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-rw-r--r--gnu/packages/statistics.scm81
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"))))