From 5713bbf157a8e82fbb194519ce3d611de8db075d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 20 Oct 2017 02:39:56 +0200 Subject: 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. --- guix/import/cran.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'guix/import') 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 @@ (define* (maybe-inputs package-inputs #:optional (type 'inputs)) `((,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 @@ (define (cran-package? package) (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 @@ (define (bioconductor-package? package) (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 @@ (define (bioconductor-data-package? package) (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) -- cgit v1.2.3