diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 257 |
1 files changed, 122 insertions, 135 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 82f97c679e..71ff921c62 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -702,14 +702,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.2-3") + (version "3.2-7") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "07h76r2y23w889257krlijcw4n4d7ssx92x7i5qb1xyv5gyvl3rx")))) + "0ila864g5b9yhjhk3jirgdpi06sksc0axa78890dmkvyv9rwsmjk")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -1415,13 +1415,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.29") + (version "1.30") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "00rcwiq8znmk5h4qgrwd0639xyb38iwbjykqjk3disz3kvrcvbn1")))) + "0gn9qwc5762a6j0iywfwhalni52g228dcy4bl4di6d52cqsv3ars")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) @@ -1965,13 +1965,13 @@ inference for statistical models.") (define-public r-coda (package (name "r-coda") - (version "0.19-3") + (version "0.19-4") (source (origin (method url-fetch) (uri (cran-uri "coda" version)) (sha256 (base32 - "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk")))) + "13z5dwfpnyyhpsbpg4xr9g5c1685jhqj90f4x4qkcykr6kykqba2")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -2034,14 +2034,14 @@ files in R. It is built on top of the libxml2 C library.") (define-public r-multitaper (package (name "r-multitaper") - (version "1.0-14") + (version "1.0-15") (source (origin (method url-fetch) (uri (cran-uri "multitaper" version)) (sha256 (base32 - "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68")))) + "1gm3wr8xqpqiby7q1dr3zxim77v0bvvrqi0hlazf5g3gnkrp2zc3")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2100,14 +2100,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.9") + (version "1.1.10") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "1mz3r6ad484xmx0i89gvmak4wzl4cp59gxdzirrci9znw1axrrvx")))) + "1pq16bf40zx441ylmqqqilj3xp39r707h56kwqp5yqklq9yln2z1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") @@ -2322,14 +2322,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "17fkc6pr8w5z3rpadg692a689p1v4j7xl5ak0y64is7c74cxgljx")))) + "0sc2skh1nz7jj65p0pq4a6bl8jza6lyi4zvmvwndzxfgivgh281l")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) @@ -2426,13 +2426,13 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "2.3.1") + (version "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "100mgighf6vqsfwv2qw5rlnd5sfvcji9l9jrmx9ii28r9fd2gyas")))) + "0vcqs4c5dfjs2ddkclv3z7zzix2zrnrxvzax8hjvjszgp8362275")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -2467,13 +2467,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.2.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac")))) + "1837vjp35npjrnis1im5xrwj1swpgnms00gkjiz7296l8yckrh1c")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -2511,22 +2511,27 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k")))) + "1fa67h4l9d30ig460xizgzl115i9pm3bk9dvsbrw6awbmf51ic82")))) (build-system r-build-system) (propagated-inputs - `(("r-clipr" ,r-clipr) + `(("r-cli" ,r-cli) + ("r-clipr" ,r-clipr) + ("r-cpp11" ,r-cpp11) ("r-crayon" ,r-crayon) - ("r-rcpp" ,r-rcpp) ("r-hms" ,r-hms) + ("r-lifecycle" ,r-lifecycle) ("r-tibble" ,r-tibble) ("r-r6" ,r-r6) + ("r-rlang" ,r-rlang) ("r-bh" ,r-bh))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/readr") (synopsis "Read tabular data") (description @@ -2690,18 +2695,17 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.3") + (version "2.4") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0vdjq4kcyxkr2m27588kk6yi5g53symjshj4jz4n0j18wz53shji")))) + (base32 "1y2156w1abik8df8vl376ilv8s1jg8i0x2w4n4dwrnm3xxgp5kf0")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-evaluate" ,r-evaluate) + `(("r-evaluate" ,r-evaluate) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) @@ -2806,13 +2810,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "1m38sj8rwbf3p2lhqabcp7c7djk7s9ng37cz39yxk706v9pi4380")))) + "0lynli9144dzb9vhxssba20v7z5h2nirawpvvy8ykv4n3ir7qlsl")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2824,6 +2828,8 @@ a column in data frame.") ("r-bit64" ,r-bit64) ("r-blob" ,r-blob) ("r-pkgconfig" ,r-pkgconfig))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rstats-db/RSQLite") (synopsis "SQLite interface for R") (description @@ -3604,13 +3610,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.56.0") + (version "0.57.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "09qgfv9x32x6ncgf19iy7yjp26fwy6p5wm8spc2xzfc0qhylmqrr")))) + "0hzkx7yi9ira476izsgw7r2bhv72ra4z2m9zr1i1f4ivrn3ihs7r")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (native-inputs @@ -4079,27 +4085,6 @@ framework, with additional code inspection and report generation tools.") hierarchical clustering dendrograms.") (license license:gpl2+))) -(define-public r-preprocesscore - (package - (name "r-preprocesscore") - (version "1.50.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "preprocessCore" version)) - (sha256 - (base32 - "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl")))) - (properties - `((upstream-name . "preprocessCore"))) - (build-system r-build-system) - (home-page "https://github.com/bmbolstad/preprocessCore") - (synopsis "Collection of pre-processing functions") - (description - "This package provides a library of core pre-processing and normalization -routines.") - (license license:lgpl2.0+))) - (define-public r-fastcluster (package (name "r-fastcluster") @@ -4217,18 +4202,17 @@ including: (define-public r-gplots (package (name "r-gplots") - (version "3.0.4") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 - "15ip3v4xiqzbanf8bc5fj90cbwdgixr72aj5jrp34jfdzdx0gxwg")))) + "05rislwgaw6v5dmhcwyvc04hi1fgaxrpb61f66kx483px45w6f24")))) (build-system r-build-system) (propagated-inputs `(("r-catools" ,r-catools) - ("r-gdata" ,r-gdata) ("r-gtools" ,r-gtools) ("r-kernsmooth" ,r-kernsmooth))) (native-inputs @@ -4927,14 +4911,14 @@ of the points.") (define-public r-fpc (package (name "r-fpc") - (version "2.2-7") + (version "2.2-8") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 - "1xnp3j36hggfg675v39mnr6rgvp7i11pfng7nmyy3k2ldgklz0j9")))) + "07a125pji1flmybn6iidcnizwnqyl6chnrckxa5jp4qxxfdqx658")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -5096,13 +5080,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.67") + (version "5.73") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "09hgch8x6x2k7wm17c0njp7l0r6rrrlcji60afrv19dm9r4596wr")))) + (base32 "0mjwwj3c7cfnprlh90ld0f1lll0mrqbx8mpnbfr7bvzg8h6072y4")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5230,13 +5214,13 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-9") + (version "3.0-10") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "1clh8c7mj87i4hz27l16w76dpw7k4mlnjbgm9mbrhrfkv0lpb63c")))) + (base32 "1w95b7xm0bna3qm637pwyv4s7294ffz9dl153naprd79zv91dqqw")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) @@ -5383,14 +5367,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.4-1") + (version "1.4-2") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb")))) + "1nb5iky4kc832627jf28lzj19wrvgwg5da6fyl3kyf0npmyx1p4m")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs @@ -5805,78 +5789,81 @@ Java package that provides routines for various statistical distributions.") (license license:gpl2+))) (define-public emacs-ess - (package - (name "emacs-ess") - (version "18.10.2") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/emacs-ess/ESS") - (commit (string-append "v" version)))) - (sha256 - (base32 - "1yq41l2bicwjrc0b731iic20cpcnz6ppigri1jn621qv2qv22vy3")) - (file-name (git-file-name name version)) - (modules '((guix build utils))) - (snippet - '(begin - ;; Stop ESS from trying to bundle an external julia-mode.el. - (substitute* "lisp/Makefile" - (("^ess-julia.elc: julia-mode.elc") "") - (("^all: julia-mode.el") - "all:")) - ;; Include *.el files in install target. - (substitute* "lisp/Makefile" - (("\t\\$\\(INSTALL) \\$\\(ELC\\) \\$\\(LISPDIR\\)" elc) - (string-append "\t$(INSTALL) $(ELS) ess-autoloads.el " - "$(LISPDIR)\n" elc))) - ;; Only build docs in info format. - (substitute* "doc/Makefile" - (("all : info text") - "all : info") - (("install: install-info install-other-docs") - "install: install-info")) - ;; Stop install-info from trying to update the info directory. - (substitute* "doc/Makefile" - ((".*\\$\\(INFODIR\\)/dir.*") "")) - ;; Fix roxygen preview test. - (substitute* "test/ess-r-tests.el" - (("Add together two numbers.\n") - "Add together two numbers. ") - (("##' add\\(10, 1\\)") "add(10, 1)")) - #t)))) - (build-system gnu-build-system) - (arguments - (let ((base-directory "/share/emacs/site-lisp")) - `(#:make-flags (list (string-append "PREFIX=" %output) - (string-append "ETCDIR=" %output - ,base-directory "/etc") - (string-append "LISPDIR=" %output - ,base-directory)) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-before 'build 'more-shebang-patching - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "Makeconf" - (("SHELL = /bin/sh") - (string-append "SHELL = " (which "sh")))) - #t)) - (replace 'check - (lambda _ - (invoke "make" "test"))))))) - (inputs - `(("emacs" ,emacs-minimal) - ("r-minimal" ,r-minimal))) - (native-inputs - `(("perl" ,perl) - ("r-roxygen2" ,r-roxygen2) - ("texinfo" ,texinfo))) - (propagated-inputs - `(("emacs-julia-mode" ,emacs-julia-mode))) - (home-page "https://ess.r-project.org/") - (synopsis "Emacs mode for statistical analysis programs") - (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU -Emacs. It is designed to support editing of scripts and interaction with -various statistical analysis programs such as R, Julia, and JAGS.") - (license license:gpl2+))) + ;; Latest release is old. This is not the latest commit either due to bug + ;; reported here: <https://github.com/emacs-ess/ESS/issues/987>. + (let ((commit "24da603184ce39246611dd5b8602e769d7ebd5bf") + (version "18.10.2") + (revision "0")) + (package + (name "emacs-ess") + (version (git-version version revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-ess/ESS") + (commit commit))) + (sha256 + (base32 "0j98lv07nzwzd54d4dgcfz01wy5gj48m0mnirxzh5r45ik2myh1r")) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + '(begin + ;; Stop ESS from trying to bundle an external julia-mode.el. + (substitute* "lisp/Makefile" + ((" \\$\\(JULIAS)") "") + (("\ttest.*julia-mode.*\\.el") "")) + ;; Only build docs in info format. + (substitute* "doc/Makefile" + (("all : info text") + "all : info") + (("install: install-info install-other-docs") + "install: install-info")) + ;; 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") + "all: lisp doc etc")) + ;; Install to correct directories. + (substitute* "Makefile" + (("mkdir -p \\$\\(ESSDESTDIR)") + "$(MAKE) -C lisp install; $(MAKE) -C doc install") + (("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/") + "$(MAKE) -C etc install")) + #t)))) + (build-system gnu-build-system) + (arguments + (let ((base-directory "/share/emacs/site-lisp")) + `(#:make-flags (list (string-append "PREFIX=" %output) + (string-append "ETCDIR=" %output + ,base-directory "/etc") + (string-append "LISPDIR=" %output + ,base-directory) + (string-append "INFODIR=" %output + "/share/info")) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check + (lambda _ (invoke "make" "test"))))))) + (native-inputs + `(("perl" ,perl) + ("r-roxygen2" ,r-roxygen2) + ("texinfo" ,texinfo))) + (inputs + `(("emacs" ,emacs-minimal) + ("r-minimal" ,r-minimal))) + (propagated-inputs + `(("emacs-julia-mode" ,emacs-julia-mode))) + (home-page "https://ess.r-project.org/") + (synopsis "Emacs mode for statistical analysis programs") + (description + "Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It +is designed to support editing of scripts and interaction with various +statistical analysis programs such as R, Julia, and JAGS.") + (license license:gpl3+)))) |