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.

2 files changed, 5 insertions, 5 deletions

diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
index c649036210..2c8a89f8de 100644
--- a/guix/build-system/r.scm
+++ b/guix/build-system/r.scm
@@ -50,7 +50,7 @@ available via the first URI, the second URI points to the archived version."
 (define (bioconductor-uri name version)
   "Return a URI string for the R package archive on Bioconductor for the
 release corresponding to NAME and VERSION."
-  (string-append "http://bioconductor.org/packages/release/bioc/src/contrib/"
+  (string-append "https://bioconductor.org/packages/release/bioc/src/contrib/"
                  name "_" version ".tar.gz"))
 
 (define %r-build-system-modules
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)