mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-26 06:18:07 -05:00
Merge branch 'master' into core-updates
This commit is contained in:
Ricardo Wurmus
commit
e0f8970357
7 changed files with 318 additions and 295 deletions
|
|
@ -64,14 +64,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm6
|
|||
(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 @@ (define-public r-hpar
|
|||
(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 @@ (define-public r-regioner
|
|||
("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 @@ (define-public r-regioner
|
|||
(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
|
||||
|
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@ -128,6 +129,8 @@ (define-public r-diffbind
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|||
("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)
|
||||
|
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@ -138,6 +141,7 @@ (define-public r-diffbind
|
|||
("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")
|
||||
|
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@ -151,14 +155,14 @@ (define-public r-diffbind
|
|||
(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 @@ (define-public r-multtest
|
|||
(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)
|
||||
|
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@ -250,6 +258,7 @@ (define-public r-chippeakanno
|
|||
("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)
|
||||
|
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@ -272,16 +281,15 @@ (define-public r-chippeakanno
|
|||
(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 @@ (define-public r-marray
|
|||
(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 @@ (define-public r-cghbase
|
|||
(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 @@ (define-public r-cghcall
|
|||
(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)
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
|
|
@ -4188,7 +4188,7 @@ (define-public emacs-projectile
|
|||
(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 @@ (define-public emacs-elfeed
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1fd1mx0q1qb9vgdzls5ppxfriyid48blg8smgjspiazp7kxakzxv"))))
|
||||
"1wkdrxr6zzqb48czqqv34l87bx8aqjk1739ddqg933aqh241kfvn"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
`(#:tests? #t
|
||||
|
|
|
|||
|
|
@ -155,14 +155,14 @@ (define-public r-diffusionmap
|
|||
(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
|
||||
|
|
|
|||
|
|
@ -113,10 +113,10 @@ (define-public pspp
|
|||
;; 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 @@ (define-public r-minimal
|
|||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"))))
|
||||
"0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:disallowed-references (,tzdata-for-tests)
|
||||
|
|
@ -217,11 +217,9 @@ (define-public r-minimal
|
|||
(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 @@ (define-public r-minimal
|
|||
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 @@ (define-public r-r-rsp
|
|||
(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)))
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@ (define* (maybe-inputs package-inputs #:optional (type 'inputs))
|
|||
(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/"
|
||||
|
|
|
|||
|
|
@ -171,7 +171,8 @@ (define* (scheme-node name modules #:optional (dependencies '())
|
|||
(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 @@ (define *system-modules*
|
|||
*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 @@ (define %nix-instantiate ;for (guix import snix)
|
|||
(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 @@ (define build
|
|||
;; 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 @@ (define* (compiled-modules name module-tree modules
|
|||
(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 @@ (define (report-compilation file total completed)
|
|||
(* 100. (/ completed total)) total)
|
||||
(force-output))
|
||||
|
||||
(define (process-directory directory output)
|
||||
(let ((files (find-files directory "\\.scm$"))
|
||||
(prefix (+ 1 (string-length directory))))
|
||||
;; Hide compilation warnings.
|
||||
(parameterize ((current-warning-port (%make-void-port "w")))
|
||||
(compile-files directory #$output
|
||||
(map (cut string-drop <> prefix) files)
|
||||
#:workers (parallel-job-count)
|
||||
#:report-load report-load
|
||||
#:report-compilation report-compilation))))
|
||||
(define (process-directory directory files output)
|
||||
;; Hide compilation warnings.
|
||||
(parameterize ((current-warning-port (%make-void-port "w")))
|
||||
(compile-files directory #$output files
|
||||
#:workers (parallel-job-count)
|
||||
#:report-load report-load
|
||||
#:report-compilation report-compilation)))
|
||||
|
||||
(setvbuf (current-output-port) _IONBF)
|
||||
(setvbuf (current-error-port) _IONBF)
|
||||
|
|
@ -579,7 +591,7 @@ (define (process-directory directory output)
|
|||
|
||||
(mkdir #$output)
|
||||
(chdir #+module-tree)
|
||||
(process-directory "." #$output)
|
||||
(process-directory "." '#+module-files #$output)
|
||||
(newline))))
|
||||
|
||||
(computed-file name build
|
||||
|
|
|
|||
Loading…
Reference in a new issue