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| author | Tobias Geerinckx-Rice <me@tobias.gr> | 2017-10-20 02:39:56 +0200 |
|---|---|---|
| committer | Tobias Geerinckx-Rice <me@tobias.gr> | 2017-10-21 17:43:40 +0200 |
| commit | 5713bbf157a8e82fbb194519ce3d611de8db075d (patch) | |
| tree | a2bc4a88780b885cf1e8f2a0947aa41b0ab1ea0d /guix/import | |
| parent | 82bdcfe82141b7696f487a9ff721a834d5ce2347 (diff) | |
| download | gnu-guix-5713bbf157a8e82fbb194519ce3d611de8db075d.tar gnu-guix-5713bbf157a8e82fbb194519ce3d611de8db075d.tar.gz | |
Use HTTPS for bioconductor.org.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
Diffstat (limited to 'guix/import')
| -rw-r--r-- | guix/import/cran.scm | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 056a7dcc7c..9b08ebfb63 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -126,7 +126,7 @@ package definition." `((,type (,'quasiquote ,(format-inputs package-inputs))))))) (define %cran-url "http://cran.r-project.org/web/packages/") -(define %bioconductor-url "http://bioconductor.org/packages/") +(define %bioconductor-url "https://bioconductor.org/packages/") ;; The latest Bioconductor release is 3.5. Bioconductor packages should be ;; updated together. @@ -446,7 +446,7 @@ dependencies." (define (bioconductor-package? package) "Return true if PACKAGE is an R package from Bioconductor." (let ((predicate (lambda (uri) - (and (string-prefix? "http://bioconductor.org" uri) + (and (string-prefix? "https://bioconductor.org" uri) ;; Data packages are neither listed in SVN nor on ;; the Github mirror, so we have to exclude them ;; from the set of bioconductor packages that can be @@ -465,7 +465,7 @@ dependencies." (define (bioconductor-data-package? package) "Return true if PACKAGE is an R data package from Bioconductor." (let ((predicate (lambda (uri) - (and (string-prefix? "http://bioconductor.org" uri) + (and (string-prefix? "https://bioconductor.org" uri) (string-contains uri "/data/annotation/"))))) (and (string-prefix? "r-" (package-name package)) (match (and=> (package-source package) origin-uri) @@ -478,7 +478,7 @@ dependencies." (define (bioconductor-experiment-package? package) "Return true if PACKAGE is an R experiment package from Bioconductor." (let ((predicate (lambda (uri) - (and (string-prefix? "http://bioconductor.org" uri) + (and (string-prefix? "https://bioconductor.org" uri) (string-contains uri "/data/experiment/"))))) (and (string-prefix? "r-" (package-name package)) (match (and=> (package-source package) origin-uri) |