diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 208 |
1 files changed, 142 insertions, 66 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c1012a635b..78afb77a8b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -32,11 +32,14 @@ #:use-module (guix hg-download) #:use-module (guix git-download) #:use-module (guix utils) + #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) + #:use-module (gnu packages algebra) + #:use-module (gnu packages bash) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) @@ -170,21 +173,15 @@ be output in text, PostScript, PDF or HTML.") ;; 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. - ;; - ;; Instead of disabling this feature, which may have unexpected - ;; consequences, we reset the mtime of generated files before - ;; passing them to the "srcfile" procedure. - (substitute* "src/library/Makefile.in" - (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line) - (string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n")) - (("@\\$\\(MAKE\\) Rdobjects" line) - (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n " - line))) - (substitute* "src/library/tools/Makefile.in" - (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line) - (string-append - line - "\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n"))) + + ;; 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. @@ -265,6 +262,9 @@ be output in text, PostScript, PDF or HTML.") ("libxt" ,libxt) ("pcre" ,pcre) ("readline" ,readline) + ;; This avoids a reference to the ungraftable static bash. R uses the + ;; detected shell for the "system" procedure. + ("bash" ,bash-minimal) ("which" ,which) ("zlib" ,zlib))) (native-search-paths @@ -318,14 +318,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-48") + (version "7.3-49") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "02q95ba909p2gxnzfp295ipxjnv14f7bm55nicxwn2kj8hizpzqd")))) + "1yjbnj1p4z0vw84wga8q5fyqiw4n6r7pc6rdwam7vsbiamyzfcqs")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -554,14 +554,14 @@ single hidden layer, and for multinomial log-linear models.") (define-public r-rpart (package (name "r-rpart") - (version "4.1-12") + (version "4.1-13") (source (origin (method url-fetch) (uri (cran-uri "rpart" version)) (sha256 (base32 - "177p03w4m0qshb3sqkdyixim3f44g2an31v3vlbjmpzjvd5ff6yq")))) + "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rpart") (synopsis "Recursive partitioning and regression trees") @@ -939,14 +939,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.1.6") + (version "1.1.7") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "122im5m8x9bqpahc0hbxmvdq6hnsmgnxwwyjpvbihyv2jq5kd44m")))) + "0nck1s2iglmkrn15ay2chrrwsy5lngcylz2sc87fxy5skxaahxdl")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -1098,20 +1098,21 @@ agnes cluster diagrams.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "103wnc8sq0iwcnj4j14hd420d2dqdyf13s3f25icsznrlyzdkhf5")))) + "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) ("pkg-config" ,pkg-config))) (inputs - `(("cairo" ,cairo))) + `(("cairo" ,cairo) + ("zlib" ,zlib))) (propagated-inputs `(("r-withr" ,r-withr))) (home-page "https://cran.r-project.org/web/packages/gdtools") @@ -1187,13 +1188,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5")))) + "16nf8flxr5vdz8yrpprfbzydy3ajixkp9hc8ibd9n7r9nc29waym")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") @@ -1330,13 +1331,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.1.16") + (version "2.1.17") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "1xlsmqal607w6c9rx86061y1fwpbyd5lqp9bad5n7cc9a0blpnkm")))) + "10y6wnv2v8k396far29haqv2s82p4zm04rrsxk183wg19gb51was")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") @@ -2232,14 +2233,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1j8smqrb79lnaf2n9icksjiy641fcazsbkhmgg916s3nnyjngjz3")))) + "1qyql5gpwf88bkm1qarjhbqbq4hn6w0d8j4pxb5x7i96is30ap30")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) @@ -2481,13 +2482,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.8.300.1.0") + (version "0.8.400.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0p6cbnwxgzigf7n5qhqvxdr3nd3pq3c2qq6pskqz7avzf813fy83")))) + "11y2ksf46zw6fcz0kk70szyfn7qqxwwd33xylrxvnyb7ldmbc5yr")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs @@ -2575,14 +2576,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "0q1y1qx87xp6vf9h7mfl77rqhmd01xl53l9ap9qj99bfvpabb572")))) + "0wq6kbhrkv3fhcy4hg5yyv9gdvf8gr4nsjwdifs4ih8lnn0dmdyb")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2595,7 +2596,11 @@ certain criterion, e.g., it contains a certain regular file.") ("r-rprojroot" ,r-rprojroot) ("r-stringr" ,r-stringr) ("r-yaml" ,r-yaml) - ("ghc-pandoc" ,ghc-pandoc))) + ;; rmarkdown works with the 2.x release of Pandoc, but with degraded + ;; functionality. For example, tabbed plots do not currently work with + ;; Pandoc 2. The authors of rmarkdown recommend the use of Pandoc 1 + ;; for the time being. + ("ghc-pandoc" ,ghc-pandoc-1))) (home-page "http://rmarkdown.rstudio.com") (synopsis "Convert R Markdown documents into a variety of formats") (description @@ -2811,6 +2816,19 @@ plotted and compared with the asymptotic curve.") "0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x")))) (properties `((upstream-name . "lambda.r"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'check 'delete-test-log + ;; The test report contains time stamps and is not important for + ;; the installed package. + (lambda* (#:key outputs #:allow-other-keys) + (delete-file-recursively + (string-append (assoc-ref outputs "out") + "/site-library/lambda.r/unitTests")) + #t))))) + (native-inputs + `(("r-runit" ,r-runit))) (home-page "https://cran.r-project.org/web/packages/lambda.r") (synopsis "Functional programming extension for R") (description @@ -3315,20 +3333,20 @@ memory-mapped files.") (define-public r-nmf (package (name "r-nmf") - (version "0.20.6") + (version "0.21.0") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z")))) + "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) - ("r-bigmemory" ,r-bigmemory) - ("r-synchronicity" ,r-synchronicity) + ("r-bigmemory" ,r-bigmemory) ; suggested + ("r-synchronicity" ,r-synchronicity) ; suggested ("r-colorspace" ,r-colorspace) ("r-digest" ,r-digest) ("r-doparallel" ,r-doparallel) @@ -3577,14 +3595,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "0b0w30yq30c7bwpaghp3hp0nncqwcmvrra9j58fhx9jihay3l68c")))) + "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw")))) (build-system r-build-system) (propagated-inputs `(("r-glue" ,r-glue) @@ -4011,14 +4029,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-1") + (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf")))) + "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -4039,6 +4057,14 @@ Zurich, including many that are related to graphics.") (base32 "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-deterministic + (lambda _ + (substitute* "R/checkReverseDependencies.R" + (("tempdir\\(\\)") "\"/tmp\"")) + #t))))) (home-page "https://cran.r-project.org/web/packages/gtools") (synopsis "Various R programming tools") (description @@ -4882,27 +4908,6 @@ functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap.") (license license:gpl2))) -(define-public r-fnn - (package - (name "r-fnn") - (version "1.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "FNN" version)) - (sha256 - (base32 - "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj")))) - (properties `((upstream-name . "FNN"))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/FNN") - (synopsis "Fast nearest neighbor search algorithms and applications") - (description - "This package provides cover-tree and kd-tree fast k-nearest neighbor -search algorithms and related applications including KNN classification, -regression and information measures.") - (license license:gpl2+))) - (define-public r-minqa (package (name "r-minqa") @@ -5356,14 +5361,14 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "0k417a1xp5gxf77ycbnx5apzpc5d25sjm83ss7wmqpbnhnr5dcav")))) + "1pzkqfiahnsdm3zx46asgn8fw43vlxvbh7r4cn70c7ffmxabzzrc")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -5445,6 +5450,7 @@ manually \"recoding\").") (uri (hg-reference (url "https://bitbucket.org/tanaylab/tgstat") (changeset changeset))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn")))) @@ -5479,6 +5485,7 @@ tools.") (uri (hg-reference (url "https://bitbucket.org/tanaylab/tgconfig") (changeset changeset))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj")))) @@ -5539,3 +5546,72 @@ inferring an appropriate positioning method.") (description "Did you ever wish you could make scatter plots with cat shaped points? Now you can!") (license license:asl2.0)))) + +(define-public r-colorout + (package + (name "r-colorout") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/jalvesaq/colorout/archive/" + "v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v")))) + (build-system r-build-system) + (home-page "https://github.com/jalvesaq/colorout") + (synopsis "Colorize output in the R REPL") + (description "@code{colorout} is an R package that colorizes R output when +running in terminal emulator. + +R STDOUT is parsed and numbers, negative numbers, dates in the standard +format, strings, and R constants are identified and wrapped by special ANSI +scape codes that are interpreted by terminal emulators as commands to colorize +the output. R STDERR is also parsed to identify the expressions warning and +error and their translations to many languages. If these expressions are +found, the output is colorized accordingly; otherwise, it is colorized as +STDERROR (blue, by default). + +You can customize the colors according to your taste, guided by the color +table made by the command @code{show256Colors()}. You can also set the colors +to any arbitrary string. In this case, it is up to you to set valid values.") + (license license:gpl3+))) + +(define-public java-jdistlib + (package + (name "java-jdistlib") + (version "0.4.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-" + version "-src.jar")) + (sha256 + (base32 + "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "jdistlib.jar" + #:jdk ,icedtea-8 + #:tests? #f ; no dedicated test directory + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-broken-encoding + (lambda _ + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* "src/jdistlib/Beta.java" + (("Scheff.+-Tukey") "Scheffe-Tukey"))) + #t))))) + (propagated-inputs + `(("java-jtransforms" ,java-jtransforms))) + (native-inputs + `(("java-junit" ,java-junit))) + (home-page "http://jdistlib.sourceforge.net/") + (synopsis "Java library of statistical distributions") + (description "JDistlib is the Java Statistical Distribution Library, a +Java package that provides routines for various statistical distributions.") + ;; The files that were translated from R code are under GPLv2+; some files + ;; are under the GPLv3, which is a mistake. The author confirmed in an + ;; email that this whole project should be under GPLv2+. + (license license:gpl2+))) |