diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 81 |
1 files changed, 32 insertions, 49 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0ae4dddb64..8afccb0737 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -39,6 +39,7 @@ #: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) @@ -172,21 +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. @@ -267,13 +262,16 @@ 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 (list (search-path-specification (variable "R_LIBS_SITE") (files (list "site-library/"))))) - (home-page "http://www.r-project.org/") + (home-page "https://www.r-project.org/") (synopsis "Environment for statistical computing and graphics") (description "R is a language and environment for statistical computing and graphics. @@ -941,14 +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))) @@ -2235,14 +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))) @@ -2598,7 +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 @@ -3331,20 +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) @@ -4027,14 +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") @@ -4906,27 +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") @@ -5037,7 +5018,7 @@ using modular prediction and response module classes.") `(("r-matrix" ,r-matrix) ("r-matrixmodels" ,r-matrixmodels) ("r-sparsem" ,r-sparsem))) - (home-page "http://www.r-project.org") + (home-page "https://www.r-project.org") (synopsis "Quantile regression") (description "This package provides an estimation and inference methods for models @@ -5469,6 +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")))) @@ -5503,6 +5485,7 @@ tools.") (uri (hg-reference (url "https://bitbucket.org/tanaylab/tgconfig") (changeset changeset))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj")))) |