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-rw-r--r--gnu/packages/statistics.scm536
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