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Merge branch 'master' into core-updates

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Ricardo Wurmus 2018-06-02 13:44:43 +02:00
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7 changed files with 318 additions and 295 deletions
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51
gnu/packages/bioconductor.scm
View file

@ -64,14 +64,14 @@ objects.")
(define-public r-hpar
(package
(name "r-hpar")
(version "1.20.0")
(version "1.22.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
"0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8"))))
"1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
@ -82,14 +82,14 @@ the Human Protein Atlas project.")
(define-public r-regioner
(package
(name "r-regioner")
(version "1.10.0")
(version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
"1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
"09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@ -98,7 +98,8 @@ the Human Protein Atlas project.")
("r-bsgenome" ,r-bsgenome)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)
("r-iranges" ,r-iranges)))
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/regioneR/")
(synopsis "Association analysis of genomic regions")
(description "This package offers a statistical framework based on
@ -109,14 +110,14 @@ region sets and other genomic features.")
(define-public r-diffbind
(package
(name "r-diffbind")
(version "2.6.6")
(version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
"1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp"))))
"1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
@ -128,6 +129,8 @@ region sets and other genomic features.")
("r-dplyr" ,r-dplyr)
("r-edger" ,r-edger)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-ggrepel" ,r-ggrepel)
("r-gplots" ,r-gplots)
("r-iranges" ,r-iranges)
@ -138,6 +141,7 @@ region sets and other genomic features.")
("r-rcpp" ,r-rcpp)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-systempiper" ,r-systempiper)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "http://bioconductor.org/packages/DiffBind")
@ -151,14 +155,14 @@ occupancy (overlap) analysis and plotting functions.")
(define-public r-ripseeker
(package
(name "r-ripseeker")
(version "1.18.0")
(version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RIPSeeker" version))
(sha256
(base32
"0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"))))
"0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
@ -222,23 +226,27 @@ expressed genes in DNA microarray experiments.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
(version "3.12.7")
(version "3.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
"1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04"))))
"1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-delayedarray" ,r-delayedarray)
("r-go-db" ,r-go-db)
("r-biomart" ,r-biomart)
("r-bsgenome" ,r-bsgenome)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-iranges" ,r-iranges)
("r-matrixstats" ,r-matrixstats)
("r-annotationdbi" ,r-annotationdbi)
("r-limma" ,r-limma)
@ -250,6 +258,7 @@ expressed genes in DNA microarray experiments.")
("r-dbi" ,r-dbi)
("r-ensembldb" ,r-ensembldb)
("r-biobase" ,r-biobase)
("r-s4vectors" ,r-s4vectors)
("r-seqinr" ,r-seqinr)
("r-idr" ,r-idr)
("r-genomicalignments" ,r-genomicalignments)
@ -272,16 +281,15 @@ enrichedGO (addGeneIDs).")
(define-public r-marray
(package
(name "r-marray")
(version "1.56.0")
(version "1.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
(base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic"))))
(base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-limma" ,r-limma)))
`(("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/marray")
(synopsis "Exploratory analysis for two-color spotted microarray data")
(description "This package contains class definitions for two-color spotted
@ -292,12 +300,12 @@ normalization and quality checking.")
(define-public r-cghbase
(package
(name "r-cghbase")
(version "1.38.0")
(version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
(base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"))))
(base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
@ -312,12 +320,12 @@ the @code{arrayCGH} packages.")
(define-public r-cghcall
(package
(name "r-cghcall")
(version "2.40.0")
(version "2.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
(base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch"))))
(base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
@ -335,16 +343,17 @@ the @code{arrayCGH} packages.")
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
(version "1.14.0")
(version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
(base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
(base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocparallel" ,r-biocparallel)
("r-cghbase" ,r-cghbase)
("r-cghcall" ,r-cghcall)
("r-dnacopy" ,r-dnacopy)

473
gnu/packages/bioinformatics.scm
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File diff suppressed because it is too large Load diff

4
gnu/packages/emacs.scm
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@ -4188,7 +4188,7 @@ If you want to mark a folder manually as a project just create an empty
(define-public emacs-elfeed
(package
(name "emacs-elfeed")
(version "2.3.0")
(version "3.0.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/skeeto/elfeed/archive/"
@ -4196,7 +4196,7 @@ If you want to mark a folder manually as a project just create an empty
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1fd1mx0q1qb9vgdzls5ppxfriyid48blg8smgjspiazp7kxakzxv"))))
"1wkdrxr6zzqb48czqqv34l87bx8aqjk1739ddqg933aqh241kfvn"))))
(build-system emacs-build-system)
(arguments
`(#:tests? #t

4
gnu/packages/graph.scm
View file

@ -155,14 +155,14 @@ model.")
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
(version "2.22.0")
(version "2.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
"1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv"))))
"1037hzfxxcn46w6y88wm3kk2nixj0s8bk0hkmnshpxih3kmnvqby"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
;; FIXME: Rgraphviz bundles the sources of an older variant of

33
gnu/packages/statistics.scm
View file

@ -113,10 +113,10 @@ be output in text, PostScript, PDF or HTML.")
;; Update this package together with the set of recommended packages: r-boot,
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
(define-public r-minimal
(define r-with-tests
(package
(name "r-minimal")
(version "3.4.4")
(name "r-with-tests")
(version "3.5.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@ -124,7 +124,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz"))
(sha256
(base32
"0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"))))
"0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
(build-system gnu-build-system)
(arguments
`(#:disallowed-references (,tzdata-for-tests)
@ -217,11 +217,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
(add-after 'build 'install-info
(lambda _ (zero? (system* "make" "install-info")))))
#:configure-flags
`(;; Do not build the recommended packages. The build system creates
;; random temporary directories and embeds their names in some
;; package files. We build these packages with the r-build-system
;; instead.
"--without-recommended-packages"
`(;; We build the recommended packages here, because they are needed in
;; order to run the test suite. We disable them in the r-minimal
;; package.
"--with-cairo"
"--with-blas=-lopenblas"
"--with-libpng"
@ -292,6 +290,19 @@ publication-quality data plots. A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
(license license:gpl3+)))
(define-public r-minimal
(package (inherit r-with-tests)
(name "r-minimal")
(arguments
`(#:tests? #f
,@(substitute-keyword-arguments (package-arguments r-with-tests)
((#:configure-flags flags)
;; Do not build the recommended packages. The build system creates
;; random temporary directories and embeds their names in some
;; package files. We build these packages with the r-build-system
;; instead.
`(cons "--without-recommended-packages" ,flags)))))))
(define-public rmath-standalone
(package (inherit r-minimal)
(name "rmath-standalone")
@ -3522,13 +3533,13 @@ vignettes.")
(define-public r-mvtnorm
(package
(name "r-mvtnorm")
(version "1.0-7")
(version "1.0-8")
(source (origin
(method url-fetch)
(uri (cran-uri "mvtnorm" version))
(sha256
(base32
"0f7hzflygdnbwvzadr3knhybhanwg7agqddclj6mhbvwqpgb0qyh"))))
"0la42lylb7cjrcrc285bn69bz9kyg556xw317iz139dp1yswl410"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)))

4
guix/import/cran.scm
View file

@ -128,9 +128,9 @@ package definition."
(define %cran-url "http://cran.r-project.org/web/packages/")
(define %bioconductor-url "https://bioconductor.org/packages/")
;; The latest Bioconductor release is 3.6. Bioconductor packages should be
;; The latest Bioconductor release is 3.7. Bioconductor packages should be
;; updated together.
(define %bioconductor-version "3.6")
(define %bioconductor-version "3.7")
(define %bioconductor-packages-list-url
(string-append "https://bioconductor.org/packages/"

36
guix/self.scm
View file

@ -171,7 +171,8 @@ must be present in the search path."
(source (imported-files (string-append name "-source")
(append module-files extra-files))))
(node name modules source dependencies
(compiled-modules name source modules
(compiled-modules name source
(map car module-files)
(map node-source dependencies)
(map node-compiled dependencies)
#:extensions extensions
@ -313,7 +314,12 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
*extra-modules* *core-modules*)
#:extensions dependencies
#:extra-files
(file-imports source "gnu/system/examples" (const #t))
(append (file-imports source "gnu/system/examples"
(const #t))
;; Build-side code that we don't build. Some of
;; these depend on guile-rsvg, the Shepherd, etc.
(file-imports source "gnu/build" (const #t)))
#:guile-for-build
guile-for-build))
@ -481,6 +487,11 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
(define (imported-files name files)
;; This is a non-monadic, simplified version of 'imported-files' from (guix
;; gexp).
(define same-target?
(match-lambda*
(((file1 . _) (file2 . _))
(string=? file1 file2))))
(define build
(with-imported-modules (source-module-closure
'((guix build utils)))
@ -497,14 +508,15 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
;; symlinks, as this makes a difference for
;; 'add-to-store'.
(copy-file store-path final-path)))
'#$files))))
'#$(delete-duplicates files same-target?)))))
;; We're just copying files around, no need to substitute or offload it.
(computed-file name build
#:options '(#:local-build? #t
#:substitutable? #f)))
#:substitutable? #f
#:env-vars (("COLUMNS" . "200")))))
(define* (compiled-modules name module-tree modules
(define* (compiled-modules name module-tree module-files
#:optional
(dependencies '())
(dependencies-compiled '())
@ -512,6 +524,9 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
(extensions '()) ;full-blown Guile packages
parallel?
guile-for-build)
"Build all the MODULE-FILES from MODULE-TREE. MODULE-FILES must be a list
like '(\"guix/foo.scm\" \"gnu/bar.scm\") and MODULE-TREE is the directory
containing MODULE-FILES and possibly other files as well."
;; This is a non-monadic, enhanced version of 'compiled-file' from (guix
;; gexp).
(define build
@ -542,16 +557,13 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
(* 100. (/ completed total)) total)
(force-output))
(define (process-directory directory output)
(let ((files (find-files directory "\\.scm$"))
(prefix (+ 1 (string-length directory))))
(define (process-directory directory files output)
;; Hide compilation warnings.
(parameterize ((current-warning-port (%make-void-port "w")))
(compile-files directory #$output
(map (cut string-drop <> prefix) files)
(compile-files directory #$output files
#:workers (parallel-job-count)
#:report-load report-load
#:report-compilation report-compilation))))
#:report-compilation report-compilation)))
(setvbuf (current-output-port) _IONBF)
(setvbuf (current-error-port) _IONBF)
@ -579,7 +591,7 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
(mkdir #$output)
(chdir #+module-tree)
(process-directory "." #$output)
(process-directory "." '#+module-files #$output)
(newline))))
(computed-file name build