GNU bug report logs - #45399
[PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 00/10] Move some Bioconductor packages to (gnu packages
 bioconductor).
Date: Wed, 23 Dec 2020 19:03:38 +0100

Hi,

Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 7
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-sushi: Move to (gnu packages bioconductor).
  gnu: r-gwascat: Move to (gnu packages bioconductor).
  gnu: r-gviz: Move to (gnu packages bioconductor).
  gnu: r-gqtlstats: Move to (gnu packages bioconductor).
  gnu: r-ldblock: Move to (gnu packages bioconductor).
  gnu: r-erma: Move to (gnu packages bioconductor).
  gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
  gnu: r-snpstats: Move to (gnu packages bioconductor).
  gnu: r-gqtlstats: Move to (gnu packages bioconductor).
  gnu: r-ggbio: Move to (gnu packages bioconductor).

 gnu/packages/bioconductor.scm   | 400 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 405 --------------------------------
 2 files changed, 400 insertions(+), 405 deletions(-)


base-commit: 4994e1f2bd9b573d2c13abf2b98ec204f510ad11
-- 
2.29.2

Message #8 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 01/10] gnu: r-sushi: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:26 +0100

* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
---
 gnu/packages/bioconductor.scm   | 22 ++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 22 ----------------------
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 33f66ce8be..3dd34e7f24 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9300,3 +9300,25 @@ graph with the mapped data.  In addition, @code{r-pathview} also seamlessly
 integrates with pathway and gene set (enrichment) analysis tools for
 large-scale and fully automated analysis.")
     (license license:gpl3+)))
+
+(define-public r-sushi
+  (package
+    (name "r-sushi")
+    (version "1.28.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Sushi" version))
+              (sha256
+               (base32
+                "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
+    (properties `((upstream-name . "Sushi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biomart" ,r-biomart)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://bioconductor.org/packages/Sushi")
+    (synopsis "Tools for visualizing genomics data")
+    (description
+     "This package provides flexible, quantitative, and integrative genomic
+visualizations for publication-quality multi-panel figures.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 96fa22f1a3..6ef93d9b62 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10867,28 +10867,6 @@ with your data.")
 EMBL-EBI GWAS catalog.")
     (license license:artistic2.0)))
 
-(define-public r-sushi
-  (package
-    (name "r-sushi")
-    (version "1.28.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Sushi" version))
-              (sha256
-               (base32
-                "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
-    (properties `((upstream-name . "Sushi")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biomart" ,r-biomart)
-       ("r-zoo" ,r-zoo)))
-    (home-page "https://bioconductor.org/packages/Sushi")
-    (synopsis "Tools for visualizing genomics data")
-    (description
-     "This package provides flexible, quantitative, and integrative genomic
-visualizations for publication-quality multi-panel figures.")
-    (license license:gpl2+)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #11 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 00/10] Move some Bioconductor packages to (gnu packages
 bioconductor).
Date: Wed, 23 Dec 2020 19:06:25 +0100

Hi,

Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 7
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-sushi: Move to (gnu packages bioconductor).
  gnu: r-gwascat: Move to (gnu packages bioconductor).
  gnu: r-gviz: Move to (gnu packages bioconductor).
  gnu: r-gqtlstats: Move to (gnu packages bioconductor).
  gnu: r-ldblock: Move to (gnu packages bioconductor).
  gnu: r-erma: Move to (gnu packages bioconductor).
  gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
  gnu: r-snpstats: Move to (gnu packages bioconductor).
  gnu: r-gqtlstats: Move to (gnu packages bioconductor).
  gnu: r-ggbio: Move to (gnu packages bioconductor).

 gnu/packages/bioconductor.scm   | 400 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 405 --------------------------------
 2 files changed, 400 insertions(+), 405 deletions(-)


base-commit: 4994e1f2bd9b573d2c13abf2b98ec204f510ad11
-- 
2.29.2

Message #14 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 02/10] gnu: r-gwascat: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:27 +0100

* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
---
 gnu/packages/bioconductor.scm   | 33 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 33 ---------------------------------
 2 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3dd34e7f24..970602a32b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,39 @@ preprocessing of cytometry data, including i) normalization using bead
 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
     (license license:gpl2+)))
 
+(define-public r-gwascat
+  (package
+    (name "r-gwascat")
+    (version "2.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gwascat" version))
+       (sha256
+        (base32
+         "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocfilecache" ,r-biocfilecache)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-readr" ,r-readr)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-snpstats" ,r-snpstats)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/gwascat")
+    (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
+    (description
+     "This package provides tools for representing and modeling data in the
+EMBL-EBI GWAS catalog.")
+    (license license:artistic2.0)))
+
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6ef93d9b62..ab187dcddd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10834,39 +10834,6 @@ grid graphics package.  This results in genomic information plotted together
 with your data.")
     (license license:artistic2.0)))
 
-(define-public r-gwascat
-  (package
-    (name "r-gwascat")
-    (version "2.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gwascat" version))
-       (sha256
-        (base32
-         "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-readr" ,r-readr)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-snpstats" ,r-snpstats)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/gwascat")
-    (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
-    (description
-     "This package provides tools for representing and modeling data in the
-EMBL-EBI GWAS catalog.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #17 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 03/10] gnu: r-gviz: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:28 +0100

* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
---
 gnu/packages/bioconductor.scm   | 49 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 49 ---------------------------------
 2 files changed, 49 insertions(+), 49 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 970602a32b..11e9a46b11 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,55 @@ preprocessing of cytometry data, including i) normalization using bead
 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
     (license license:gpl2+)))
 
+(define-public r-gviz
+  (package
+    (name "r-gviz")
+    (version "1.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Gviz" version))
+       (sha256
+        (base32
+         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
+    (properties `((upstream-name . "Gviz")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-digest" ,r-digest)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-latticeextra" ,r-latticeextra)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/Gviz")
+    (synopsis "Plotting data and annotation information along genomic coordinates")
+    (description
+     "Genomic data analyses requires integrated visualization of known genomic
+information and new experimental data.  Gviz uses the biomaRt and the
+rtracklayer packages to perform live annotation queries to Ensembl and UCSC
+and translates this to e.g. gene/transcript structures in viewports of the
+grid graphics package.  This results in genomic information plotted together
+with your data.")
+    (license license:artistic2.0)))
+
 (define-public r-gwascat
   (package
     (name "r-gwascat")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab187dcddd..caa505fdab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10785,55 +10785,6 @@ interpretation of members of a collection of association statistics on a
 family of feature/genome hypotheses.")
     (license license:artistic2.0)))
 
-(define-public r-gviz
-  (package
-    (name "r-gviz")
-    (version "1.34.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Gviz" version))
-       (sha256
-        (base32
-         "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
-    (properties `((upstream-name . "Gviz")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-digest" ,r-digest)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-latticeextra" ,r-latticeextra)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/Gviz")
-    (synopsis "Plotting data and annotation information along genomic coordinates")
-    (description
-     "Genomic data analyses requires integrated visualization of known genomic
-information and new experimental data.  Gviz uses the biomaRt and the
-rtracklayer packages to perform live annotation queries to Ensembl and UCSC
-and translates this to e.g. gene/transcript structures in viewports of the
-grid graphics package.  This results in genomic information plotted together
-with your data.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #20 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 04/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:29 +0100

* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
---
 gnu/packages/bioconductor.scm   | 56 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 56 ---------------------------------
 2 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 11e9a46b11..1bf9a49272 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,62 @@ preprocessing of cytometry data, including i) normalization using bead
 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
     (license license:gpl2+)))
 
+(define-public r-gqtlstats
+  (package
+    (name "r-gqtlstats")
+    (version "1.21.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gQTLstats" version))
+       (sha256
+        (base32
+         "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
+    (properties `((upstream-name . "gQTLstats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-batchjobs" ,r-batchjobs)
+       ("r-bbmisc" ,r-bbmisc)
+       ("r-beeswarm" ,r-beeswarm)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dplyr" ,r-dplyr)
+       ("r-erma" ,r-erma)
+       ("r-ffbase" ,r-ffbase)
+       ("r-foreach" ,r-foreach)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gqtlbase" ,r-gqtlbase)
+       ("r-hardyweinberg" ,r-hardyweinberg)
+       ("r-homo-sapiens" ,r-homo-sapiens)
+       ("r-iranges" ,r-iranges)
+       ("r-limma" ,r-limma)
+       ("r-mgcv" ,r-mgcv)
+       ("r-plotly" ,r-plotly)
+       ("r-reshape2" ,r-reshape2)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shiny" ,r-shiny)
+       ("r-snpstats" ,r-snpstats)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/gQTLstats")
+    (synopsis "Computationally efficient analysis for eQTL and allied studies")
+    (description
+     "This package provides tools for the computationally efficient analysis
+of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
+The software in this package aims to support refinements and functional
+interpretation of members of a collection of association statistics on a
+family of feature/genome hypotheses.")
+    (license license:artistic2.0)))
+
 (define-public r-gviz
   (package
     (name "r-gviz")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index caa505fdab..67b4c4cb73 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10729,62 +10729,6 @@ handling of existing population-level data for the purpose of flexibly
 defining LD blocks.")
     (license license:artistic2.0)))
 
-(define-public r-gqtlstats
-  (package
-    (name "r-gqtlstats")
-    (version "1.21.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gQTLstats" version))
-       (sha256
-        (base32
-         "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
-    (properties `((upstream-name . "gQTLstats")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-batchjobs" ,r-batchjobs)
-       ("r-bbmisc" ,r-bbmisc)
-       ("r-beeswarm" ,r-beeswarm)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-erma" ,r-erma)
-       ("r-ffbase" ,r-ffbase)
-       ("r-foreach" ,r-foreach)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggbeeswarm" ,r-ggbeeswarm)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gqtlbase" ,r-gqtlbase)
-       ("r-hardyweinberg" ,r-hardyweinberg)
-       ("r-homo-sapiens" ,r-homo-sapiens)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-mgcv" ,r-mgcv)
-       ("r-plotly" ,r-plotly)
-       ("r-reshape2" ,r-reshape2)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-snpstats" ,r-snpstats)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/gQTLstats")
-    (synopsis "Computationally efficient analysis for eQTL and allied studies")
-    (description
-     "This package provides tools for the computationally efficient analysis
-of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
-The software in this package aims to support refinements and functional
-interpretation of members of a collection of association statistics on a
-family of feature/genome hypotheses.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #23 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 05/10] gnu: r-ldblock: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:30 +0100

* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
---
 gnu/packages/bioconductor.scm   | 34 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 34 ---------------------------------
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1bf9a49272..40a02dbe7f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9405,6 +9405,40 @@ maintaining all essential pathway attributes.  The package offers
 functionalities including parsing, graph operation, visualization and etc.")
     (license license:gpl2+)))
 
+(define-public r-ldblock
+  (package
+    (name "r-ldblock")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ldblock" version))
+       (sha256
+        (base32
+         "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-httr" ,r-httr)
+       ("r-matrix" ,r-matrix)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-snpstats" ,r-snpstats)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/ldblock")
+    (synopsis "Data structures for linkage disequilibrium measures in populations")
+    (description
+     "This package defines data structures for @dfn{linkage
+disequilibrium} (LD) measures in populations.  Its purpose is to simplify
+handling of existing population-level data for the purpose of flexibly
+defining LD blocks.")
+    (license license:artistic2.0)))
+
 (define-public r-pathview
   (package
     (name "r-pathview")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67b4c4cb73..25021f1ee8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10695,40 +10695,6 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
 by Ernst and Kellis.")
     (license license:artistic2.0)))
 
-(define-public r-ldblock
-  (package
-    (name "r-ldblock")
-    (version "1.20.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ldblock" version))
-       (sha256
-        (base32
-         "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-httr" ,r-httr)
-       ("r-matrix" ,r-matrix)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-snpstats" ,r-snpstats)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/ldblock")
-    (synopsis "Data structures for linkage disequilibrium measures in populations")
-    (description
-     "This package defines data structures for @dfn{linkage
-disequilibrium} (LD) measures in populations.  Its purpose is to simplify
-handling of existing population-level data for the purpose of flexibly
-defining LD blocks.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #26 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 06/10] gnu: r-erma: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:31 +0100

* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
---
 gnu/packages/bioconductor.scm   | 40 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 40 ---------------------------------
 2 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 40a02dbe7f..466bb71101 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9241,6 +9241,46 @@ preprocessing of cytometry data, including i) normalization using bead
 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
     (license license:gpl2+)))
 
+(define-public r-erma
+  (package
+    (name "r-erma")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "erma" version))
+       (sha256
+        (base32
+         "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-homo-sapiens" ,r-homo-sapiens)
+       ("r-iranges" ,r-iranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shiny" ,r-shiny)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/erma")
+    (synopsis "Epigenomic road map adventures")
+    (description
+     "The epigenomics road map describes locations of epigenetic marks in DNA
+from a variety of cell types.  Of interest are locations of histone
+modifications, sites of DNA methylation, and regions of accessible chromatin.
+This package presents a selection of elements of the road map including
+metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
+by Ernst and Kellis.")
+    (license license:artistic2.0)))
+
 (define-public r-gqtlstats
   (package
     (name "r-gqtlstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 25021f1ee8..1c59d7a690 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10655,46 +10655,6 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
 several related annotation packages.")
     (license license:artistic2.0)))
 
-(define-public r-erma
-  (package
-    (name "r-erma")
-    (version "1.6.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "erma" version))
-       (sha256
-        (base32
-         "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-homo-sapiens" ,r-homo-sapiens)
-       ("r-iranges" ,r-iranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shiny" ,r-shiny)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/erma")
-    (synopsis "Epigenomic road map adventures")
-    (description
-     "The epigenomics road map describes locations of epigenetic marks in DNA
-from a variety of cell types.  Of interest are locations of histone
-modifications, sites of DNA methylation, and regions of accessible chromatin.
-This package presents a selection of elements of the road map including
-metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
-by Ernst and Kellis.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #29 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 07/10] gnu: r-homo-sapiens: Move to (gnu packages
 bioconductor).
Date: Wed, 23 Dec 2020 19:06:32 +0100

* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
---
 gnu/packages/bioconductor.scm   | 27 +++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 32 --------------------------------
 2 files changed, 27 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 466bb71101..3b8dce30e5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-homo-sapiens
+  (package
+    (name "r-homo-sapiens")
+    (version "1.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
+              (sha256
+               (base32
+                "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
+    (properties
+     `((upstream-name . "Homo.sapiens")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-go-db" ,r-go-db)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
+       ("r-organismdbi" ,r-organismdbi)
+       ("r-annotationdbi" ,r-annotationdbi)))
+    (home-page "https://bioconductor.org/packages/Homo.sapiens/")
+    (synopsis "Annotation package for the Homo.sapiens object")
+    (description
+     "This package contains the Homo.sapiens object to access data from
+several related annotation packages.")
+    (license license:artistic2.0)))
+
 (define-public r-org-ce-eg-db
   (package
     (name "r-org-ce-eg-db")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c59d7a690..2a6ac38505 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10623,38 +10623,6 @@ and more.")
 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
     (license license:gpl3)))
 
-(define-public r-homo-sapiens
-  (package
-    (name "r-homo-sapiens")
-    (version "1.3.1")
-    (source (origin
-              (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "Homo.sapiens_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
-    (properties
-     `((upstream-name . "Homo.sapiens")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-go-db" ,r-go-db)
-       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "https://bioconductor.org/packages/Homo.sapiens/")
-    (synopsis "Annotation package for the Homo.sapiens object")
-    (description
-     "This package contains the Homo.sapiens object to access data from
-several related annotation packages.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #32 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 08/10] gnu: r-snpstats: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:33 +0100

* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
---
 gnu/packages/bioconductor.scm   | 27 +++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 27 ---------------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3b8dce30e5..ff9e26bbde 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9540,6 +9540,33 @@ integrates with pathway and gene set (enrichment) analysis tools for
 large-scale and fully automated analysis.")
     (license license:gpl3+)))
 
+(define-public r-snpstats
+  (package
+    (name "r-snpstats")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "snpStats" version))
+       (sha256
+        (base32
+         "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
+    (properties `((upstream-name . "snpStats")))
+    (build-system r-build-system)
+    (inputs `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-matrix" ,r-matrix)
+       ("r-survival" ,r-survival)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://bioconductor.org/packages/snpStats")
+    (synopsis "Methods for SNP association studies")
+    (description
+     "This package provides classes and statistical methods for large
+@dfn{single-nucleotide polymorphism} (SNP) association studies.  This extends
+the earlier snpMatrix package, allowing for uncertainty in genotypes.")
+    (license license:gpl3)))
+
 (define-public r-sushi
   (package
     (name "r-sushi")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2a6ac38505..76236929de 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10596,33 +10596,6 @@ of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
 and more.")
     (license license:artistic2.0)))
 
-(define-public r-snpstats
-  (package
-    (name "r-snpstats")
-    (version "1.40.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "snpStats" version))
-       (sha256
-        (base32
-         "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
-    (properties `((upstream-name . "snpStats")))
-    (build-system r-build-system)
-    (inputs `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-matrix" ,r-matrix)
-       ("r-survival" ,r-survival)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "https://bioconductor.org/packages/snpStats")
-    (synopsis "Methods for SNP association studies")
-    (description
-     "This package provides classes and statistical methods for large
-@dfn{single-nucleotide polymorphism} (SNP) association studies.  This extends
-the earlier snpMatrix package, allowing for uncertainty in genotypes.")
-    (license license:gpl3)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #35 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 09/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:34 +0100

* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
---
 gnu/packages/bioconductor.scm   | 47 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 47 ---------------------------------
 2 files changed, 47 insertions(+), 47 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ff9e26bbde..a3dd93e763 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9308,6 +9308,53 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
 by Ernst and Kellis.")
     (license license:artistic2.0)))
 
+(define-public r-gqtlbase
+  (package
+    (name "r-gqtlbase")
+    (version "1.21.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gQTLBase" version))
+       (sha256
+        (base32
+         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
+    (properties `((upstream-name . "gQTLBase")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This is an upstream bug.
+         (add-after 'unpack 'fix-imports
+           (lambda _
+             (substitute* "NAMESPACE"
+               ((".*maxffmode.*") "")
+               (("importFrom\\(ff,.*") "import(ff)\n"))
+             #t)))))
+    (propagated-inputs
+     `(("r-batchjobs" ,r-batchjobs)
+       ("r-bbmisc" ,r-bbmisc)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-bit" ,r-bit)
+       ("r-doparallel" ,r-doparallel)
+       ("r-ff" ,r-ff)
+       ("r-ffbase" ,r-ffbase)
+       ("r-foreach" ,r-foreach)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/gQTLBase")
+    (synopsis "Infrastructure for eQTL, mQTL and similar studies")
+    (description
+     "The purpose of this package is to simplify the storage and interrogation
+of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
+and more.")
+    (license license:artistic2.0)))
+
 (define-public r-gqtlstats
   (package
     (name "r-gqtlstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 76236929de..bc483e6f13 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10549,53 +10549,6 @@ views.  High-level plots include sequence fragment length, edge-linked
 interval to data view, mismatch pileup, and several splicing summaries.")
     (license license:artistic2.0)))
 
-(define-public r-gqtlbase
-  (package
-    (name "r-gqtlbase")
-    (version "1.21.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gQTLBase" version))
-       (sha256
-        (base32
-         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
-    (properties `((upstream-name . "gQTLBase")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; This is an upstream bug.
-         (add-after 'unpack 'fix-imports
-           (lambda _
-             (substitute* "NAMESPACE"
-               ((".*maxffmode.*") "")
-               (("importFrom\\(ff,.*") "import(ff)\n"))
-             #t)))))
-    (propagated-inputs
-     `(("r-batchjobs" ,r-batchjobs)
-       ("r-bbmisc" ,r-bbmisc)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-bit" ,r-bit)
-       ("r-doparallel" ,r-doparallel)
-       ("r-ff" ,r-ff)
-       ("r-ffbase" ,r-ffbase)
-       ("r-foreach" ,r-foreach)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/gQTLBase")
-    (synopsis "Infrastructure for eQTL, mQTL and similar studies")
-    (description
-     "The purpose of this package is to simplify the storage and interrogation
-of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
-and more.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #38 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 10/10] gnu: r-ggbio: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:35 +0100

* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
---
 gnu/packages/bioconductor.scm   | 65 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 65 ---------------------------------
 2 files changed, 65 insertions(+), 65 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a3dd93e763..55df9bf7d1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9308,6 +9308,71 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
 by Ernst and Kellis.")
     (license license:artistic2.0)))
 
+(define-public r-ggbio
+  (package
+    (name "r-ggbio")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ggbio" version))
+       (sha256
+        (base32
+         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; See https://github.com/tengfei/ggbio/issues/117
+         ;; This fix will be included in the next release.
+         (add-after 'unpack 'fix-typo
+           (lambda _
+             (substitute* "R/GGbio-class.R"
+               (("fechable") "fetchable"))
+             #t)))))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggally" ,r-ggally)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-gtable" ,r-gtable)
+       ("r-hmisc" ,r-hmisc)
+       ("r-iranges" ,r-iranges)
+       ("r-organismdbi" ,r-organismdbi)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "http://www.tengfei.name/ggbio/")
+    (synopsis "Visualization tools for genomic data")
+    (description
+     "The ggbio package extends and specializes the grammar of graphics for
+biological data.  The graphics are designed to answer common scientific
+questions, in particular those often asked of high throughput genomics data.
+All core Bioconductor data structures are supported, where appropriate.  The
+package supports detailed views of particular genomic regions, as well as
+genome-wide overviews.  Supported overviews include ideograms and grand linear
+views.  High-level plots include sequence fragment length, edge-linked
+interval to data view, mismatch pileup, and several splicing summaries.")
+    (license license:artistic2.0)))
+
 (define-public r-gqtlbase
   (package
     (name "r-gqtlbase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bc483e6f13..512abcd8fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10484,71 +10484,6 @@ high-level packages for biological data visualization.  This saves development
 effort and encourages consistency.")
     (license license:artistic2.0)))
 
-(define-public r-ggbio
-  (package
-    (name "r-ggbio")
-    (version "1.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ggbio" version))
-       (sha256
-        (base32
-         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; See https://github.com/tengfei/ggbio/issues/117
-         ;; This fix will be included in the next release.
-         (add-after 'unpack 'fix-typo
-           (lambda _
-             (substitute* "R/GGbio-class.R"
-               (("fechable") "fetchable"))
-             #t)))))
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggally" ,r-ggally)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-gtable" ,r-gtable)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-organismdbi" ,r-organismdbi)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "http://www.tengfei.name/ggbio/")
-    (synopsis "Visualization tools for genomic data")
-    (description
-     "The ggbio package extends and specializes the grammar of graphics for
-biological data.  The graphics are designed to answer common scientific
-questions, in particular those often asked of high throughput genomics data.
-All core Bioconductor data structures are supported, where appropriate.  The
-package supports detailed views of particular genomic regions, as well as
-genome-wide overviews.  Supported overviews include ideograms and grand linear
-views.  High-level plots include sequence fragment length, edge-linked
-interval to data view, mismatch pileup, and several splicing summaries.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

Message #43 received at 45399-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 45399-done <at> debbugs.gnu.org
Subject: Re: [bug#45399] [PATCH 00/10] Move some Bioconductor packages to
 (gnu packages bioconductor).
Date: Tue, 29 Dec 2020 17:42:16 +0100

zimoun <zimon.toutoune <at> gmail.com> writes:

> Hi,
>
> Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
> bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 7
> pacth set like this one are coming...
>
> 1: <https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html>

Excellent!

Pushed with commit 610cd6a170.

Thanks!

-- 
Ricardo

Message #46 received at 45399-done <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 45399-done <at> debbugs.gnu.org
Subject: Re: [bug#45399] [PATCH 00/10] Move some Bioconductor packages to
 (gnu packages bioconductor).
Date: Wed, 30 Dec 2020 10:13:29 +0100

Hi Ricardo,

On Tue, 29 Dec 2020 at 17:42, Ricardo Wurmus <rekado <at> elephly.net> wrote:

>> Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
>> bioinformatics) to (gnu packages bioconductor).  Far to be complete; still 7
>> pacth set like this one are coming...
>>
>> 1: <https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html>
>
> Excellent!
>
> Pushed with commit 610cd6a170.

Thanks.  Well, I should change my workflow since I have missed [2].


2: <https://lists.gnu.org/archive/html/guix-devel/2020-12/msg00316.html>


Cheers,
simon

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