03/03: gnu: Use HTTPS for bioconductor.org.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit 99db6db7be7a51a6250584dfe896afd797c73812
Author: Tobias Geerinckx-Rice <address@hidden>
AuthorDate: Tue Jan 21 23:50:29 2020 +0100

    gnu: Use HTTPS for bioconductor.org.
    
    * gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS.
    * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked,
    r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno,
    r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise.
    * gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
---
 gnu/packages/bioconductor.scm   | 18 +++++++++---------
 gnu/packages/bioinformatics.scm |  2 +-
 gnu/packages/graph.scm          |  2 +-
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ef34b99..e2b4f6e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -297,7 +297,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings 
objects.")
      `(("r-bsgenome" ,r-bsgenome)
        ("r-bsgenome-mmusculus-ucsc-mm9"
         ,r-bsgenome-mmusculus-ucsc-mm9)))
-    (home-page 
"http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/";)
+    (home-page 
"https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/";)
     (synopsis "Full masked genome sequences for Mouse")
     (description
      "This package provides full genome sequences for Mus musculus (Mouse) as
@@ -1400,7 +1400,7 @@ problems in genomics, brain imaging, astrophysics, and 
data mining.")
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-systempiper" ,r-systempiper)))
-    (home-page "http://bioconductor.org/packages/DiffBind";)
+    (home-page "https://bioconductor.org/packages/DiffBind";)
     (synopsis "Differential binding analysis of ChIP-Seq peak data")
     (description
      "This package computes differentially bound sites from multiple
@@ -1429,7 +1429,7 @@ occupancy (overlap) analysis and plotting functions.")
        ("r-rsamtools" ,r-rsamtools)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-rtracklayer" ,r-rtracklayer)))
-    (home-page "http://bioconductor.org/packages/RIPSeeker";)
+    (home-page "https://bioconductor.org/packages/RIPSeeker";)
     (synopsis
      "Identifying protein-associated transcripts from RIP-seq experiments")
     (description
@@ -1458,7 +1458,7 @@ processing to visualization and annotation.")
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-biobase" ,r-biobase)
        ("r-mass" ,r-mass)))
-    (home-page "http://bioconductor.org/packages/multtest";)
+    (home-page "https://bioconductor.org/packages/multtest";)
     (synopsis "Resampling-based multiple hypothesis testing")
     (description
      "This package can do non-parametric bootstrap and permutation
@@ -1569,7 +1569,7 @@ determining dependencies between variables, code 
improvement suggestions.")
        ("r-seqinr" ,r-seqinr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-venndiagram" ,r-venndiagram)))
-    (home-page "http://bioconductor.org/packages/ChIPpeakAnno";)
+    (home-page "https://bioconductor.org/packages/ChIPpeakAnno";)
     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
     (description
      "The package includes functions to retrieve the sequences around the peak,
@@ -1594,7 +1594,7 @@ enrichedGO (addGeneIDs).")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
-    (home-page "http://bioconductor.org/packages/marray";)
+    (home-page "https://bioconductor.org/packages/marray";)
     (synopsis "Exploratory analysis for two-color spotted microarray data")
     (description "This package contains class definitions for two-color spotted
 microarray data.  It also includes functions for data input, diagnostic plots,
@@ -1615,7 +1615,7 @@ normalization and quality checking.")
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-marray" ,r-marray)))
-   (home-page "http://bioconductor.org/packages/CGHbase";)
+   (home-page "https://bioconductor.org/packages/CGHbase";)
    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
 the @code{arrayCGH} packages.")
@@ -1638,7 +1638,7 @@ the @code{arrayCGH} packages.")
       ("r-impute" ,r-impute)
       ("r-dnacopy" ,r-dnacopy)
       ("r-snowfall" ,r-snowfall)))
-   (home-page "http://bioconductor.org/packages/CGHcall";)
+   (home-page "https://bioconductor.org/packages/CGHcall";)
    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
 @code{arrayCGH} packages.")
@@ -1667,7 +1667,7 @@ the @code{arrayCGH} packages.")
        ("r-matrixstats" ,r-matrixstats)
        ("r-r-utils" ,r-r-utils)
        ("r-rsamtools" ,r-rsamtools)))
-    (home-page "http://bioconductor.org/packages/QDNAseq";)
+    (home-page "https://bioconductor.org/packages/QDNAseq";)
     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
     (description "The genome is divided into non-overlapping fixed-sized bins,
 number of sequence reads in each counted, adjusted with a simultaneous
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a84273..edfccac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10161,7 +10161,7 @@ the earlier snpMatrix package, allowing for uncertainty 
in genotypes.")
               (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/"
                                   "Homo.sapiens_"
                                   version ".tar.gz"))
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 4095926..982def6 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -183,7 +183,7 @@ model.")
      `(("r-graph" ,r-graph)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-    (home-page "http://bioconductor.org/packages/Rgraphviz";)
+    (home-page "https://bioconductor.org/packages/Rgraphviz";)
     (synopsis "Plotting capabilities for R graph objects")
     (description
      "This package interfaces R with the graphviz library for plotting R graph