diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 200 |
1 files changed, 92 insertions, 108 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 70a85e8b60..60f39fa0a9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -429,14 +429,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-52") + (version "7.3-53") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "0c4scl7r4m0bikr0wmdrnn7wfzy1vg5v7gsq6bms2vknzs9ymhxp")))) + "0f2bwsbqr3nzsqxva051lg8wd068naqif3vc48hac0m3mmq4x0j1")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -1026,14 +1026,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.4.6") + (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1mkgxzf000zdgbbbvg2vf4md4l501n5lfksffq8vdg6pbgd6fgv3")))) + "0420f7zn5knyyvd3a3xa7059l4kadw0m67rfpivacqn9xn6iwkr2")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -1135,13 +1135,13 @@ aesthetic attributes.") (define-public r-ggdendro (package (name "r-ggdendro") - (version "0.1.21") + (version "0.1.22") (source (origin (method url-fetch) (uri (cran-uri "ggdendro" version)) (sha256 (base32 - "0jcjdkhd3wirjgv4v3gb9rw8idyymwhwnxplg3wi8wa3mwr9rhq2")))) + "0skbj487b6f6pj2iz4yq2b9gbgb39cv5dyzhdl3w7ay1k0s5z9ph")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2598,13 +2598,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.9.900.2.0") + (version "0.9.900.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "03dfy0avzpiaf1jk8h18y2gyj3zwlfvvfixi13q3zq5qaz93by2r")))) + "0x8jm6cvfvp1kyckwwqxyy5hfkr8na28fih3k0lhi55wry3ml30q")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -4079,27 +4079,6 @@ 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") @@ -4522,20 +4501,22 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh")))) + "04d5pg4xi9nhgcbam71b5mp3q1g804ng864v90add1kddfyl3f9h")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/wilkelab/cowplot") (synopsis "Streamlined plot theme and plot annotations for ggplot2") (description @@ -5094,13 +5075,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.61") + (version "5.67") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "0kby1crnzkdg5sczwqapfpkr58apyzrrx85khigcqggmhhwl44wk")))) + (base32 "09hgch8x6x2k7wm17c0njp7l0r6rrrlcji60afrv19dm9r4596wr")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5803,78 +5784,81 @@ 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+)))) |