[bug#47010] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

[bug#47010] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

[zimoun]

Hi,

Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 6
pacth set like this one are coming...

1: <https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html>


To transfer the Copyright, I use:

   git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r-<name>

Then, after the move, I run:

   ./pre-inst-env guix build r-<name> --no-grafts
   ./pre-inst-env guix build r-<name> --no-grafts --check

and at the end of the series, I run:

    make as-derivation

to check that "guix pull" is not broken; just in case.

Last, I have not carefully checked the imported modules, so it could
be possible to perhaps remove couple of #:use-module (gnu packages <useless>)
in gnu/packages/bioinformatics.scm.

All the best,
simon

zimoun (10):
  gnu: r-genefilter: Move to (gnu packages bioconductor).
  gnu: r-deseq2: Move to (gnu packages bioconductor).
  gnu: r-dexseq: Move to (gnu packages bioconductor).
  gnu: r-annotationforge: Move to (gnu packages bioconductor).
  gnu: r-rbgl: Move to (gnu packages bioconductor).
  gnu: r-gseabase: Move to (gnu packages bioconductor).
  gnu: r-category: Move to (gnu packages bioconductor).
  gnu: r-gostats: Move to (gnu packages bioconductor).
  gnu: r-shortread: Move to (gnu packages bioconductor).
  gnu: r-systempiper: Move to (gnu packages bioconductor).

 gnu/packages/bioconductor.scm   | 354 ++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 354 --------------------------------
 2 files changed, 354 insertions(+), 354 deletions(-)


base-commit: 612dc6dbe0904f39238a89d3b63ee66abd861b51
-- 
2.30.1

[bug#47010] [PATCH 01/10] gnu: r-genefilter: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
---
 gnu/packages/bioconductor.scm   | 28 ++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 28 ----------------------------
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 89b191585b..e15984d0e3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1487,6 +1487,34 @@ structure.")
 microarrays.")
     (license license:artistic2.0)))
 
+(define-public r-genefilter
+  (package
+    (name "r-genefilter")
+    (version "1.72.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "genefilter" version))
+       (sha256
+        (base32
+         "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)
+       ("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-annotate" ,r-annotate)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-survival" ,r-survival)))
+    (home-page "https://bioconductor.org/packages/genefilter")
+    (synopsis "Filter genes from high-throughput experiments")
+    (description
+     "This package provides basic functions for filtering genes from
+high-throughput sequencing experiments.")
+    (license license:artistic2.0)))
+
 (define-public r-hpar
   (package
     (name "r-hpar")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index be07bd18a3..258c3ca409 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,34 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-genefilter
-  (package
-    (name "r-genefilter")
-    (version "1.72.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "genefilter" version))
-       (sha256
-        (base32
-         "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)
-       ("r-knitr" ,r-knitr)))
-    (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-survival" ,r-survival)))
-    (home-page "https://bioconductor.org/packages/genefilter")
-    (synopsis "Filter genes from high-throughput experiments")
-    (description
-     "This package provides basic functions for filtering genes from
-high-throughput sequencing experiments.")
-    (license license:artistic2.0)))
-
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-- 
2.30.1

[bug#47010] [PATCH 02/10] gnu: r-deseq2: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
---
 gnu/packages/bioconductor.scm   | 38 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 38 ---------------------------------
 2 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e15984d0e3..f2dd4bb70b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1487,6 +1487,44 @@ structure.")
 microarrays.")
     (license license:artistic2.0)))
 
+(define-public r-deseq2
+  (package
+    (name "r-deseq2")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DESeq2" version))
+       (sha256
+        (base32
+         "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
+    (properties `((upstream-name . "DESeq2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-genefilter" ,r-genefilter)
+       ("r-geneplotter" ,r-geneplotter)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-locfit" ,r-locfit)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/DESeq2")
+    (synopsis "Differential gene expression analysis")
+    (description
+     "This package provides functions to estimate variance-mean dependence in
+count data from high-throughput nucleotide sequencing assays and test for
+differential expression based on a model using the negative binomial
+distribution.")
+    (license license:lgpl3+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 258c3ca409..64585127e6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,44 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-deseq2
-  (package
-    (name "r-deseq2")
-    (version "1.30.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DESeq2" version))
-       (sha256
-        (base32
-         "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
-    (properties `((upstream-name . "DESeq2")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genefilter" ,r-genefilter)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-locfit" ,r-locfit)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/DESeq2")
-    (synopsis "Differential gene expression analysis")
-    (description
-     "This package provides functions to estimate variance-mean dependence in
-count data from high-throughput nucleotide sequencing assays and test for
-differential expression based on a model using the negative binomial
-distribution.")
-    (license license:lgpl3+)))
-
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-- 
2.30.1

[bug#47010] [PATCH 03/10] gnu: r-dexseq: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
---
 gnu/packages/bioconductor.scm   | 45 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 45 ---------------------------------
 2 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f2dd4bb70b..883b6df2fb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1525,6 +1525,51 @@ differential expression based on a model using the negative binomial
 distribution.")
     (license license:lgpl3+)))
 
+(define-public r-dexseq
+  (package
+    (name "r-dexseq")
+    (version "1.36.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DEXSeq" version))
+       (sha256
+        (base32
+         "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
+    (properties `((upstream-name . "DEXSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biomart" ,r-biomart)
+       ("r-deseq2" ,r-deseq2)
+       ("r-genefilter" ,r-genefilter)
+       ("r-geneplotter" ,r-geneplotter)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-hwriter" ,r-hwriter)
+       ("r-iranges" ,r-iranges)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-statmod" ,r-statmod)
+       ("r-stringr" ,r-stringr)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (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
+exon counts between samples with different experimental designs.  It provides
+functions that allows the user to make the necessary statistical tests based
+on a model that uses the negative binomial distribution to estimate the
+variance between biological replicates and generalized linear models for
+testing.  The package also provides functions for the visualization and
+exploration of the results.")
+    (license license:gpl3+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 64585127e6..4fa4a1e354 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,51 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-dexseq
-  (package
-    (name "r-dexseq")
-    (version "1.36.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DEXSeq" version))
-       (sha256
-        (base32
-         "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
-    (properties `((upstream-name . "DEXSeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biomart" ,r-biomart)
-       ("r-deseq2" ,r-deseq2)
-       ("r-genefilter" ,r-genefilter)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-hwriter" ,r-hwriter)
-       ("r-iranges" ,r-iranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-statmod" ,r-statmod)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (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
-exon counts between samples with different experimental designs.  It provides
-functions that allows the user to make the necessary statistical tests based
-on a model that uses the negative binomial distribution to estimate the
-variance between biological replicates and generalized linear models for
-testing.  The package also provides functions for the visualization and
-exploration of the results.")
-    (license license:gpl3+)))
-
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-- 
2.30.1

[bug#47010] [PATCH 04/10] gnu: r-annotationforge: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
---
 gnu/packages/bioconductor.scm   | 32 ++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 32 --------------------------------
 2 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 883b6df2fb..706b87b207 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1487,6 +1487,38 @@ structure.")
 microarrays.")
     (license license:artistic2.0)))
 
+(define-public r-annotationforge
+  (package
+    (name "r-annotationforge")
+    (version "1.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationForge" version))
+       (sha256
+        (base32
+         "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
+    (properties
+     `((upstream-name . "AnnotationForge")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-dbi" ,r-dbi)
+       ("r-rcurl" ,r-rcurl)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xml" ,r-xml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (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
+databases.  Packages produced are intended to be used with AnnotationDbi.")
+    (license license:artistic2.0)))
+
 (define-public r-deseq2
   (package
     (name "r-deseq2")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4fa4a1e354..3212641af9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,38 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-annotationforge
-  (package
-    (name "r-annotationforge")
-    (version "1.32.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "AnnotationForge" version))
-       (sha256
-        (base32
-         "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
-    (properties
-     `((upstream-name . "AnnotationForge")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xml" ,r-xml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (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
-databases.  Packages produced are intended to be used with AnnotationDbi.")
-    (license license:artistic2.0)))
-
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-- 
2.30.1

[bug#47010] [PATCH 05/10] gnu: r-rbgl: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
---
 gnu/packages/bioconductor.scm   | 23 +++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 23 -----------------------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 706b87b207..0a9dc4f9ba 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1650,6 +1650,29 @@ high-throughput sequencing experiments.")
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-rbgl
+  (package
+    (name "r-rbgl")
+    (version "1.66.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RBGL" version))
+       (sha256
+        (base32
+         "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
+    (properties `((upstream-name . "RBGL")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-graph" ,r-graph)))
+    (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
+the graph algorithms contained in the Boost library.")
+    (license license:artistic2.0)))
+
 (define-public r-regioner
   (package
     (name "r-regioner")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3212641af9..0f96ffc02e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,29 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-rbgl
-  (package
-    (name "r-rbgl")
-    (version "1.66.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "RBGL" version))
-       (sha256
-        (base32
-         "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
-    (properties `((upstream-name . "RBGL")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-bh" ,r-bh)
-       ("r-graph" ,r-graph)))
-    (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
-the graph algorithms contained in the Boost library.")
-    (license license:artistic2.0)))
-
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-- 
2.30.1

[bug#47010] [PATCH 06/10] gnu: r-gseabase: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
---
 gnu/packages/bioconductor.scm   | 29 +++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 29 -----------------------------
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0a9dc4f9ba..a17c6beeef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1630,6 +1630,35 @@ exploration of the results.")
 high-throughput sequencing experiments.")
     (license license:artistic2.0)))
 
+(define-public r-gseabase
+  (package
+    (name "r-gseabase")
+    (version "1.52.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GSEABase" version))
+       (sha256
+        (base32
+         "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
+    (properties `((upstream-name . "GSEABase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotate" ,r-annotate)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-graph" ,r-graph)
+       ("r-xml" ,r-xml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (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
+Enrichment Analysis} (GSEA).")
+    (license license:artistic2.0)))
+
 (define-public r-hpar
   (package
     (name "r-hpar")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0f96ffc02e..23b8ce6892 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,35 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-gseabase
-  (package
-    (name "r-gseabase")
-    (version "1.52.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "GSEABase" version))
-       (sha256
-        (base32
-         "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
-    (properties `((upstream-name . "GSEABase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-graph" ,r-graph)
-       ("r-xml" ,r-xml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (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
-Enrichment Analysis} (GSEA).")
-    (license license:artistic2.0)))
-
 (define-public r-category
   (package
     (name "r-category")
-- 
2.30.1

[bug#47010] [PATCH 07/10] gnu: r-category: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
---
 gnu/packages/bioconductor.scm   | 31 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a17c6beeef..4e3dd25d61 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1519,6 +1519,37 @@ microarrays.")
 databases.  Packages produced are intended to be used with AnnotationDbi.")
     (license license:artistic2.0)))
 
+(define-public r-category
+  (package
+    (name "r-category")
+    (version "2.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Category" version))
+       (sha256
+        (base32
+         "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
+    (properties `((upstream-name . "Category")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotate" ,r-annotate)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genefilter" ,r-genefilter)
+       ("r-graph" ,r-graph)
+       ("r-gseabase" ,r-gseabase)
+       ("r-matrix" ,r-matrix)
+       ("r-rbgl" ,r-rbgl)
+       ("r-dbi" ,r-dbi)))
+    (home-page "https://bioconductor.org/packages/Category")
+    (synopsis "Category analysis")
+    (description
+     "This package provides a collection of tools for performing category
+analysis.")
+    (license license:artistic2.0)))
+
 (define-public r-deseq2
   (package
     (name "r-deseq2")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 23b8ce6892..6b32f3416c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,37 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-category
-  (package
-    (name "r-category")
-    (version "2.56.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Category" version))
-       (sha256
-        (base32
-         "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
-    (properties `((upstream-name . "Category")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genefilter" ,r-genefilter)
-       ("r-graph" ,r-graph)
-       ("r-gseabase" ,r-gseabase)
-       ("r-matrix" ,r-matrix)
-       ("r-rbgl" ,r-rbgl)
-       ("r-dbi" ,r-dbi)))
-    (home-page "https://bioconductor.org/packages/Category")
-    (synopsis "Category analysis")
-    (description
-     "This package provides a collection of tools for performing category
-analysis.")
-    (license license:artistic2.0)))
-
 (define-public r-gostats
   (package
     (name "r-gostats")
-- 
2.30.1

[bug#47010] [PATCH 08/10] gnu: r-gostats: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
---
 gnu/packages/bioconductor.scm   | 31 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4e3dd25d61..4f4088db27 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1661,6 +1661,37 @@ exploration of the results.")
 high-throughput sequencing experiments.")
     (license license:artistic2.0)))
 
+(define-public r-gostats
+  (package
+    (name "r-gostats")
+    (version "2.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GOstats" version))
+       (sha256
+        (base32
+         "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
+    (properties `((upstream-name . "GOstats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotate" ,r-annotate)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationforge" ,r-annotationforge)
+       ("r-biobase" ,r-biobase)
+       ("r-category" ,r-category)
+       ("r-go-db" ,r-go-db)
+       ("r-graph" ,r-graph)
+       ("r-rgraphviz" ,r-rgraphviz)
+       ("r-rbgl" ,r-rbgl)))
+    (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
+microarray data.  A variety of basic manipulation tools for graphs, hypothesis
+testing and other simple calculations.")
+    (license license:artistic2.0)))
+
 (define-public r-gseabase
   (package
     (name "r-gseabase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6b32f3416c..186b051865 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,37 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-gostats
-  (package
-    (name "r-gostats")
-    (version "2.56.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "GOstats" version))
-       (sha256
-        (base32
-         "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
-    (properties `((upstream-name . "GOstats")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationforge" ,r-annotationforge)
-       ("r-biobase" ,r-biobase)
-       ("r-category" ,r-category)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-rgraphviz" ,r-rgraphviz)
-       ("r-rbgl" ,r-rbgl)))
-    (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
-microarray data.  A variety of basic manipulation tools for graphs, hypothesis
-testing and other simple calculations.")
-    (license license:artistic2.0)))
-
 (define-public r-shortread
   (package
     (name "r-shortread")
-- 
2.30.1

[bug#47010] [PATCH 09/10] gnu: r-shortread: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
---
 gnu/packages/bioconductor.scm   | 43 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 43 ---------------------------------
 2 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f4088db27..05077b422e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1845,6 +1845,49 @@ reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-shortread
+  (package
+    (name "r-shortread")
+    (version "1.48.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ShortRead" version))
+       (sha256
+        (base32
+         "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
+    (properties `((upstream-name . "ShortRead")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-hwriter" ,r-hwriter)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-latticeextra" ,r-latticeextra)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://bioconductor.org/packages/ShortRead")
+    (synopsis "FASTQ input and manipulation tools")
+    (description
+     "This package implements sampling, iteration, and input of FASTQ files.
+It includes functions for filtering and trimming reads, and for generating a
+quality assessment report.  Data are represented as
+@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
+purposes.  The package also contains legacy support for early single-end,
+ungapped alignment formats.")
+    (license license:artistic2.0)))
+
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 186b051865..fda4516052 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,49 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-shortread
-  (package
-    (name "r-shortread")
-    (version "1.48.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ShortRead" version))
-       (sha256
-        (base32
-         "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
-    (properties `((upstream-name . "ShortRead")))
-    (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-hwriter" ,r-hwriter)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "https://bioconductor.org/packages/ShortRead")
-    (synopsis "FASTQ input and manipulation tools")
-    (description
-     "This package implements sampling, iteration, and input of FASTQ files.
-It includes functions for filtering and trimming reads, and for generating a
-quality assessment report.  Data are represented as
-@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
-purposes.  The package also contains legacy support for early single-end,
-ungapped alignment formats.")
-    (license license:artistic2.0)))
-
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-- 
2.30.1

[bug#47010] [PATCH 10/10] gnu: r-systempiper: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
---
 gnu/packages/bioconductor.scm   | 54 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 54 ---------------------------------
 2 files changed, 54 insertions(+), 54 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 05077b422e..d7be5e66a2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1888,6 +1888,60 @@ purposes.  The package also contains legacy support for early single-end,
 ungapped alignment formats.")
     (license license:artistic2.0)))
 
+(define-public r-systempiper
+  (package
+    (name "r-systempiper")
+    (version "1.24.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "systemPipeR" version))
+       (sha256
+        (base32
+         "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
+    (properties `((upstream-name . "systemPipeR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotate" ,r-annotate)
+       ("r-assertthat" ,r-assertthat)
+       ("r-batchtools" ,r-batchtools)
+       ("r-biostrings" ,r-biostrings)
+       ("r-deseq2" ,r-deseq2)
+       ("r-dot" ,r-dot)
+       ("r-edger" ,r-edger)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-go-db" ,r-go-db)
+       ("r-gostats" ,r-gostats)
+       ("r-iranges" ,r-iranges)
+       ("r-limma" ,r-limma)
+       ("r-magrittr" ,r-magrittr)
+       ("r-pheatmap" ,r-pheatmap)
+       ("r-rjson" ,r-rjson)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rsvg" ,r-rsvg)
+       ("r-shortread" ,r-shortread)
+       ("r-stringr" ,r-stringr)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-yaml" ,r-yaml)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/tgirke/systemPipeR")
+    (synopsis "Next generation sequencing workflow and reporting environment")
+    (description
+     "This R package provides tools for building and running automated
+end-to-end analysis workflows for a wide range of @dfn{next generation
+sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
+Important features include a uniform workflow interface across different NGS
+applications, automated report generation, and support for running both R and
+command-line software, such as NGS aligners or peak/variant callers, on local
+computers or compute clusters.  Efficient handling of complex sample sets and
+experimental designs is facilitated by a consistently implemented sample
+annotation infrastructure.")
+    (license license:artistic2.0)))
+
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fda4516052..072c0582be 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7385,60 +7385,6 @@ includes software to
 ")
       (license license:cc0))))
 
-(define-public r-systempiper
-  (package
-    (name "r-systempiper")
-    (version "1.24.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "systemPipeR" version))
-       (sha256
-        (base32
-         "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
-    (properties `((upstream-name . "systemPipeR")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotate" ,r-annotate)
-       ("r-assertthat" ,r-assertthat)
-       ("r-batchtools" ,r-batchtools)
-       ("r-biostrings" ,r-biostrings)
-       ("r-deseq2" ,r-deseq2)
-       ("r-dot" ,r-dot)
-       ("r-edger" ,r-edger)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-go-db" ,r-go-db)
-       ("r-gostats" ,r-gostats)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-magrittr" ,r-magrittr)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-rjson" ,r-rjson)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rsvg" ,r-rsvg)
-       ("r-shortread" ,r-shortread)
-       ("r-stringr" ,r-stringr)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-yaml" ,r-yaml)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/tgirke/systemPipeR")
-    (synopsis "Next generation sequencing workflow and reporting environment")
-    (description
-     "This R package provides tools for building and running automated
-end-to-end analysis workflows for a wide range of @dfn{next generation
-sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
-Important features include a uniform workflow interface across different NGS
-applications, automated report generation, and support for running both R and
-command-line software, such as NGS aligners or peak/variant callers, on local
-computers or compute clusters.  Efficient handling of complex sample sets and
-experimental designs is facilitated by a consistently implemented sample
-annotation infrastructure.")
-    (license license:artistic2.0)))
-
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-- 
2.30.1

bug#47010: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

[Ricardo Wurmus]

Thank you, pushed to the “master” branch with commit df6b3c25bb.
-- 
Ricardo