diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
-rw-r--r-- | gnu/packages/statistics.scm | 536 |
1 files changed, 282 insertions, 254 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 80d8ff2f93..aa8c586cc0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2017 Alex Kost <alezost@gmail.com> ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com> ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com> -;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2021, 2022, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com> ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net> ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com> @@ -228,157 +228,162 @@ 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)")) + (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\")")) + ;; 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"))) + ;; 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. + ;; 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 <- \ + ;; 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')\""))) + ;; 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))) + (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")))) + ;; 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, + ;; 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 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R @@ -443,45 +448,44 @@ available, greatly increasing its breadth and scope.") (package (inherit r-with-tests) (name "r-minimal") (arguments - `(#:tests? #f - ,@(substitute-keyword-arguments (package-arguments r-with-tests) - ((#:disallowed-references refs '()) - (cons perl refs)) - ((#:configure-flags flags) - ;; Do not build the recommended packages. The build system creates - ;; random temporary directories and embeds their names in some - ;; package files. We build these packages with the r-build-system - ;; instead. - `(cons "--without-recommended-packages" ,flags)) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (add-after 'install 'remove-extraneous-references - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* (string-append out "/lib/R/etc/Makeconf") - (("^# configure.*") - "# Removed to avoid extraneous references\n")) - (substitute* (string-append out "/lib/R/bin/libtool") - (((string-append - "(-L)?(" - (format #false - "~a/[^-]+-(~{~a~^|~})-[^/]+" - (%store-directory) - '("bzip2" - "file" - "glibc-utf8-locales" - "graphite2" - "libselinux" - "libsepol" - "perl" - "texinfo" - "texlive-bin" - "util-macros" - "xz")) - "|" - (format #false "~a/[^-]+-glibc-[^-]+-static" - (%store-directory)) - ")/lib")) "")))))))))))) + (substitute-keyword-arguments (package-arguments r-with-tests) + ((#:tests? #f #f) #f) + ((#:disallowed-references refs '()) + (cons perl refs)) + ((#:configure-flags flags) + ;; Do not build the recommended packages. The build system creates + ;; random temporary directories and embeds their names in some + ;; package files. We build these packages with the r-build-system + ;; instead. + #~(cons "--without-recommended-packages" #$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) @@ -525,14 +529,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-60") + (version "7.3-60.0.1") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "1hphf8m1zny4582rvfnl262ydf3f2w0kayxj2b8n855hx87l20mq")))) + "1gdd2gyqngvgnm0bxc3a33nykrx2rbfmxj82i7bh7f1961cr7pvl")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "https://www.stats.ox.ac.uk/pub/MASS4/") @@ -673,14 +677,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.6-4") + (version "1.6-5") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "00dv2xv69fr3c8h5a2qvr31lffamw5kx08q5v8vli3g6xkd7pjkh")))) + "0zdrrss4q0g7jify9bp1vvzrdpy62fc6fx3awzbd2wvfc938sv3j")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -962,13 +966,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.33") + (version "0.6.34") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "06bq696wpmn8ivbrpxw0qlcf835kc515m8jfv9zbwf8ndf42qw5y")))) + (base32 "1na47pywh059g9ymf56z232h5yxbj0gn755cb10ms5igjd97awqb")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -1409,13 +1413,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "1g4c2qfyjwbjwbsczhk83xmx74764nn53gnqzb6xxrwqjbxj4dpn")))) + "0w7dpp1zg8w0mback1mk0a0vp51hf4njmrxz1i3j1xq5b1jfyiz4")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1991,13 +1995,13 @@ 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 +2138,7 @@ 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 +2147,7 @@ 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 +2186,7 @@ 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 +2195,7 @@ 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 +2254,15 @@ 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)) @@ -2296,13 +2309,13 @@ building design matrices.") (define-public python-mapie (package (name "python-mapie") - (version "0.7.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "MAPIE" version)) (sha256 (base32 - "1nvi547avvwrck1n7rf5jh7d0ml6jaqjs2p59iwcq2a5xjmdsmsc")))) + "185nnsl6ag2xzkfxpmc86d9dd8wf2v87b2psan10sma399fbqd0x")))) (build-system pyproject-build-system) (native-inputs (list python-pandas python-pytest)) (propagated-inputs (list python-numpy python-scikit-learn)) @@ -2485,13 +2498,13 @@ 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 +2793,14 @@ 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 +2816,13 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.2.3") + (version "7.3.1") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "1nhn0jhnxzlyqx0qnpd7k7q3azzngyn0j4zs8awmlmyjfywzli6q")))) + "1j72arkadw93f4wrzxhryn3666jwnablr1bhk0zv6g77q2lrypi1")))) (build-system r-build-system) (propagated-inputs (list r-brew @@ -2991,13 +3004,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.5.2") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "01a27nqlrrf1pws57hi9631f3aj33a9dashd640m5nlgf9nzmdnm")))) + "1rz0pgm1bg3cnc09s8q8yyg83lmf8bv9arlasciqqr0fdpgfwy4c")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3342,13 +3355,13 @@ 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 +3426,13 @@ 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 +3547,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "2.0-1") + (version "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "0r3l39sihncrmhs6y3nydr6izp5ss86rfwjyhwf2x0clvqq2gkz9")))) + "0ym5z2zngkqvs1cd7c3k16k9ipsli6xc6qp0nmr77va34d8v0n4q")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") @@ -4277,13 +4290,13 @@ 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 @@ -4430,13 +4443,13 @@ 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 +4521,27 @@ 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 +4605,13 @@ 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/" @@ -4984,14 +4997,14 @@ hierarchical clustering dendrograms.") (define-public r-fastcluster (package (name "r-fastcluster") - (version "1.2.3") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "fastcluster" version)) (sha256 (base32 - "009amz7i5yndqw2008fgd3p11n4fsb291k2ypg3pip6dw4lr28hz")))) + "06cd3w62ijf0yx2yq0xgx6qw5lcrnn1033ygx6bl9dmhix2haal5")))) (build-system r-build-system) (home-page "http://danifold.net/fastcluster.html") (synopsis "Fast hierarchical clustering routines") @@ -5009,14 +5022,14 @@ 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") @@ -5390,14 +5403,14 @@ 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)) @@ -5637,14 +5650,14 @@ 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 +5695,14 @@ 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)) @@ -6668,14 +6681,14 @@ 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 +6717,15 @@ 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 @@ -6819,7 +6838,9 @@ Java package that provides routines for various statistical distributions.") #~(modify-phases %standard-phases (delete 'configure) (add-before 'check 'skip-failing-tests - ;; XXX: Skip 10 failing tests (out of 187). + ;; 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 @@ -6831,7 +6852,22 @@ 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" @@ -6841,26 +6877,18 @@ 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"))) - ;; The two tests below use a different syntax. - (emacs-batch-edit-file "test/ess-test-r-eval.el" - '(progn - (mapc (lambda (test) - (goto-char (point-min)) - (search-forward (format "etest-deftest %s " test)) - (beginning-of-line) - (kill-sexp)) - '("ess-r-eval-ns-env-roxy-tracebug-test" - "ess-r-eval-sink-freeze-test")) - (basic-save-buffer))))) + "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"))))) (replace 'check (lambda _ (invoke "make" "test"))))))) - (native-inputs - (list perl r-roxygen2 texinfo)) - (inputs - (list emacs-minimal r-minimal)) - (propagated-inputs - (list emacs-julia-mode)) + (native-inputs (list perl r-roxygen2 texinfo)) + (inputs (list emacs-minimal r-minimal)) + (propagated-inputs (list emacs-julia-mode)) (home-page "https://ess.r-project.org/") (synopsis "Emacs mode for statistical analysis programs") (description @@ -7197,14 +7225,14 @@ 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 @@ -7431,13 +7459,13 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.52") + (version "0.99.53") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "147p9brnzyhibffq15wcn0dza3cx14w57b2zc9na8wmmc3wpv6cl")))) + (base32 "0b7an97ns7zjc5qqqhrbb0wzzvcx7wcd0980fxlnpbzj5z2idl0p")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (propagated-inputs |