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.

doc/guix.texi

@@ -5881,7 +5881,7 @@ dependency graph of the given upstream package recursively and generate
 package expressions for all those packages that are not yet in Guix.
 
 When @code{--archive=bioconductor} is added, metadata is imported from
-@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R
+@uref{https://www.bioconductor.org/, Bioconductor}, a repository of R
 packages for for the analysis and comprehension of high-throughput
 genomic data in bioinformatics.
 
@@ -6236,7 +6236,7 @@ the updater for @uref{http://elpa.gnu.org/, ELPA} packages;
 @item cran
 the updater for @uref{http://cran.r-project.org/, CRAN} packages;
 @item bioconductor
-the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages;
+the updater for @uref{https://www.bioconductor.org/, Bioconductor} R packages;
 @item cpan
 the updater for @uref{http://www.cpan.org/, CPAN} packages;
 @item pypi

gnu/packages/bioinformatics.scm

@@ -5747,7 +5747,7 @@ (define-public r-annotate
        ("r-xml" ,r-xml)
        ("r-xtable" ,r-xtable)))
     (home-page
-     "http://bioconductor.org/packages/annotate")
+     "https://bioconductor.org/packages/annotate")
     (synopsis "Annotation for microarrays")
     (description "This package provides R environments for the annotation of
 microarrays.")
@@ -5772,7 +5772,7 @@ (define-public r-geneplotter
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-lattice" ,r-lattice)
        ("r-rcolorbrewer" ,r-rcolorbrewer)))
-    (home-page "http://bioconductor.org/packages/geneplotter")
+    (home-page "https://bioconductor.org/packages/geneplotter")
     (synopsis "Graphics functions for genomic data")
     (description
      "This package provides functions for plotting genomic data.")
@@ -5798,7 +5798,7 @@ (define-public r-genefilter
        ("r-biobase" ,r-biobase)
        ("r-s4vectors" ,r-s4vectors)
        ("r-survival" ,r-survival)))
-    (home-page "http://bioconductor.org/packages/genefilter")
+    (home-page "https://bioconductor.org/packages/genefilter")
     (synopsis "Filter genes from high-throughput experiments")
     (description
      "This package provides basic functions for filtering genes from
@@ -5833,7 +5833,7 @@ (define-public r-deseq2
        ("r-rcpparmadillo" ,r-rcpparmadillo)
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (home-page "http://bioconductor.org/packages/DESeq2")
+    (home-page "https://bioconductor.org/packages/DESeq2")
     (synopsis "Differential gene expression analysis")
     (description
      "This package provides functions to estimate variance-mean dependence in
@@ -5873,7 +5873,7 @@ (define-public r-dexseq
        ("r-statmod" ,r-statmod)
        ("r-stringr" ,r-stringr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (home-page "http://bioconductor.org/packages/DEXSeq")
+    (home-page "https://bioconductor.org/packages/DEXSeq")
     (synopsis "Inference of differential exon usage in RNA-Seq")
     (description
      "This package is focused on finding differential exon usage using RNA-seq
@@ -5908,7 +5908,7 @@ (define-public r-annotationforge
        ("r-rsqlite" ,r-rsqlite)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xml" ,r-xml)))
-    (home-page "http://bioconductor.org/packages/AnnotationForge")
+    (home-page "https://bioconductor.org/packages/AnnotationForge")
     (synopsis "Code for building annotation database packages")
     (description
      "This package provides code for generating Annotation packages and their
@@ -5929,7 +5929,7 @@ (define-public r-rbgl
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs `(("r-graph" ,r-graph)))
-    (home-page "http://www.bioconductor.org/packages/RBGL")
+    (home-page "https://www.bioconductor.org/packages/RBGL")
     (synopsis "Interface to the Boost graph library")
     (description
      "This package provides a fairly extensive and comprehensive interface to
@@ -5956,7 +5956,7 @@ (define-public r-gseabase
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-graph" ,r-graph)
        ("r-xml" ,r-xml)))
-    (home-page "http://bioconductor.org/packages/GSEABase")
+    (home-page "https://bioconductor.org/packages/GSEABase")
     (synopsis "Gene set enrichment data structures and methods")
     (description
      "This package provides classes and methods to support @dfn{Gene Set
@@ -5987,7 +5987,7 @@ (define-public r-category
        ("r-matrix" ,r-matrix)
        ("r-rbgl" ,r-rbgl)
        ("r-rsqlite" ,r-rsqlite)))
-    (home-page "http://bioconductor.org/packages/Category")
+    (home-page "https://bioconductor.org/packages/Category")
     (synopsis "Category analysis")
     (description
      "This package provides a collection of tools for performing category
@@ -6016,7 +6016,7 @@ (define-public r-gostats
        ("r-go-db" ,r-go-db)
        ("r-graph" ,r-graph)
        ("r-rbgl" ,r-rbgl)))
-    (home-page "http://bioconductor.org/packages/GOstats")
+    (home-page "https://bioconductor.org/packages/GOstats")
     (synopsis "Tools for manipulating GO and microarrays")
     (description
      "This package provides a set of tools for interacting with GO and
@@ -6055,7 +6055,7 @@ (define-public r-shortread
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)
        ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "http://bioconductor.org/packages/ShortRead")
+    (home-page "https://bioconductor.org/packages/ShortRead")
     (synopsis "FASTQ input and manipulation tools")
     (description
      "This package implements sampling, iteration, and input of FASTQ files.
@@ -6147,7 +6147,7 @@ (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://bioconductor.org/packages/"
+              (uri (string-append "https://bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib"
                                   "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
                                   version ".tar.gz"))
@@ -6163,7 +6163,7 @@ (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
     (propagated-inputs
      `(("r-genomicfeatures" ,r-genomicfeatures)))
     (home-page
-     "http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
+     "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
     (synopsis "Annotation package for human genome in TxDb format")
     (description
      "This package provides an annotation database of Homo sapiens genome
@@ -6444,7 +6444,7 @@ (define-public r-biocgenerics
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
-    (home-page "http://bioconductor.org/packages/BiocGenerics")
+    (home-page "https://bioconductor.org/packages/BiocGenerics")
     (synopsis "S4 generic functions for Bioconductor")
     (description
      "This package provides S4 generic functions needed by many Bioconductor
@@ -6464,7 +6464,7 @@ (define-public r-biocinstaller
     (properties
      `((upstream-name . "BiocInstaller")))
     (build-system r-build-system)
-    (home-page "http://bioconductor.org/packages/BiocInstaller")
+    (home-page "https://bioconductor.org/packages/BiocInstaller")
     (synopsis "Install Bioconductor packages")
     (description "This package is used to install and update R packages from
 Bioconductor, CRAN, and Github.")
@@ -6491,7 +6491,7 @@ (define-public r-biocviews
        ("r-xml" ,r-xml)
        ("r-knitr" ,r-knitr)
        ("r-runit" ,r-runit)))
-    (home-page "http://bioconductor.org/packages/biocViews")
+    (home-page "https://bioconductor.org/packages/biocViews")
     (synopsis "Bioconductor package categorization helper")
     (description "The purpose of biocViews is to create HTML pages that
 categorize packages in a Bioconductor package repository according to keywords,
@@ -6538,7 +6538,7 @@ (define-public r-biocstyle
        ("r-knitr" ,r-knitr)
        ("r-rmarkdown" ,r-rmarkdown)
        ("r-yaml" ,r-yaml)))
-    (home-page "http://bioconductor.org/packages/BiocStyle")
+    (home-page "https://bioconductor.org/packages/BiocStyle")
     (synopsis "Bioconductor formatting styles")
     (description "This package provides standard formatting styles for
 Bioconductor PDF and HTML documents.  Package vignettes illustrate use and
@@ -6586,7 +6586,7 @@ (define-public r-bioccheck
        ("r-optparse" ,r-optparse)
        ("r-biocinstaller" ,r-biocinstaller)
        ("r-biocviews" ,r-biocviews)))
-    (home-page "http://bioconductor.org/packages/BiocCheck")
+    (home-page "https://bioconductor.org/packages/BiocCheck")
     (synopsis "Executes Bioconductor-specific package checks")
     (description "This package contains tools to perform additional quality
 checks on R packages that are to be submitted to the Bioconductor repository.")
@@ -6674,7 +6674,7 @@ (define-public r-s4vectors
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
-    (home-page "http://bioconductor.org/packages/S4Vectors")
+    (home-page "https://bioconductor.org/packages/S4Vectors")
     (synopsis "S4 implementation of vectors and lists")
     (description
      "The S4Vectors package defines the @code{Vector} and @code{List} virtual
@@ -6727,7 +6727,7 @@ (define-public r-iranges
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-s4vectors" ,r-s4vectors)))
-    (home-page "http://bioconductor.org/packages/IRanges")
+    (home-page "https://bioconductor.org/packages/IRanges")
     (synopsis "Infrastructure for manipulating intervals on sequences")
     (description
      "This package provides efficient low-level and highly reusable S4 classes
@@ -6757,7 +6757,7 @@ (define-public r-genomeinfodbdata
     (properties
      `((upstream-name . "GenomeInfoDbData")))
     (build-system r-build-system)
-    (home-page "http://bioconductor.org/packages/GenomeInfoDbData")
+    (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
     (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
     (description "This package contains data for mapping between NCBI taxonomy
 ID and species.  It is used by functions in the GenomeInfoDb package.")
@@ -6782,7 +6782,7 @@ (define-public r-genomeinfodb
        ("r-iranges" ,r-iranges)
        ("r-rcurl" ,r-rcurl)
        ("r-s4vectors" ,r-s4vectors)))
-    (home-page "http://bioconductor.org/packages/GenomeInfoDb")
+    (home-page "https://bioconductor.org/packages/GenomeInfoDb")
     (synopsis "Utilities for manipulating chromosome identifiers")
     (description
      "This package contains data and functions that define and allow
@@ -6904,7 +6904,7 @@ (define-public r-xvector
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-iranges" ,r-iranges)
        ("r-s4vectors" ,r-s4vectors)))
-    (home-page "http://bioconductor.org/packages/XVector")
+    (home-page "https://bioconductor.org/packages/XVector")
     (synopsis "Representation and manpulation of external sequences")
     (description
      "This package provides memory efficient S4 classes for storing sequences
@@ -6930,7 +6930,7 @@ (define-public r-genomicranges
        ("r-iranges" ,r-iranges)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))
-    (home-page "http://bioconductor.org/packages/GenomicRanges")
+    (home-page "https://bioconductor.org/packages/GenomicRanges")
     (synopsis "Representation and manipulation of genomic intervals")
     (description
      "This package provides tools to efficiently represent and manipulate
@@ -6955,7 +6955,7 @@ (define-public r-biobase
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
-    (home-page "http://bioconductor.org/packages/Biobase")
+    (home-page "https://bioconductor.org/packages/Biobase")
     (synopsis "Base functions for Bioconductor")
     (description
      "This package provides functions that are needed by many other packages
@@ -6982,7 +6982,7 @@ (define-public r-annotationdbi
        ("r-iranges" ,r-iranges)
        ("r-rsqlite" ,r-rsqlite)
        ("r-s4vectors" ,r-s4vectors)))
-    (home-page "http://bioconductor.org/packages/AnnotationDbi")
+    (home-page "https://bioconductor.org/packages/AnnotationDbi")
     (synopsis "Annotation database interface")
     (description
      "This package provides user interface and database connection code for
@@ -7006,7 +7006,7 @@ (define-public r-biomart
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-rcurl" ,r-rcurl)
        ("r-xml" ,r-xml)))
-    (home-page "http://bioconductor.org/packages/biomaRt")
+    (home-page "https://bioconductor.org/packages/biomaRt")
     (synopsis "Interface to BioMart databases")
     (description
      "biomaRt provides an interface to a growing collection of databases
@@ -7035,7 +7035,7 @@ (define-public r-biocparallel
     (propagated-inputs
      `(("r-futile-logger" ,r-futile-logger)
        ("r-snow" ,r-snow)))
-    (home-page "http://bioconductor.org/packages/BiocParallel")
+    (home-page "https://bioconductor.org/packages/BiocParallel")
     (synopsis "Bioconductor facilities for parallel evaluation")
     (description
      "This package provides modified versions and novel implementation of
@@ -7061,7 +7061,7 @@ (define-public r-biostrings
        ("r-iranges" ,r-iranges)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))
-    (home-page "http://bioconductor.org/packages/Biostrings")
+    (home-page "https://bioconductor.org/packages/Biostrings")
     (synopsis "String objects and algorithms for biological sequences")
     (description
      "This package provides memory efficient string containers, string
@@ -7104,7 +7104,7 @@ (define-public r-rsamtools
        ("r-iranges" ,r-iranges)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))
-    (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
+    (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
     (synopsis "Interface to samtools, bcftools, and tabix")
     (description
      "This package provides an interface to the 'samtools', 'bcftools', and
@@ -7131,7 +7131,7 @@ (define-public r-delayedarray
        ("r-s4vectors" ,r-s4vectors)
        ("r-iranges" ,r-iranges)
        ("r-matrixstats" ,r-matrixstats)))
-    (home-page "http://bioconductor.org/packages/DelayedArray")
+    (home-page "https://bioconductor.org/packages/DelayedArray")
     (synopsis "Delayed operations on array-like objects")
     (description
      "Wrapping an array-like object (typically an on-disk object) in a
@@ -7165,7 +7165,7 @@ (define-public r-summarizedexperiment
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
        ("r-s4vectors" ,r-s4vectors)))
-    (home-page "http://bioconductor.org/packages/SummarizedExperiment")
+    (home-page "https://bioconductor.org/packages/SummarizedExperiment")
     (synopsis "Container for representing genomic ranges by sample")
     (description
      "The SummarizedExperiment container contains one or more assays, each
@@ -7197,7 +7197,7 @@ (define-public r-genomicalignments
        ("r-rsamtools" ,r-rsamtools)
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (home-page "http://bioconductor.org/packages/GenomicAlignments")
+    (home-page "https://bioconductor.org/packages/GenomicAlignments")
     (synopsis "Representation and manipulation of short genomic alignments")
     (description
      "This package provides efficient containers for storing and manipulating
@@ -7242,7 +7242,7 @@ (define-public r-rtracklayer
        ("r-s4vectors" ,r-s4vectors)
        ("r-xml" ,r-xml)
        ("r-xvector" ,r-xvector)))
-    (home-page "http://bioconductor.org/packages/rtracklayer")
+    (home-page "https://bioconductor.org/packages/rtracklayer")
     (synopsis "R interface to genome browsers and their annotation tracks")
     (description
      "rtracklayer is an extensible framework for interacting with multiple
@@ -7280,7 +7280,7 @@ (define-public r-genomicfeatures
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))
-    (home-page "http://bioconductor.org/packages/GenomicFeatures")
+    (home-page "https://bioconductor.org/packages/GenomicFeatures")
     (synopsis "Tools for working with transcript centric annotations")
     (description
      "This package provides a set of tools and methods for making and
@@ -7299,7 +7299,7 @@ (define-public r-go-db
     (version "3.4.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/GO.db_"
                                   version ".tar.gz"))
               (sha256
@@ -7310,7 +7310,7 @@ (define-public r-go-db
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "http://bioconductor.org/packages/GO.db")
+    (home-page "https://bioconductor.org/packages/GO.db")
     (synopsis "Annotation maps describing the entire Gene Ontology")
     (description
      "The purpose of this GO.db annotation package is to provide detailed
@@ -7330,7 +7330,7 @@ (define-public r-graph
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
-    (home-page "http://bioconductor.org/packages/graph")
+    (home-page "https://bioconductor.org/packages/graph")
     (synopsis "Handle graph data structures in R")
     (description
      "This package implements some simple graph handling capabilities for R.")
@@ -7359,7 +7359,7 @@ (define-public r-topgo
        ("r-lattice" ,r-lattice)
        ("r-matrixstats" ,r-matrixstats)
        ("r-sparsem" ,r-sparsem)))
-    (home-page "http://bioconductor.org/packages/topGO")
+    (home-page "https://bioconductor.org/packages/topGO")
     (synopsis "Enrichment analysis for gene ontology")
     (description
      "The topGO package provides tools for testing @dfn{gene ontology} (GO)
@@ -7392,7 +7392,7 @@ (define-public r-bsgenome
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))
-    (home-page "http://bioconductor.org/packages/BSgenome")
+    (home-page "https://bioconductor.org/packages/BSgenome")
     (synopsis "Infrastructure for Biostrings-based genome data packages")
     (description
      "This package provides infrastructure shared by all Biostrings-based
@@ -7407,7 +7407,7 @@ (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "BSgenome.Hsapiens.1000genomes.hs37d5_"
                                   version ".tar.gz"))
@@ -7423,7 +7423,7 @@ (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
-     "http://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
+     "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
     (synopsis "Full genome sequences for Homo sapiens")
     (description
      "This package provides full genome sequences for Homo sapiens from
@@ -7443,7 +7443,7 @@ (define-public r-impute
     (inputs
      `(("gfortran" ,gfortran)))
     (build-system r-build-system)
-    (home-page "http://bioconductor.org/packages/impute")
+    (home-page "https://bioconductor.org/packages/impute")
     (synopsis "Imputation for microarray data")
     (description
      "This package provides a function to impute missing gene expression
@@ -7469,7 +7469,7 @@ (define-public r-seqpattern
        ("r-iranges" ,r-iranges)
        ("r-kernsmooth" ,r-kernsmooth)
        ("r-plotrix" ,r-plotrix)))
-    (home-page "http://bioconductor.org/packages/seqPattern")
+    (home-page "https://bioconductor.org/packages/seqPattern")
     (synopsis "Visualising oligonucleotide patterns and motif occurrences")
     (description
      "This package provides tools to visualize oligonucleotide patterns and
@@ -7562,7 +7562,7 @@ (define-public r-org-hs-eg-db
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "org.Hs.eg.db_" version ".tar.gz"))
               (sha256
@@ -7573,7 +7573,7 @@ (define-public r-org-hs-eg-db
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/")
+    (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
     (synopsis "Genome wide annotation for Human")
     (description
      "This package provides mappings from Entrez gene identifiers to various
@@ -7588,7 +7588,7 @@ (define-public r-org-ce-eg-db
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "org.Ce.eg.db_" version ".tar.gz"))
               (sha256
@@ -7599,7 +7599,7 @@ (define-public r-org-ce-eg-db
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/")
+    (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
     (synopsis "Genome wide annotation for Worm")
     (description
      "This package provides mappings from Entrez gene identifiers to various
@@ -7614,7 +7614,7 @@ (define-public r-org-dm-eg-db
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "org.Dm.eg.db_" version ".tar.gz"))
               (sha256
@@ -7625,7 +7625,7 @@ (define-public r-org-dm-eg-db
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/")
+    (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
     (synopsis "Genome wide annotation for Fly")
     (description
      "This package provides mappings from Entrez gene identifiers to various
@@ -7640,7 +7640,7 @@ (define-public r-org-mm-eg-db
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "org.Mm.eg.db_" version ".tar.gz"))
               (sha256
@@ -7651,7 +7651,7 @@ (define-public r-org-mm-eg-db
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/")
+    (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
     (synopsis "Genome wide annotation for Mouse")
     (description
      "This package provides mappings from Entrez gene identifiers to various
@@ -7671,7 +7671,7 @@ (define-public r-seqlogo
          "19d5zmy7m8svljwgbmrb4vxkq18slq0f3all6k2ayv42b8w44h6q"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
-    (home-page "http://bioconductor.org/packages/seqLogo")
+    (home-page "https://bioconductor.org/packages/seqLogo")
     (synopsis "Sequence logos for DNA sequence alignments")
     (description
      "seqLogo takes the position weight matrix of a DNA sequence motif and
@@ -7687,7 +7687,7 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "BSgenome.Hsapiens.UCSC.hg19_"
                                   version ".tar.gz"))
@@ -7703,7 +7703,7 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
-     "http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
+     "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
     (synopsis "Full genome sequences for Homo sapiens")
     (description
      "This package provides full genome sequences for Homo sapiens as provided
@@ -7718,7 +7718,7 @@ (define-public r-bsgenome-mmusculus-ucsc-mm9
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "BSgenome.Mmusculus.UCSC.mm9_"
                                   version ".tar.gz"))
@@ -7734,7 +7734,7 @@ (define-public r-bsgenome-mmusculus-ucsc-mm9
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
-     "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
+     "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
     (synopsis "Full genome sequences for Mouse")
     (description
      "This package provides full genome sequences for Mus musculus (Mouse) as
@@ -7749,7 +7749,7 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "BSgenome.Mmusculus.UCSC.mm10_"
                                   version ".tar.gz"))
@@ -7765,7 +7765,7 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
-     "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
+     "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
     (synopsis "Full genome sequences for Mouse")
     (description
      "This package provides full genome sequences for Mus
@@ -7781,7 +7781,7 @@ (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "TxDb.Mmusculus.UCSC.mm10.knownGene_"
                                   version ".tar.gz"))
@@ -7799,7 +7799,7 @@ (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-annotationdbi" ,r-annotationdbi)))
     (home-page
-     "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
+     "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
     (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
     (description
      "This package loads a TxDb object, which is an R interface to
@@ -7816,7 +7816,7 @@ (define-public r-bsgenome-celegans-ucsc-ce6
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "BSgenome.Celegans.UCSC.ce6_"
                                   version ".tar.gz"))
@@ -7832,7 +7832,7 @@ (define-public r-bsgenome-celegans-ucsc-ce6
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
-     "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
+     "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
     (synopsis "Full genome sequences for Worm")
     (description
      "This package provides full genome sequences for Caenorhabditis
@@ -7848,7 +7848,7 @@ (define-public r-bsgenome-celegans-ucsc-ce10
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "BSgenome.Celegans.UCSC.ce10_"
                                   version ".tar.gz"))
@@ -7864,7 +7864,7 @@ (define-public r-bsgenome-celegans-ucsc-ce10
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
-     "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
+     "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
     (synopsis "Full genome sequences for Worm")
     (description
      "This package provides full genome sequences for Caenorhabditis
@@ -7880,7 +7880,7 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
               ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/data/annotation/src/contrib/"
                                   "BSgenome.Dmelanogaster.UCSC.dm3_"
                                   version ".tar.gz"))
@@ -7896,7 +7896,7 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
-     "http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
+     "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
     (synopsis "Full genome sequences for Fly")
     (description
      "This package provides full genome sequences for Drosophila
@@ -7924,7 +7924,7 @@ (define-public r-motifrg
        ("r-iranges" ,r-iranges)
        ("r-seqlogo" ,r-seqlogo)
        ("r-xvector" ,r-xvector)))
-    (home-page "http://bioconductor.org/packages/motifRG")
+    (home-page "https://bioconductor.org/packages/motifRG")
     (synopsis "Discover motifs in high throughput sequencing data")
     (description
      "This package provides tools for discriminative motif discovery in high
@@ -8046,7 +8046,7 @@ (define-public r-bamsignals
        ("r-zlibbioc" ,r-zlibbioc)))
     (inputs
      `(("zlib" ,zlib)))
-    (home-page "http://bioconductor.org/packages/bamsignals")
+    (home-page "https://bioconductor.org/packages/bamsignals")
     (synopsis "Extract read count signals from bam files")
     (description
      "This package allows to efficiently obtain count vectors from indexed bam
@@ -8175,7 +8175,7 @@ (define-public r-mutationalpatterns
        ("r-reshape2" ,r-reshape2)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-variantannotation" ,r-variantannotation)))
-    (home-page "http://bioconductor.org/packages/MutationalPatterns/")
+    (home-page "https://bioconductor.org/packages/MutationalPatterns/")
     (synopsis "Extract and visualize mutational patterns in genomic data")
     (description "This package provides an extensive toolset for the
 characterization and visualization of a wide range of mutational patterns
@@ -8331,7 +8331,7 @@ (define-public r-tximport
                (base32
                 "1mklb02bj4gnbjlmb7vv6k4lr3w9fp3pzli9rddbrwd0y5n8fcpx"))))
     (build-system r-build-system)
-    (home-page "http://bioconductor.org/packages/tximport")
+    (home-page "https://bioconductor.org/packages/tximport")
     (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
     (description
      "This package provides tools to import transcript-level abundance,
@@ -8373,7 +8373,7 @@ (define-public r-rhdf5
     (inputs
      `(("perl" ,perl)
        ("zlib" ,zlib)))
-    (home-page "http://bioconductor.org/packages/rhdf5")
+    (home-page "https://bioconductor.org/packages/rhdf5")
     (synopsis "HDF5 interface to R")
     (description
      "This R/Bioconductor package provides an interface between HDF5 and R.
@@ -8692,7 +8692,7 @@ (define-public r-chipseq
        ("r-iranges" ,r-iranges)
        ("r-s4vectors" ,r-s4vectors)
        ("r-shortread" ,r-shortread)))
-    (home-page "http://bioconductor.org/packages/chipseq")
+    (home-page "https://bioconductor.org/packages/chipseq")
     (synopsis "Package for analyzing ChIPseq data")
     (description
      "This package provides tools for processing short read data from ChIPseq
@@ -8706,7 +8706,7 @@ (define-public r-copyhelper
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "http://bioconductor.org/packages/release/"
+       (uri (string-append "https://bioconductor.org/packages/release/"
                            "data/experiment/src/contrib/CopyhelpeR_"
                            version ".tar.gz"))
        (sha256
@@ -8714,7 +8714,7 @@ (define-public r-copyhelper
          "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
     (properties `((upstream-name . "CopyhelpeR")))
     (build-system r-build-system)
-    (home-page "http://bioconductor.org/packages/CopyhelpeR/")
+    (home-page "https://bioconductor.org/packages/CopyhelpeR/")
     (synopsis "Helper files for CopywriteR")
     (description
      "This package contains the helper files that are required to run the
@@ -8829,7 +8829,7 @@ (define-public r-sva
        ("r-biocparallel" ,r-biocparallel)
        ("r-matrixstats" ,r-matrixstats)
        ("r-limma" ,r-limma)))
-    (home-page "http://bioconductor.org/packages/sva")
+    (home-page "https://bioconductor.org/packages/sva")
     (synopsis "Surrogate variable analysis")
     (description
      "This package contains functions for removing batch effects and other
@@ -9017,7 +9017,7 @@ (define-public r-affy
        ("r-biocinstaller" ,r-biocinstaller)
        ("r-preprocesscore" ,r-preprocesscore)
        ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "http://bioconductor.org/packages/affy")
+    (home-page "https://bioconductor.org/packages/affy")
     (synopsis "Methods for affymetrix oligonucleotide arrays")
     (description
      "This package contains functions for exploratory oligonucleotide array
@@ -9043,7 +9043,7 @@ (define-public r-vsn
        ("r-hexbin" ,r-hexbin)
        ("r-lattice" ,r-lattice)
        ("r-limma" ,r-limma)))
-    (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
+    (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
     (synopsis "Variance stabilization and calibration for microarray data")
     (description
      "The package implements a method for normalising microarray intensities,
@@ -9080,7 +9080,7 @@ (define-public r-mzid
        ("r-protgenerics" ,r-protgenerics)
        ("r-rcpp" ,r-rcpp)
        ("r-xml" ,r-xml)))
-    (home-page "http://bioconductor.org/packages/mzID")
+    (home-page "https://bioconductor.org/packages/mzID")
     (synopsis "Parser for mzIdentML files")
     (description
      "This package provides a parser for mzIdentML files implemented using the
@@ -9187,7 +9187,7 @@ (define-public r-msnid
        ("r-r-cache" ,r-r-cache)
        ("r-rcpp" ,r-rcpp)
        ("r-reshape2" ,r-reshape2)))
-    (home-page "http://bioconductor.org/packages/MSnID")
+    (home-page "https://bioconductor.org/packages/MSnID")
     (synopsis "Utilities for LC-MSn proteomics identifications")
     (description
      "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
@@ -9391,7 +9391,7 @@ (define-public r-interactivedisplaybase
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-shiny" ,r-shiny)))
-    (home-page "http://bioconductor.org/packages/interactiveDisplayBase")
+    (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
     (synopsis "Base package for web displays of Bioconductor objects")
     (description
      "This package contains the basic methods needed to generate interactive
@@ -9420,7 +9420,7 @@ (define-public r-annotationhub
        ("r-rsqlite" ,r-rsqlite)
        ("r-s4vectors" ,r-s4vectors)
        ("r-yaml" ,r-yaml)))
-    (home-page "http://bioconductor.org/packages/AnnotationHub")
+    (home-page "https://bioconductor.org/packages/AnnotationHub")
     (synopsis "Client to access AnnotationHub resources")
     (description
      "This package provides a client for the Bioconductor AnnotationHub web

gnu/packages/statistics.scm

@@ -2718,7 +2718,7 @@ (define-public r-rcurl
     (version "1.95-0.1.2")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://www.bioconductor.org/packages/"
+              (uri (string-append "https://www.bioconductor.org/packages/"
                                   "release/extra/src/"
                                   "contrib/RCurl_" version ".tar.gz"))
               (sha256

guix/build-system/r.scm

@@ -50,7 +50,7 @@ (define (cran-uri name 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

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)