perl refs)) - ((#:configure-flags flags) - ;; Do not build the recommended packages. The build system creates - ;; random temporary directories and embeds their names in some - ;; package files. We build these packages with the r-build-system - ;; instead. - `(cons "--without-recommended-packages" ,flags)) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (add-after 'install 'remove-extraneous-references - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* (string-append out "/lib/R/etc/Makeconf") - (("^# configure.*") - "# Removed to avoid extraneous references\n")) - (substitute* (string-append out "/lib/R/bin/libtool") - (((string-append - "(-L)?(" - (format #false - "~a/[^-]+-(~{~a~^|~})-[^/]+" - (%store-directory) - '("bzip2" - "file" - "glibc-utf8-locales" - "graphite2" - "libselinux" - "libsepol" - "perl" - "texinfo" - "texlive-bin" - "util-macros" - "xz")) - "|" - (format #false "~a/[^-]+-glibc-[^-]+-static" - (%store-directory)) - ")/lib")) "")))))))))))) + (substitute-keyword-arguments (package-arguments r-with-tests) + ((#:tests? #f #f) #f) + ((#:disallowed-references refs '()) + (cons perl refs)) + ((#:configure-flags flags) + ;; Do not build the recommended packages. The build system creates + ;; random temporary directories and embeds their names in some + ;; package files. We build these packages with the r-build-system + ;; instead. + #~(cons "--without-recommended-packages" #$flags)) + ((#:phases phases '%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extraneous-references + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* (string-append #$output "/lib/R/etc/Makeconf") + (("^# configure.*") + "# Removed to avoid extraneous references\n")) + (substitute* (string-append #$output "/lib/R/bin/libtool") + (((string-append + "(-L)?(" + (format #false + "~a/[^-]+-(~{~a~^|~})-[^/]+" + (%store-directory) + '("bzip2" + "file" + "glibc-utf8-locales" + "graphite2" + "libselinux" + "libsepol" + "perl" + "texinfo" + "texlive-bin" + "util-macros" + "xz")) + "|" + (format #false "~a/[^-]+-glibc-[^-]+-static" + (%store-directory)) + ")/lib")) "")))))))))) (define-public rmath-standalone (package (inherit r-minimal) @@ -504,14 +514,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-28.1") + (version "1.3-30") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "0lzz08fpn80qzm197s4806hr6skanr3r3rlx6bx7zk4cripygkfl")))) + "15zysf5manfsap7x0zvjzgdvs9whv137iasjydp1php6sqmxc2am")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -797,14 +807,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.5-7") + (version "3.5-8") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "0bi76kr5xkcs98r795lz9nvsj6zzxq0w6zn1938z0ffx5b9js3nm")))) + "1d0qvw4200mjldna9n0acis0fk8xj28wwzqb8c3d4537l92zivbi")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) @@ -993,19 +1003,20 @@ OpenSSL should be used.") (define-public r-estimability (package (name "r-estimability") - (version "1.4.1") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "estimability" version)) (sha256 (base32 - "090i1xwdp4fwj8jr8nk13w49516lfkk5mq1w7l0lff9g8lgaynn6")))) + "0s6w8vnq0jc136d2mpf6pgg45rbxccrlsgdy89pgksnbaxhmyb5k")))) (build-system r-build-system) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/estimability") (synopsis "Tools for assessing estimability of linear predictions") - (description "Provides tools for determining estimability of linear -functions of regression coefficients, and @code{epredict} methods that handle -non-estimable cases correctly.") + (description "This package provides tools for determining estimability of +linear functions of regression coefficients, and @code{epredict} methods that +handle non-estimable cases correctly.") (license license:gpl2+))) (define-public r-labeling @@ -1253,13 +1264,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.4.4") + (version "3.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "0iiywrzv8j0npasvzgkxwhw0zqisf4xmpx06jl0lsq1ybl3fqxid")))) + (base32 "1qlh231dwsa7j0pzlw6xdm68d7r0v64916p66bg9lh1dw3a1ryh7")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -1291,13 +1302,13 @@ aesthetic attributes.") (define-public r-ggdendro (package (name "r-ggdendro") - (version "0.1.23") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "ggdendro" version)) (sha256 (base32 - "1f4fz9llmbpb8gh90aid7dvriadx16xdhsl7832yw4pyqj4fjcrs")))) + "0sdayyzvhkbli0ha68mc0f7cgp36njv9ign37d63l21hvd6w6h0r")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-mass)) @@ -1317,14 +1328,14 @@ agnes cluster diagrams.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "155qa55wr9vf2j2j4qjqqlkdaqlvvlvsm2wmysnhli47bfh6vd4c")))) + "1d1sidm2qi1nrp1hhf010xji66aj8sn833fv4a39gli2c560p4i6")))) (build-system r-build-system) (native-inputs (list pkg-config)) @@ -1409,13 +1420,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "0w7dpp1zg8w0mback1mk0a0vp51hf4njmrxz1i3j1xq5b1jfyiz4")))) + "10d7sl9nk1gkkbinmvplyp2hg9zgxgs03llamrvbf4a5cnrs0mcd")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1514,6 +1525,36 @@ it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.") (license license:gpl3+))) +(define-public r-httpgd + (let ((commit "3f5f55822c4dce930155b91cedcfd4d483e3294e") + (revision "1")) + (package + (name "r-httpgd") + (version (git-version "2.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nx10/httpgd") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14i7mhbv1vcz2886w9lii9zhgr4zhhc844349syb989nhhzg552n")))) + (properties `((upstream-name . "httpgd"))) + (build-system r-build-system) + (propagated-inputs (list r-asioheaders r-cpp11 r-unigd)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/nx10/httpgd") + (synopsis "'HTTP' Server Graphics Device") + (description + "This package provides a graphics device for R that is accessible via +network protocols. This package was created to make it easier to embed live R +graphics in integrated development environments and other applications. The +included HTML/@code{JavaScript} client (plot viewer) aims to provide a better +overall user experience when dealing with R graphics. The device +asynchronously serves graphics via HTTP and @code{WebSockets}'.") + (license license:gpl2+)))) + (define-public r-mime (package (name "r-mime") @@ -1602,18 +1643,19 @@ generation in R using Literate Programming techniques.") (define-public r-knitrbootstrap (package (name "r-knitrbootstrap") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "knitrBootstrap" version)) (sha256 (base32 - "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3")))) + "157mn2gm7djfiw1b55vdr2ylrmgxlpfg95bmm82ghv5g6vr26smd")))) (properties `((upstream-name . "knitrBootstrap"))) (build-system r-build-system) (propagated-inputs - (list r-knitr r-rmarkdown r-markdown)) + (list r-knitr r-markdown r-rmarkdown)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jimhester/knitrBootstrap") (synopsis "Knitr bootstrap framework") (description @@ -1991,13 +2033,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.14.10") + (version "1.15.0") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "0zk2g0lnjrw5wk6avwq07xw0cd7hpcpkmamf9d8avpd8f7ml2jq1")))) + "0qhh4ii10b6rbimhh83160gsax82gbrm3hqbqqddkzknpifxpdrr")))) (properties `((upstream-name . "data.table"))) (build-system r-build-system) (inputs @@ -2134,7 +2176,7 @@ machine learning, computer vision, and high-dimensional statistics.") (define-public python-arviz (package (name "python-arviz") - (version "0.16.1") + (version "0.17.0") (source (origin (method git-fetch) ; PyPI misses some test files (uri (git-reference @@ -2143,7 +2185,7 @@ machine learning, computer vision, and high-dimensional statistics.") (file-name (git-file-name name version)) (sha256 (base32 - "19phaqbpls82300z7ghicrldjxyjq4ilmmwsmd9zkl8c7ld5cb4j")))) + "0rmv7nniciq2jjnmk3qslc777wm8mjp7vsbk5dqx87a94dp7198f")))) (build-system pyproject-build-system) (arguments ;; FIXME: matplotlib tests fail because of the "--save" test flag. @@ -2182,7 +2224,7 @@ comparison and diagnostics.") (define-public python-pymc (package (name "python-pymc") - (version "5.10.0") + (version "5.10.3") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference @@ -2191,7 +2233,7 @@ comparison and diagnostics.") (file-name (git-file-name name version)) (sha256 (base32 - "17gb7ny2isfgyps7qffdxq18a9p43qy1fhqhbh75cnqd5wv1yxzb")))) + "0ydngbki4xb0i4j0nayzqqrvwlxp30fp56kiwm95n2i7iwgmki02")))) (build-system pyproject-build-system) (arguments (list #:tests? #f ; tests are too computationally intensive @@ -2250,6 +2292,15 @@ inference (VI) algorithms.") (base32 "1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m")))) (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; The deprecation warnings break the tests. + (add-after 'unpack 'dont-treat-deprecation-warnings-as-error + (lambda _ + (substitute* "pyproject.toml" + (("\"error::DeprecationWarning\",") ""))))))) (propagated-inputs (list python-importlib-metadata python-numpoly python-numpy python-scipy)) (native-inputs (list python-pytest python-scikit-learn)) @@ -2485,13 +2536,13 @@ functionalities needed to treat uncertainties in studies.") (define-public r-coda (package (name "r-coda") - (version "0.19-4") + (version "0.19-4.1") (source (origin (method url-fetch) (uri (cran-uri "coda" version)) (sha256 (base32 - "13z5dwfpnyyhpsbpg4xr9g5c1685jhqj90f4x4qkcykr6kykqba2")))) + "1mlaf3ffql3phc12vlfss0vqqdj415mxsg84vsdgymmvdzc53d7l")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -2780,14 +2831,14 @@ other packages.") (define-public r-commonmark (package (name "r-commonmark") - (version "1.9.0") + (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 - "13slfv9xpd5fhccw6xgm274d338gmpvc4sdzd943dm684rd1ml3d")))) + "0fxm1nn4al0yn79iqix9cp5j5chr8jq56d29ayqrpag49hzs25wm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") @@ -2803,13 +2854,13 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.3.0") + (version "7.3.1") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "05vzmln9cwcns1pcs568ivxpvf823xcw671d3wi77c3ixzmj3p7q")))) + "1j72arkadw93f4wrzxhryn3666jwnablr1bhk0zv6g77q2lrypi1")))) (build-system r-build-system) (propagated-inputs (list r-brew @@ -3128,13 +3179,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.12.6.6.1") + (version "0.12.8.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1h7z1l2zf4qv8azi9c4wj0klshhcqihpabvjhln7ra61i8lvssls")))) + "0pkn4334dh4k6hqfx4xln2nfvajyxdbfnfddajb8875il0f7kp0x")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -3342,13 +3393,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.3.4") + (version "2.3.5") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "1sy4zgacr7f7svv0a1vd7s40llk7g2989qwf19l6zkngncdwikbk")))) + "1wvfadwcr8iv0z6pddfpvl60dq4p8l68v16p9daa002srgzpwlw1")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -3413,13 +3464,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.16") + (version "3.99-0.16.1") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "0ny93jlx0fpv0hs9qjm9cbcv4fh5rh0kkyhk6g0dm8wvp6x3f39m")))) + "1i7fs9i2f6bdkxb45w2bck7sshlwxy2s32hi9fwa4nfmw2iy62m3")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -3534,14 +3585,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "2.0-1") + (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "0r3l39sihncrmhs6y3nydr6izp5ss86rfwjyhwf2x0clvqq2gkz9")))) + "1f89v6zbxwl6yhx3qi7wrr3rndnxfwaf49mygw357f7cf3i8ma77")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") @@ -3779,13 +3830,13 @@ using the multicore functionality of the parallel package.") "datatables-extensions/Buttons")))) (package (name "r-dt") - (version "0.31") + (version "0.32") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "11wwd76x1bk9aswi8w4bmvbf51j8hlmb5gsyqzfjdi6ihjkl4vwm")) + "0nvj2bc441b9h13085fa7q281f86lgx4k0d8lr64xgdpbmbvkl21")) (modules '((guix build utils) (ice-9 match))) (snippet @@ -4277,13 +4328,13 @@ want to migrate to S4.") (define-public r-r-oo (package (name "r-r-oo") - (version "1.25.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (cran-uri "R.oo" version)) (sha256 (base32 - "1vxy8yw4yblb3vgl64yh0b6zf1d51rnc2c23kmyyw629fxhr1cdq")))) + "0ra3sjs7sqqif3dlcdry7p40vd4jxm0407d3s6sgn5i2ihw2nq7p")))) (properties `((upstream-name . "R.oo"))) (build-system r-build-system) (propagated-inputs @@ -4349,13 +4400,13 @@ persistent (on the file system).") (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.45.0") + (version "0.46.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "192x8cvna1j0sx37xh3ha8bjjyx39pn5wnxzn5gs3z5j93a4d055")))) + "1frkgjc2mzvjnay8g5nky1bvxv60wvsypmmdj6mbsfjnzq7ni7qs")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (arguments @@ -4430,13 +4481,13 @@ memory usage.") (define-public r-viridis (package (name "r-viridis") - (version "0.6.4") + (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "viridis" version)) (sha256 (base32 - "1p6n85js15lx0zx07v2dxnb6wx4xzlbvrljf0x6vxy4gqf5si8hb")))) + "0p00s24d8bsifw3r0afwrx98bqixnf5krpbw42hfwp8ipsv5qaw6")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-viridislite)) @@ -4508,27 +4559,27 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "178a9sb07rph4mh7cz004ls0g7d4b7jk065m4ycfrlzxcs9jnlwd")))) + "0pc3ad9k36lk3c5qbgx4blhs8aihqyysfxljyirgahsmrdhw4878")))) (build-system r-build-system) (propagated-inputs (list r-cli r-cpp11 r-dplyr - r-magrittr r-glue r-lifecycle + r-magrittr r-purrr r-rlang r-stringr - r-tidyselect r-tibble + r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) @@ -4592,13 +4643,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.10.3") + (version "4.10.4") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "13sxmanx2xck8dn0prn2fplgx4bafb7h2kk2wjmci21h8hk6qylb")) + "0ryqcs9y7zan36zs6n1hxxy91pajldpax8q7cwcimlsmxnvrbafg")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib/" @@ -4943,14 +4994,14 @@ conversion of R objects to LaTeX code, and recoding variables.") (define-public r-runit (package (name "r-runit") - (version "0.4.32") + (version "0.4.33") (source (origin (method url-fetch) (uri (cran-uri "RUnit" version)) (sha256 (base32 - "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3")))) + "0pybwvd57vf71vvlxdrynw5n6s5gnbqnwvq0qpd395ggqypwb95j")))) (properties `((upstream-name . "RUnit"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RUnit") @@ -5009,14 +5060,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-16") + (version "1.1-17") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0v2325f3115yp48s0ddiiqwxlg2zf5xzc21xxd0cbziw3rk4l6si")))) + "06ih8zljs57scy7jfnv32yxijgv1i60vggmlyyblwnff6mr2fm60")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -5087,14 +5138,14 @@ including: (define-public r-gplots (package (name "r-gplots") - (version "3.1.3") + (version "3.1.3.1") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 - "05k7a8x62qs5g6mps62vb3mwjdnfjzvjb20yws3x0r2j42g3p1cz")))) + "1whs45axg1vp2p3jjya4aq68bl6vp11g059saj2av0vmyaadxq8s")))) (build-system r-build-system) (propagated-inputs (list r-catools r-gtools r-kernsmooth)) @@ -5268,13 +5319,13 @@ data at that region, and avoids over-plotting.") (define-public r-ggthemes (package (name "r-ggthemes") - (version "5.0.0") + (version "5.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggthemes" version)) (sha256 (base32 - "1iddxlcxbj5pq0llbhjh5gvxq8j4kzby0cahy0sgzzca074i7aan")))) + "03mxigi34nd05wjigm8lpcbyhp4c8jxz7zm04qs27clbzsn1jj07")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -5390,14 +5441,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "1ppsg3rbqz9a16zq87izdj5w8ylb6jb6v13xb01k7m3n2h4mv4f6")))) + "0wxjynpbamyimpms7psbac7xgwswzlidczpc037q20y5yld9fml7")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gtable r-rlang r-scales)) @@ -5568,14 +5619,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "6.0.1") + (version "6.1") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0zsk89r2l73zi1dy0195k84n4dqdp97yisll5kg16amxs5pxx4hf")))) + "0mchdxkc3y0v6dw8fzjnlqd6f3zrafm3xf1c53s6ps529b66kx2x")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5637,14 +5688,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.99-1") + (version "0.99-2") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "0n3qxw633hk391mr07pd7c9572v3zgdffvmaq4q2w5q4x3n1n6mf")))) + "0i6dzri3bfkpmp7h0h5nyzigs9rjzdd3c4ilapmvadmfywl9d9mn")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -5682,14 +5733,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.7-4") + (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "0jkm2w38kbzicfx2542rb90r7kcrbm7hiaasajw1zq8gb7ffshb3")))) + "0cxhs0plbd8b01hmnpaphshhk34rw1bwg56rackb2pmngw3rbifz")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mvtnorm r-pcapp r-robustbase)) @@ -5733,14 +5784,14 @@ generally.") (define-public r-robust (package (name "r-robust") - (version "0.7-3") + (version "0.7-4") (source (origin (method url-fetch) (uri (cran-uri "robust" version)) (sha256 (base32 - "0pj7qinp11rjsibixl7axvxp9alaqr4pjr1l52vq8cl8h6j159w9")))) + "0qh816ha18v0n021cccjan1kplmyj0xyb7jmkmrnb6gxf8kma3b3")))) (build-system r-build-system) (propagated-inputs (list r-fit-models r-lattice r-mass r-robustbase r-rrcov)) @@ -6235,14 +6286,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.5-5") + (version "1.5-6") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "15jl1srsn0m0r5qafbkqsvnh44j30nh3yhipw030mdfa4qkbz3gw")))) + "1p7y58mklcwq76msh1q8pm2v6v19ja6fy07xg1j07d2zw2wa0phy")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs @@ -6668,14 +6719,14 @@ completion.") (define-public python-rpy2 (package (name "python-rpy2") - (version "3.5.5") + (version "3.5.15") (source (origin (method url-fetch) (uri (pypi-uri "rpy2" version)) (sha256 (base32 - "0dyhb3xn2p6s67yxhgh4qd4hp45mhb5zvgqkdsn26kyg447c8lm2")))) + "0asvybb7kmr48pfkibp1qi3h3vlq2fl0mazaf0xj6zywhi5awks4")))) (build-system python-build-system) (arguments '(#:phases @@ -6704,9 +6755,15 @@ completion.") r-rsqlite r-dplyr r-dbplyr - python-numpy)) + python-numpy + zlib)) (native-inputs - (list zlib python-pytest)) + (list python-coverage + python-ipython + python-numpy + python-pandas + python-pytest + python-pytest-cov)) (home-page "https://rpy2.github.io") (synopsis "Python interface to the R language") (description "rpy2 is a redesign and rewrite of rpy. It is providing a @@ -6756,8 +6813,8 @@ Java package that provides routines for various statistical distributions.") (license license:gpl2+))) (define-public emacs-ess - (let ((commit "3691ecc642eab5d016887e42699648e0eeeef566") - (version "18.10.2") + (let ((commit "ab2faeca1ba6c456333312c58f58ef9e5ef4aa8b") + (version "24.01.1") (revision "1")) (package (name "emacs-ess") @@ -6769,7 +6826,7 @@ Java package that provides routines for various statistical distributions.") (url "https://github.com/emacs-ess/ESS") (commit commit))) (sha256 - (base32 "19p8djsbgvahpsx1w8i6h3qvpbdr4isjwm3wi82yk2648ri0qsq1")) + (base32 "0jfdfqpa3x1zm65cllkzhqir057xd3hxi4z2ddii1i26zy56iikf")) (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet @@ -6787,9 +6844,6 @@ Java package that provides routines for various statistical distributions.") ;; Stop install-info from trying to update the info directory. (substitute* "doc/Makefile" ((".*/dir.*") "")) - ;; Fix r-help-mode test. - (substitute* "test/ess-test-r.el" - (("\\(equal ess-help-object \"plot.default\")") "t")) ;; Avoid generating ess-autoloads.el twice. (substitute* "Makefile" (("all: lisp doc etc autoloads") @@ -6819,9 +6873,6 @@ Java package that provides routines for various statistical distributions.") #~(modify-phases %standard-phases (delete 'configure) (add-before 'check 'skip-failing-tests - ;; The command-without-trailing-newline-test and other - ;; tests fail for unknown reasons (see: - ;; https://github.com/emacs-ess/ESS/issues/1272). (lambda _ (let-syntax ((disable-tests @@ -6833,22 +6884,7 @@ Java package that provides routines for various statistical distributions.") (((string-append "^\\(ert-deftest " test-name ".*") all) (string-append all "(skip-unless nil)\n")) - ...)))) - (disable-etests ;different test syntax - (syntax-rules () - ((_ file ()) - (syntax-error "test names list must not be empty")) - ((_ file (test-name ...)) - (emacs-batch-edit-file file - '(progn - (mapc (lambda (test) - (goto-char (point-min)) - (search-forward - (format "etest-deftest %s " test)) - (beginning-of-line) - (kill-sexp)) - (list test-name ...)) - (basic-save-buffer))))))) + ...))))) (disable-tests (list "test/ess-test-inf.el" "test/ess-test-r.el") ("ess--derive-connection-path" @@ -6858,15 +6894,10 @@ Java package that provides routines for various statistical distributions.") "ess-r-load-ESSR-github-fetch-no" "ess-r-load-ESSR-github-fetch-yes" "ess-set-working-directory-test" - "ess-test-r-startup-directory")) - (disable-etests "test/ess-test-r-eval.el" - ("ess-r-eval-ns-env-roxy-tracebug-test" - "ess-r-eval-sink-freeze-test")) - (disable-etests - "test/ess-test-inf.el" - ("command-without-trailing-newline-test"))))) + "ess-test-r-startup-directory"))))) (replace 'check - (lambda _ (invoke "make" "test"))))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? (invoke "make" "test")))))))) (native-inputs (list perl r-roxygen2 texinfo)) (inputs (list emacs-minimal r-minimal)) (propagated-inputs (list emacs-julia-mode)) @@ -7206,14 +7237,14 @@ various statistical models with linear predictors.") (define-public r-bayesfactor (package (name "r-bayesfactor") - (version "0.9.12-4.6") + (version "0.9.12-4.7") (source (origin (method url-fetch) (uri (cran-uri "BayesFactor" version)) (sha256 (base32 - "1nvm26m5m8xi8iw1fj8ca79z3aqln4l3c0hvh38yvm9p584nwpzx")))) + "0z9p9vdcmcdwqmixaiqnhli2b06whbap6y4pqx4a5gcdgxlj09zr")))) (properties `((upstream-name . "BayesFactor"))) (build-system r-build-system) (propagated-inputs @@ -7440,13 +7471,13 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.52") + (version "0.99.54") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "147p9brnzyhibffq15wcn0dza3cx14w57b2zc9na8wmmc3wpv6cl")))) + (base32 "16qbm1l1281yj1cg6fp8xgd8xdshpz9a09f0b9cyimsjbm01c2j7")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (propagated-inputs @@ -7755,3 +7786,40 @@ weighting schemes.") statistical summary in arrays and enumerables.") (home-page "https://github.com/mrkn/enumerable-statistics") (license license:expat))) + +(define-public python-pgmpy + (package + (name "python-pgmpy") + (version "0.1.24") + (source + (origin + (method git-fetch) ;pypi package does not include test data + (uri (git-reference + (url "https://github.com/pgmpy/pgmpy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-daft + python-joblib + python-networkx + python-numpy + python-opt-einsum + python-pandas + python-pyparsing + python-pytorch + python-scikit-learn + python-scipy + python-statsmodels + python-tqdm)) + (native-inputs (list python-mock + python-pytest)) + (home-page "https://github.com/pgmpy/pgmpy") + (synopsis "Probabilistic Graphical Models library") + (description "This package provides a library for Probabilistic +Graphical Models. It can be used for learning (Structure and Parameter), +inference (Probabilistic and Causal), and simulations in Bayesian +Networks.") + (license license:expat))) |