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

DoneSubmitted by zimoun.
Details
3 participants
  • Leo Famulari
  • Ricardo Wurmus
  • zimoun
Owner
unassigned
Severity
normal
Z
Z
zimoun wrote on 15 Mar 2021 19:07
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180714.8233-1-zimon.toutoune@gmail.com
Hi,

Janitor [1] patch set. It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor). Far to be complete; still 4
pacth set like this one are coming...



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-limma: Move to (gnu packages bioconductor).
gnu: r-xvector: Move to (gnu packages bioconductor).
gnu: r-genomicranges: Move to (gnu packages bioconductor).
gnu: r-biobase: Move to (gnu packages bioconductor).
gnu: r-annotationdbi: Move to (gnu packages bioconductor).
gnu: r-biomart: Move to (gnu packages bioconductor).
gnu: r-biocparallel: Move to (gnu packages bioconductor).
gnu: r-biostrings: Move to (gnu packages bioconductor).
gnu: r-rsamtools: Move to (gnu packages bioconductor).
gnu: r-delayedarray: Move to (gnu packages bioconductor).

gnu/packages/bioconductor.scm | 305 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 305 --------------------------------
2 files changed, 305 insertions(+), 305 deletions(-)


base-commit: 266d55dc3080475544bf45e72359c9b9bbcecd53
--
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:08
[PATCH 01/10] gnu: r-limma: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-1-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
---
gnu/packages/bioconductor.scm | 19 +++++++++++++++++++
gnu/packages/bioinformatics.scm | 19 -------------------
2 files changed, 19 insertions(+), 19 deletions(-)

Toggle diff (62 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d611f3a491..379b6c30c0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1850,6 +1850,25 @@ Enrichment Analysis} (GSEA).")
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-limma
+  (package
+    (name "r-limma")
+    (version "3.46.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "limma" version))
+              (sha256
+               (base32
+                "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
+    (build-system r-build-system)
+    (home-page "http://bioinf.wehi.edu.au/limma")
+    (synopsis "Package for linear models for microarray and RNA-seq data")
+    (description "This package can be used for the analysis of gene expression
+studies, especially the use of linear models for analysing designed experiments
+and the assessment of differential expression.  The analysis methods apply to
+different technologies, including microarrays, RNA-seq, and quantitative PCR.")
+    (license license:gpl2+)))
+
 (define-public r-rbgl
   (package
     (name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d9afe2c56f..9774b442a3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,25 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-limma
-  (package
-    (name "r-limma")
-    (version "3.46.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "limma" version))
-              (sha256
-               (base32
-                "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
-    (build-system r-build-system)
-    (home-page "http://bioinf.wehi.edu.au/limma")
-    (synopsis "Package for linear models for microarray and RNA-seq data")
-    (description "This package can be used for the analysis of gene expression
-studies, especially the use of linear models for analysing designed experiments
-and the assessment of differential expression.  The analysis methods apply to
-different technologies, including microarrays, RNA-seq, and quantitative PCR.")
-    (license license:gpl2+)))
-
 (define-public r-xvector
   (package
     (name "r-xvector")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:08
[PATCH 02/10] gnu: r-xvector: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-2-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
---
gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 36 ---------------------------------
2 files changed, 36 insertions(+), 36 deletions(-)

Toggle diff (96 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 379b6c30c0..fdb2f7c7ac 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2108,6 +2108,42 @@ annotation infrastructure.")
 coding changes and predict coding outcomes.")
     (license license:artistic2.0)))
 
+(define-public r-xvector
+  (package
+    (name "r-xvector")
+    (version "0.30.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "XVector" version))
+              (sha256
+               (base32
+                "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
+    (properties
+     `((upstream-name . "XVector")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-zlib
+           (lambda _
+             (substitute* "DESCRIPTION"
+               (("zlibbioc, ") ""))
+             (substitute* "NAMESPACE"
+               (("import\\(zlibbioc\\)") ""))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/XVector")
+    (synopsis "Representation and manpulation of external sequences")
+    (description
+     "This package provides memory efficient S4 classes for storing sequences
+\"externally\" (behind an R external pointer, or on disk).")
+    (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 9774b442a3..65db983461 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,42 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-xvector
-  (package
-    (name "r-xvector")
-    (version "0.30.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "XVector" version))
-              (sha256
-               (base32
-                "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
-    (properties
-     `((upstream-name . "XVector")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-zlib
-           (lambda _
-             (substitute* "DESCRIPTION"
-               (("zlibbioc, ") ""))
-             (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/XVector")
-    (synopsis "Representation and manpulation of external sequences")
-    (description
-     "This package provides memory efficient S4 classes for storing sequences
-\"externally\" (behind an R external pointer, or on disk).")
-    (license license:artistic2.0)))
-
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:08
[PATCH 03/10] gnu: r-genomicranges: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-3-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
---
gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 31 insertions(+), 31 deletions(-)

Toggle diff (86 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fdb2f7c7ac..ec273cae70 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1770,6 +1770,37 @@ translation between different chromosome sequence naming conventions (e.g.,
 names in their natural, rather than lexicographic, order.")
     (license license:artistic2.0)))
 
+(define-public r-genomicranges
+  (package
+    (name "r-genomicranges")
+    (version "1.42.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicRanges" version))
+              (sha256
+               (base32
+                "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
+    (properties
+     `((upstream-name . "GenomicRanges")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/GenomicRanges")
+    (synopsis "Representation and manipulation of genomic intervals")
+    (description
+     "This package provides tools to efficiently represent and manipulate
+genomic annotations and alignments is playing a central role when it comes to
+analyzing high-throughput sequencing data (a.k.a. NGS data).  The
+GenomicRanges package defines general purpose containers for storing and
+manipulating genomic intervals and variables defined along a genome.")
+    (license license:artistic2.0)))
+
 (define-public r-gostats
   (package
     (name "r-gostats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 65db983461..4889c148e4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,37 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomicranges
-  (package
-    (name "r-genomicranges")
-    (version "1.42.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicRanges" version))
-              (sha256
-               (base32
-                "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
-    (properties
-     `((upstream-name . "GenomicRanges")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/GenomicRanges")
-    (synopsis "Representation and manipulation of genomic intervals")
-    (description
-     "This package provides tools to efficiently represent and manipulate
-genomic annotations and alignments is playing a central role when it comes to
-analyzing high-throughput sequencing data (a.k.a. NGS data).  The
-GenomicRanges package defines general purpose containers for storing and
-manipulating genomic intervals and variables defined along a genome.")
-    (license license:artistic2.0)))
-
 (define-public r-biobase
   (package
     (name "r-biobase")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:08
[PATCH 04/10] gnu: r-biobase: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-4-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
---
gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 22 ----------------------
2 files changed, 22 insertions(+), 22 deletions(-)

Toggle diff (68 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ec273cae70..b7308848c0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1570,6 +1570,28 @@ microarrays.")
 databases.  Packages produced are intended to be used with AnnotationDbi.")
     (license license:artistic2.0)))
 
+(define-public r-biobase
+  (package
+    (name "r-biobase")
+    (version "2.50.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Biobase" version))
+              (sha256
+               (base32
+                "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
+    (properties
+     `((upstream-name . "Biobase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)))
+    (home-page "https://bioconductor.org/packages/Biobase")
+    (synopsis "Base functions for Bioconductor")
+    (description
+     "This package provides functions that are needed by many other packages
+on Bioconductor or which replace R functions.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4889c148e4..b73862ff86 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,28 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-biobase
-  (package
-    (name "r-biobase")
-    (version "2.50.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Biobase" version))
-              (sha256
-               (base32
-                "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
-    (properties
-     `((upstream-name . "Biobase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)))
-    (home-page "https://bioconductor.org/packages/Biobase")
-    (synopsis "Base functions for Bioconductor")
-    (description
-     "This package provides functions that are needed by many other packages
-on Bioconductor or which replace R functions.")
-    (license license:artistic2.0)))
-
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:08
[PATCH 05/10] gnu: r-annotationdbi: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-5-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
---
gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 29 -----------------------------
2 files changed, 29 insertions(+), 29 deletions(-)

Toggle diff (82 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b7308848c0..2ae212dfac 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1538,6 +1538,35 @@ structure.")
 microarrays.")
     (license license:artistic2.0)))
 
+(define-public r-annotationdbi
+  (package
+    (name "r-annotationdbi")
+    (version "1.52.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnnotationDbi" version))
+              (sha256
+               (base32
+                "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
+    (properties
+     `((upstream-name . "AnnotationDbi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-dbi" ,r-dbi)
+       ("r-iranges" ,r-iranges)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/AnnotationDbi")
+    (synopsis "Annotation database interface")
+    (description
+     "This package provides user interface and database connection code for
+annotation data packages using SQLite data storage.")
+    (license license:artistic2.0)))
+
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b73862ff86..a45196bc5b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,35 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-annotationdbi
-  (package
-    (name "r-annotationdbi")
-    (version "1.52.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "AnnotationDbi" version))
-              (sha256
-               (base32
-                "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
-    (properties
-     `((upstream-name . "AnnotationDbi")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-iranges" ,r-iranges)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/AnnotationDbi")
-    (synopsis "Annotation database interface")
-    (description
-     "This package provides user interface and database connection code for
-annotation data packages using SQLite data storage.")
-    (license license:artistic2.0)))
-
 (define-public r-biomart
   (package
     (name "r-biomart")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:09
[PATCH 06/10] gnu: r-biomart: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-6-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 38 ---------------------------------
2 files changed, 38 insertions(+), 38 deletions(-)

Toggle diff (100 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2ae212dfac..897e85dfe3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1621,6 +1621,44 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 on Bioconductor or which replace R functions.")
     (license license:artistic2.0)))
 
+(define-public r-biomart
+  (package
+    (name "r-biomart")
+    (version "2.46.3")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "biomaRt" version))
+              (sha256
+               (base32
+                "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
+    (properties
+     `((upstream-name . "biomaRt")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocfilecache" ,r-biocfilecache)
+       ("r-httr" ,r-httr)
+       ("r-openssl" ,r-openssl)
+       ("r-progress" ,r-progress)
+       ("r-rappdirs" ,r-rappdirs)
+       ("r-stringr" ,r-stringr)
+       ("r-xml" ,r-xml)
+       ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/biomaRt")
+    (synopsis "Interface to BioMart databases")
+    (description
+     "biomaRt provides an interface to a growing collection of databases
+implementing the @url{BioMart software suite, http://www.biomart.org}.  The
+package enables retrieval of large amounts of data in a uniform way without
+the need to know the underlying database schemas or write complex SQL queries.
+Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
+Wormbase and dbSNP mapped to Ensembl.  These major databases give biomaRt
+users direct access to a diverse set of data and enable a wide range of
+powerful online queries from gene annotation to database mining.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a45196bc5b..289a96f572 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-biomart
-  (package
-    (name "r-biomart")
-    (version "2.46.3")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "biomaRt" version))
-              (sha256
-               (base32
-                "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
-    (properties
-     `((upstream-name . "biomaRt")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-httr" ,r-httr)
-       ("r-openssl" ,r-openssl)
-       ("r-progress" ,r-progress)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-stringr" ,r-stringr)
-       ("r-xml" ,r-xml)
-       ("r-xml2" ,r-xml2)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/biomaRt")
-    (synopsis "Interface to BioMart databases")
-    (description
-     "biomaRt provides an interface to a growing collection of databases
-implementing the @url{BioMart software suite, http://www.biomart.org}.  The
-package enables retrieval of large amounts of data in a uniform way without
-the need to know the underlying database schemas or write complex SQL queries.
-Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
-Wormbase and dbSNP mapped to Ensembl.  These major databases give biomaRt
-users direct access to a diverse set of data and enable a wide range of
-powerful online queries from gene annotation to database mining.")
-    (license license:artistic2.0)))
-
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:09
[PATCH 07/10] gnu: r-biocparallel: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-7-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 27 ---------------------------
2 files changed, 27 insertions(+), 27 deletions(-)

Toggle diff (78 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 897e85dfe3..6482d8e4c1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1659,6 +1659,33 @@ users direct access to a diverse set of data and enable a wide range of
 powerful online queries from gene annotation to database mining.")
     (license license:artistic2.0)))
 
+(define-public r-biocparallel
+  (package
+    (name "r-biocparallel")
+    (version "1.24.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BiocParallel" version))
+              (sha256
+               (base32
+                "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
+    (properties
+     `((upstream-name . "BiocParallel")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-futile-logger" ,r-futile-logger)
+       ("r-snow" ,r-snow)
+       ("r-bh" ,r-bh)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/BiocParallel")
+    (synopsis "Bioconductor facilities for parallel evaluation")
+    (description
+     "This package provides modified versions and novel implementation of
+functions for parallel evaluation, tailored to use with Bioconductor
+objects.")
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public r-category
   (package
     (name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 289a96f572..af3fa36b19 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,33 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-biocparallel
-  (package
-    (name "r-biocparallel")
-    (version "1.24.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BiocParallel" version))
-              (sha256
-               (base32
-                "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
-    (properties
-     `((upstream-name . "BiocParallel")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-futile-logger" ,r-futile-logger)
-       ("r-snow" ,r-snow)
-       ("r-bh" ,r-bh)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/BiocParallel")
-    (synopsis "Bioconductor facilities for parallel evaluation")
-    (description
-     "This package provides modified versions and novel implementation of
-functions for parallel evaluation, tailored to use with Bioconductor
-objects.")
-    (license (list license:gpl2+ license:gpl3+))))
-
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:09
[PATCH 08/10] gnu: r-biostrings: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-8-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
---
gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 27 ---------------------------
2 files changed, 27 insertions(+), 27 deletions(-)

Toggle diff (78 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6482d8e4c1..2b7d65023d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1686,6 +1686,33 @@ functions for parallel evaluation, tailored to use with Bioconductor
 objects.")
     (license (list license:gpl2+ license:gpl3+))))
 
+(define-public r-biostrings
+  (package
+    (name "r-biostrings")
+    (version "2.58.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Biostrings" version))
+              (sha256
+               (base32
+                "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
+    (properties
+     `((upstream-name . "Biostrings")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-crayon" ,r-crayon)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/Biostrings")
+    (synopsis "String objects and algorithms for biological sequences")
+    (description
+     "This package provides memory efficient string containers, string
+matching algorithms, and other utilities, for fast manipulation of large
+biological sequences or sets of sequences.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index af3fa36b19..415210085e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,33 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-biostrings
-  (package
-    (name "r-biostrings")
-    (version "2.58.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Biostrings" version))
-              (sha256
-               (base32
-                "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
-    (properties
-     `((upstream-name . "Biostrings")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-crayon" ,r-crayon)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/Biostrings")
-    (synopsis "String objects and algorithms for biological sequences")
-    (description
-     "This package provides memory efficient string containers, string
-matching algorithms, and other utilities, for fast manipulation of large
-biological sequences or sets of sequences.")
-    (license license:artistic2.0)))
-
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:09
[PATCH 09/10] gnu: r-rsamtools: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-9-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 43 ---------------------------------
2 files changed, 43 insertions(+), 43 deletions(-)

Toggle diff (110 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2b7d65023d..c659bdd09e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-rsamtools
+  (package
+    (name "r-rsamtools")
+    (version "2.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Rsamtools" version))
+              (sha256
+               (base32
+                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+    (properties
+     `((upstream-name . "Rsamtools")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-zlib
+           (lambda _
+             (substitute* "DESCRIPTION"
+               (("zlibbioc, ") ""))
+             (substitute* "NAMESPACE"
+               (("import\\(zlibbioc\\)") ""))
+             #t)))))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bitops" ,r-bitops)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
+    (synopsis "Interface to samtools, bcftools, and tabix")
+    (description
+     "This package provides an interface to the @code{samtools},
+@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
+Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
+tab-delimited (tabix) files.")
+    (license license:expat)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 415210085e..05805d1a8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,49 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-rsamtools
-  (package
-    (name "r-rsamtools")
-    (version "2.6.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Rsamtools" version))
-              (sha256
-               (base32
-                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
-    (properties
-     `((upstream-name . "Rsamtools")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-zlib
-           (lambda _
-             (substitute* "DESCRIPTION"
-               (("zlibbioc, ") ""))
-             (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bitops" ,r-bitops)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
-    (synopsis "Interface to samtools, bcftools, and tabix")
-    (description
-     "This package provides an interface to the @code{samtools},
-@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
-Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
-tab-delimited (tabix) files.")
-    (license license:expat)))
-
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-- 
2.30.1
Z
Z
zimoun wrote on 15 Mar 2021 19:09
[PATCH 10/10] gnu: r-delayedarray: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20210315180904.8346-10-zimon.toutoune@gmail.com
* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
---
gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 33 ---------------------------------
2 files changed, 33 insertions(+), 33 deletions(-)

Toggle diff (90 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c659bdd09e..9212165706 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1212,6 +1212,39 @@ data.  In addition, provides numerous plotting functions for commonly
 used visualizations.")
    (license license:artistic2.0)))
 
+(define-public r-delayedarray
+  (package
+    (name "r-delayedarray")
+    (version "0.16.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DelayedArray" version))
+              (sha256
+               (base32
+                "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0"))))
+    (properties
+     `((upstream-name . "DelayedArray")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixgenerics" ,r-matrixgenerics)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/DelayedArray")
+    (synopsis "Delayed operations on array-like objects")
+    (description
+     "Wrapping an array-like object (typically an on-disk object) in a
+@code{DelayedArray} object allows one to perform common array operations on it
+without loading the object in memory.  In order to reduce memory usage and
+optimize performance, operations on the object are either delayed or executed
+using a block processing mechanism.  Note that this also works on in-memory
+array-like objects like @code{DataFrame} objects (typically with Rle columns),
+@code{Matrix} objects, and ordinary arrays and data frames.")
+    (license license:artistic2.0)))
+
 (define-public r-bluster
   (package
    (name "r-bluster")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 05805d1a8b..bc342b5de8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,39 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-delayedarray
-  (package
-    (name "r-delayedarray")
-    (version "0.16.2")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "DelayedArray" version))
-              (sha256
-               (base32
-                "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0"))))
-    (properties
-     `((upstream-name . "DelayedArray")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixgenerics" ,r-matrixgenerics)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/DelayedArray")
-    (synopsis "Delayed operations on array-like objects")
-    (description
-     "Wrapping an array-like object (typically an on-disk object) in a
-@code{DelayedArray} object allows one to perform common array operations on it
-without loading the object in memory.  In order to reduce memory usage and
-optimize performance, operations on the object are either delayed or executed
-using a block processing mechanism.  Note that this also works on in-memory
-array-like objects like @code{DataFrame} objects (typically with Rle columns),
-@code{Matrix} objects, and ordinary arrays and data frames.")
-    (license license:artistic2.0)))
-
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-- 
2.30.1
R
R
Ricardo Wurmus wrote on 15 Mar 2021 23:33
Re: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 47171-done@debbugs.gnu.org)
87pn00m4ig.fsf@elephly.net
Hi,

Toggle quote (12 lines)
> zimoun (10):
> gnu: r-limma: Move to (gnu packages bioconductor).
> gnu: r-xvector: Move to (gnu packages bioconductor).
> gnu: r-genomicranges: Move to (gnu packages bioconductor).
> gnu: r-biobase: Move to (gnu packages bioconductor).
> gnu: r-annotationdbi: Move to (gnu packages bioconductor).
> gnu: r-biomart: Move to (gnu packages bioconductor).
> gnu: r-biocparallel: Move to (gnu packages bioconductor).
> gnu: r-biostrings: Move to (gnu packages bioconductor).
> gnu: r-rsamtools: Move to (gnu packages bioconductor).
> gnu: r-delayedarray: Move to (gnu packages bioconductor).

Thanks, I’ve pushed them all.

--
Ricardo
Closed
L
L
Leo Famulari wrote on 16 Mar 2021 00:56
Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).
YE/0IpB2HTm8XwWT@jasmine.lan
On Mon, Mar 15, 2021 at 11:33:11PM +0100, Ricardo Wurmus wrote:
Toggle quote (16 lines)
> Hi,
>
> > zimoun (10):
> > gnu: r-limma: Move to (gnu packages bioconductor).
> > gnu: r-xvector: Move to (gnu packages bioconductor).
> > gnu: r-genomicranges: Move to (gnu packages bioconductor).
> > gnu: r-biobase: Move to (gnu packages bioconductor).
> > gnu: r-annotationdbi: Move to (gnu packages bioconductor).
> > gnu: r-biomart: Move to (gnu packages bioconductor).
> > gnu: r-biocparallel: Move to (gnu packages bioconductor).
> > gnu: r-biostrings: Move to (gnu packages bioconductor).
> > gnu: r-rsamtools: Move to (gnu packages bioconductor).
> > gnu: r-delayedarray: Move to (gnu packages bioconductor).
>
> Thanks, I’ve pushed them all.

These commits caused `guix pull` to fail, as described here:


I think we just needed to import the bioconductor module in the cran
module, but I wasn't sure so I reverted them in order to fix the problem
quickly.
Z
Z
zimoun wrote on 16 Mar 2021 13:27
(name . Leo Famulari)(address . leo@famulari.name)
CAJ3okZ0+tMAOQtpL+1FN5x6dNs10gOUGGrtRrXBj3kZphgU2wg@mail.gmail.com
Hi Leo,

On Tue, 16 Mar 2021 at 00:56, Leo Famulari <leo@famulari.name> wrote:
Toggle quote (24 lines)
> On Mon, Mar 15, 2021 at 11:33:11PM +0100, Ricardo Wurmus wrote:

> > > zimoun (10):
> > > gnu: r-limma: Move to (gnu packages bioconductor).
> > > gnu: r-xvector: Move to (gnu packages bioconductor).
> > > gnu: r-genomicranges: Move to (gnu packages bioconductor).
> > > gnu: r-biobase: Move to (gnu packages bioconductor).
> > > gnu: r-annotationdbi: Move to (gnu packages bioconductor).
> > > gnu: r-biomart: Move to (gnu packages bioconductor).
> > > gnu: r-biocparallel: Move to (gnu packages bioconductor).
> > > gnu: r-biostrings: Move to (gnu packages bioconductor).
> > > gnu: r-rsamtools: Move to (gnu packages bioconductor).
> > > gnu: r-delayedarray: Move to (gnu packages bioconductor).
> >
> > Thanks, I’ve pushed them all.
>
> These commits caused `guix pull` to fail, as described here:
>
> https://git.savannah.gnu.org/cgit/guix.git/commit/?id=8ec0ca8faff62f19426f22aeb1bd59a8950ca05a
>
> I think we just needed to import the bioconductor module in the cran
> module, but I wasn't sure so I reverted them in order to fix the problem
> quickly.

Sorry for the annoyance. I did "make as-derivation" and it reports
nothing. But indeed, "./pre-inst-env guix pull -p /tmp/new
--url=$(pwd) --disable-authentication --branch=test" breaks.
I do not know if I do something wrong (run make in a worktree for the branch).

Well, thanks for the report and I confirm that adding the bioconductor
import in cran fixes "guix pull". But in my memories, this import
was adding circular dependency. Ricardo, WDYT?


Cheers,
simon
R
R
Ricardo Wurmus wrote on 16 Mar 2021 14:20
(name . zimoun)(address . zimon.toutoune@gmail.com)
87h7lbme0c.fsf@elephly.net
zimoun <zimon.toutoune@gmail.com> writes:

Toggle quote (4 lines)
> Well, thanks for the report and I confirm that adding the bioconductor
> import in cran fixes "guix pull". But in my memories, this import
> was adding circular dependency. Ricardo, WDYT?

The point of having (gnu packages cran) and (gnu packages bioconductor)
be separate modules is to separate independent packages.

I’d like to keep it that way and not let (gnu packages cran) depend on
(gnu packages bioconductor).

--
Ricardo
Z
Z
zimoun wrote on 16 Mar 2021 14:30
(name . Ricardo Wurmus)(address . rekado@elephly.net)
CAJ3okZ30sxLJyaz8zJE6OSTcjDdnZYrDXg1+y=YyQkumqFq+AA@mail.gmail.com
Hi,

On Tue, 16 Mar 2021 at 14:20, Ricardo Wurmus <rekado@elephly.net> wrote:
Toggle quote (12 lines)
> zimoun <zimon.toutoune@gmail.com> writes:
>
> > Well, thanks for the report and I confirm that adding the bioconductor
> > import in cran fixes "guix pull". But in my memories, this import
> > was adding circular dependency. Ricardo, WDYT?
>
> The point of having (gnu packages cran) and (gnu packages bioconductor)
> be separate modules is to separate independent packages.
>
> I’d like to keep it that way and not let (gnu packages cran) depend on
> (gnu packages bioconductor).

Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea
packages from (gnu packages cran) to (gnu packages bioconductor)
because they depend on the Bioconductor package r-biobase (and
r-limma). Right?
How do I proceed? Submit a patch moving these 2 packages and then
another patch reverting the revert?

Thanks,
simon
R
R
Ricardo Wurmus wrote on 16 Mar 2021 17:08
(name . zimoun)(address . zimon.toutoune@gmail.com)
87eegfm689.fsf@elephly.net
zimoun <zimon.toutoune@gmail.com> writes:

Toggle quote (20 lines)
> Hi,
>
> On Tue, 16 Mar 2021 at 14:20, Ricardo Wurmus <rekado@elephly.net> wrote:
>> zimoun <zimon.toutoune@gmail.com> writes:
>>
>> > Well, thanks for the report and I confirm that adding the bioconductor
>> > import in cran fixes "guix pull". But in my memories, this import
>> > was adding circular dependency. Ricardo, WDYT?
>>
>> The point of having (gnu packages cran) and (gnu packages bioconductor)
>> be separate modules is to separate independent packages.
>>
>> I’d like to keep it that way and not let (gnu packages cran) depend on
>> (gnu packages bioconductor).
>
> Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea
> packages from (gnu packages cran) to (gnu packages bioconductor)
> because they depend on the Bioconductor package r-biobase (and
> r-limma). Right?

Correct. We don’t want any CRAN packages to depend on Bioconductor
things. When this is unavoidable, though, we move them to (gnu packages
bioconductor) with a comment.

Toggle quote (3 lines)
> How do I proceed? Submit a patch moving these 2 packages and then
> another patch reverting the revert?

Sounds good. (You could do this all in the same issue.)

--
Ricardo
Z
Z
zimoun wrote on 16 Mar 2021 17:36
(name . Ricardo Wurmus)(address . rekado@elephly.net)
CAJ3okZ2SXpoLFr7F3PSmZo2hvc_DYMwrcGXwQ7fewG1ht4=nPQ@mail.gmail.com
On Tue, 16 Mar 2021 at 17:08, Ricardo Wurmus <rekado@elephly.net> wrote:

Toggle quote (9 lines)
> > Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea
> > packages from (gnu packages cran) to (gnu packages bioconductor)
> > because they depend on the Bioconductor package r-biobase (and
> > r-limma). Right?
>
> Correct. We don’t want any CRAN packages to depend on Bioconductor
> things. When this is unavoidable, though, we move them to (gnu packages
> bioconductor) with a comment.

Ok.


Toggle quote (5 lines)
> > How do I proceed? Submit a patch moving these 2 packages and then
> > another patch reverting the revert?
>
> Sounds good. (You could do this all in the same issue.)

By the same issue, do you mean the same guix-patches number? Or the
same commit?


Cheers,
simon
R
R
Ricardo Wurmus wrote on 16 Mar 2021 23:04
(name . zimoun)(address . zimon.toutoune@gmail.com)
871rcen4b4.fsf@elephly.net
zimoun <zimon.toutoune@gmail.com> writes:

Toggle quote (8 lines)
>> > How do I proceed? Submit a patch moving these 2 packages and then
>> > another patch reverting the revert?
>>
>> Sounds good. (You could do this all in the same issue.)
>
> By the same issue, do you mean the same guix-patches number? Or the
> same commit?

I meant the same guix-patches issue number; separate commits.

--
Ricardo
Z
Z
zimoun wrote on 17 Mar 2021 21:14
[PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)
20210317201414.10811-1-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-bisquerna): Move this variable from here...
* gnu/packages/bioconductor.scm (r-bisquerna): ...to here.
---
gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
gnu/packages/cran.scm | 25 -------------------------
2 files changed, 26 insertions(+), 25 deletions(-)

Toggle diff (77 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d611f3a491..b5ac2750f3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1294,6 +1294,32 @@ naming and share the same rich and consistent \"Vector API\" as much as
 possible.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
+(define-public r-bisquerna
+  (package
+   (name "r-bisquerna")
+   (version "1.0.4")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "BisqueRNA" version))
+            (sha256
+             (base32
+              "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
+   (properties `((upstream-name . "BisqueRNA")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biobase" ,r-biobase)
+      ("r-limsolve" ,r-limsolve)))
+   (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
+   (synopsis "Decomposition of bulk expression with single-cell sequencing")
+   (description "This package provides tools to accurately estimate cell type
+abundances from heterogeneous bulk expression.  A reference-based method
+utilizes single-cell information to generate a signature matrix and
+transformation of bulk expression for accurate regression based estimates.
+A marker-based method utilizes known cell-specific marker genes to measure
+relative abundances across samples.")
+   (license license:gpl3)))
+
 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
 ;; from Bioconductor.
 (define-public r-deconstructsigs
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5617383cbc..93fe44c25c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2838,31 +2838,6 @@ where the bound function accepts additional arguments.")
 bindings that call a C++ function.")
     (license license:expat)))
 
-(define-public r-bisquerna
-  (package
-   (name "r-bisquerna")
-   (version "1.0.4")
-   (source (origin
-            (method url-fetch)
-            (uri (cran-uri "BisqueRNA" version))
-            (sha256
-             (base32
-              "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
-   (properties `((upstream-name . "BisqueRNA")))
-   (build-system r-build-system)
-   (propagated-inputs
-    `(("r-biobase" ,r-biobase)
-      ("r-limsolve" ,r-limsolve)))
-   (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
-   (synopsis "Decomposition of bulk expression with single-cell sequencing")
-   (description "This package provides tools to accurately estimate cell type
-abundances from heterogeneous bulk expression.  A reference-based method
-utilizes single-cell information to generate a signature matrix and
-transformation of bulk expression for accurate regression based estimates.
-A marker-based method utilizes known cell-specific marker genes to measure
-relative abundances across samples.")
-   (license license:gpl3)))
-
 (define-public r-auc
   (package
     (name "r-auc")

base-commit: d79d63e7829d53f6a501d8df7e264ff70033abca
-- 
2.30.1
Z
Z
zimoun wrote on 17 Mar 2021 21:14
[PATCH v2 2/3] gnu: r-absfiltergsea: Move to (gnu packages bioconductor).
(address . 47171@debbugs.gnu.org)
20210317201414.10811-2-zimon.toutoune@gmail.com
* gnu/packages/cran.scm (r-absfiltergsea): Move this variable from here...
* gnu/packages/bioconductor.scm (r-absfiltergsea): ...to here.
---
gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
gnu/packages/cran.scm | 27 ---------------------------
2 files changed, 28 insertions(+), 27 deletions(-)

Toggle diff (79 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b5ac2750f3..6530a31fb5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1294,6 +1294,34 @@ naming and share the same rich and consistent \"Vector API\" as much as
 possible.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
+(define-public r-absfiltergsea
+  (package
+    (name "r-absfiltergsea")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AbsFilterGSEA" version))
+       (sha256
+        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+    (properties `((upstream-name . "AbsFilterGSEA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-deseq" ,r-deseq)
+       ("r-limma" ,r-limma)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+    (description
+     "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+  Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
 (define-public r-bisquerna
   (package
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 93fe44c25c..54d895e9fe 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -26591,33 +26591,6 @@ include Markov models of discrete and continuous trait evolution and constant
 rate speciation and extinction.")
     (license license:gpl2+)))
 
-(define-public r-absfiltergsea
-  (package
-    (name "r-absfiltergsea")
-    (version "1.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "AbsFilterGSEA" version))
-       (sha256
-        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
-    (properties `((upstream-name . "AbsFilterGSEA")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-deseq" ,r-deseq)
-       ("r-limma" ,r-limma)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcpparmadillo" ,r-rcpparmadillo)))
-    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
-    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
-    (description
-     "This package provides a function that performs gene-permuting of a gene-set
-enrichment analysis (GSEA) calculation with or without the absolute filtering.
-  Without filtering, users can perform (original) two-tailed or one-tailed
-absolute GSEA.")
-    (license license:gpl2)))
-
 (define-public r-calculus
   (package
     (name "r-calculus")
-- 
2.30.1
Z
Z
zimoun wrote on 17 Mar 2021 21:14
[PATCH v2 3/3] Revert "Revert some commits that caused `guix pull` to fail."
(address . 47171@debbugs.gnu.org)
20210317201414.10811-3-zimon.toutoune@gmail.com
This reverts commit 8ec0ca8faff62f19426f22aeb1bd59a8950ca05a.
---
gnu/packages/bioconductor.scm | 333 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 305 -----------------------------
2 files changed, 333 insertions(+), 305 deletions(-)

Toggle diff (704 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6530a31fb5..d9e938db5c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1212,6 +1212,39 @@ data.  In addition, provides numerous plotting functions for commonly
 used visualizations.")
    (license license:artistic2.0)))
 
+(define-public r-delayedarray
+  (package
+    (name "r-delayedarray")
+    (version "0.16.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DelayedArray" version))
+              (sha256
+               (base32
+                "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0"))))
+    (properties
+     `((upstream-name . "DelayedArray")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixgenerics" ,r-matrixgenerics)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/DelayedArray")
+    (synopsis "Delayed operations on array-like objects")
+    (description
+     "Wrapping an array-like object (typically an on-disk object) in a
+@code{DelayedArray} object allows one to perform common array operations on it
+without loading the object in memory.  In order to reduce memory usage and
+optimize performance, operations on the object are either delayed or executed
+using a block processing mechanism.  Note that this also works on in-memory
+array-like objects like @code{DataFrame} objects (typically with Rle columns),
+@code{Matrix} objects, and ordinary arrays and data frames.")
+    (license license:artistic2.0)))
+
 (define-public r-bluster
   (package
    (name "r-bluster")
@@ -1592,6 +1625,35 @@ structure.")
 microarrays.")
     (license license:artistic2.0)))
 
+(define-public r-annotationdbi
+  (package
+    (name "r-annotationdbi")
+    (version "1.52.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnnotationDbi" version))
+              (sha256
+               (base32
+                "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
+    (properties
+     `((upstream-name . "AnnotationDbi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-dbi" ,r-dbi)
+       ("r-iranges" ,r-iranges)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/AnnotationDbi")
+    (synopsis "Annotation database interface")
+    (description
+     "This package provides user interface and database connection code for
+annotation data packages using SQLite data storage.")
+    (license license:artistic2.0)))
+
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
@@ -1624,6 +1686,148 @@ microarrays.")
 databases.  Packages produced are intended to be used with AnnotationDbi.")
     (license license:artistic2.0)))
 
+(define-public r-biobase
+  (package
+    (name "r-biobase")
+    (version "2.50.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Biobase" version))
+              (sha256
+               (base32
+                "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
+    (properties
+     `((upstream-name . "Biobase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)))
+    (home-page "https://bioconductor.org/packages/Biobase")
+    (synopsis "Base functions for Bioconductor")
+    (description
+     "This package provides functions that are needed by many other packages
+on Bioconductor or which replace R functions.")
+    (license license:artistic2.0)))
+
+(define-public r-biomart
+  (package
+    (name "r-biomart")
+    (version "2.46.3")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "biomaRt" version))
+              (sha256
+               (base32
+                "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
+    (properties
+     `((upstream-name . "biomaRt")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocfilecache" ,r-biocfilecache)
+       ("r-httr" ,r-httr)
+       ("r-openssl" ,r-openssl)
+       ("r-progress" ,r-progress)
+       ("r-rappdirs" ,r-rappdirs)
+       ("r-stringr" ,r-stringr)
+       ("r-xml" ,r-xml)
+       ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/biomaRt")
+    (synopsis "Interface to BioMart databases")
+    (description
+     "biomaRt provides an interface to a growing collection of databases
+implementing the @url{BioMart software suite, http://www.biomart.org}.  The
+package enables retrieval of large amounts of data in a uniform way without
+the need to know the underlying database schemas or write complex SQL queries.
+Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
+Wormbase and dbSNP mapped to Ensembl.  These major databases give biomaRt
+users direct access to a diverse set of data and enable a wide range of
+powerful online queries from gene annotation to database mining.")
+    (license license:artistic2.0)))
+
+(define-public r-biocparallel
+  (package
+    (name "r-biocparallel")
+    (version "1.24.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BiocParallel" version))
+              (sha256
+               (base32
+                "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
+    (properties
+     `((upstream-name . "BiocParallel")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-reproducible
+           (lambda _
+             ;; Remove generated documentation.
+             (for-each delete-file
+                       '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
+                         "inst/doc/Introduction_To_BiocParallel.pdf"
+                         "inst/doc/Errors_Logs_And_Debugging.pdf"
+                         "inst/doc/BiocParallel_BatchtoolsParam.R"
+                         "inst/doc/Introduction_To_BiocParallel.R"
+                         "inst/doc/Errors_Logs_And_Debugging.R"))
+
+             ;; Remove time-dependent macro
+             (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
+                            "inst/doc/Introduction_To_BiocParallel.Rnw"
+                            "inst/doc/Errors_Logs_And_Debugging.Rnw"
+                            "vignettes/BiocParallel_BatchtoolsParam.Rnw"
+                            "vignettes/Introduction_To_BiocParallel.Rnw"
+                            "vignettes/Errors_Logs_And_Debugging.Rnw")
+               (("\\today") "later"))
+
+             ;; Initialize the random number generator seed when building.
+             (substitute* "R/internal_rng_stream.R"
+               (("\"L'Ecuyer-CMRG\"\\)" m)
+                (string-append
+                 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
+    (propagated-inputs
+     `(("r-futile-logger" ,r-futile-logger)
+       ("r-snow" ,r-snow)
+       ("r-bh" ,r-bh)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/BiocParallel")
+    (synopsis "Bioconductor facilities for parallel evaluation")
+    (description
+     "This package provides modified versions and novel implementation of
+functions for parallel evaluation, tailored to use with Bioconductor
+objects.")
+    (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-biostrings
+  (package
+    (name "r-biostrings")
+    (version "2.58.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Biostrings" version))
+              (sha256
+               (base32
+                "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
+    (properties
+     `((upstream-name . "Biostrings")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-crayon" ,r-crayon)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/Biostrings")
+    (synopsis "String objects and algorithms for biological sequences")
+    (description
+     "This package provides memory efficient string containers, string
+matching algorithms, and other utilities, for fast manipulation of large
+biological sequences or sets of sequences.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
@@ -1824,6 +2028,37 @@ translation between different chromosome sequence naming conventions (e.g.,
 names in their natural, rather than lexicographic, order.")
     (license license:artistic2.0)))
 
+(define-public r-genomicranges
+  (package
+    (name "r-genomicranges")
+    (version "1.42.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicRanges" version))
+              (sha256
+               (base32
+                "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
+    (properties
+     `((upstream-name . "GenomicRanges")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/GenomicRanges")
+    (synopsis "Representation and manipulation of genomic intervals")
+    (description
+     "This package provides tools to efficiently represent and manipulate
+genomic annotations and alignments is playing a central role when it comes to
+analyzing high-throughput sequencing data (a.k.a. NGS data).  The
+GenomicRanges package defines general purpose containers for storing and
+manipulating genomic intervals and variables defined along a genome.")
+    (license license:artistic2.0)))
+
 (define-public r-gostats
   (package
     (name "r-gostats")
@@ -1904,6 +2139,25 @@ Enrichment Analysis} (GSEA).")
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-limma
+  (package
+    (name "r-limma")
+    (version "3.46.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "limma" version))
+              (sha256
+               (base32
+                "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
+    (build-system r-build-system)
+    (home-page "http://bioinf.wehi.edu.au/limma")
+    (synopsis "Package for linear models for microarray and RNA-seq data")
+    (description "This package can be used for the analysis of gene expression
+studies, especially the use of linear models for analysing designed experiments
+and the assessment of differential expression.  The analysis methods apply to
+different technologies, including microarrays, RNA-seq, and quantitative PCR.")
+    (license license:gpl2+)))
+
 (define-public r-rbgl
   (package
     (name "r-rbgl")
@@ -2008,6 +2262,49 @@ reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-rsamtools
+  (package
+    (name "r-rsamtools")
+    (version "2.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "Rsamtools" version))
+              (sha256
+               (base32
+                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+    (properties
+     `((upstream-name . "Rsamtools")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-zlib
+           (lambda _
+             (substitute* "DESCRIPTION"
+               (("zlibbioc, ") ""))
+             (substitute* "NAMESPACE"
+               (("import\\(zlibbioc\\)") ""))
+             #t)))))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bitops" ,r-bitops)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
+    (synopsis "Interface to samtools, bcftools, and tabix")
+    (description
+     "This package provides an interface to the @code{samtools},
+@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
+Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
+tab-delimited (tabix) files.")
+    (license license:expat)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
@@ -2143,6 +2440,42 @@ annotation infrastructure.")
 coding changes and predict coding outcomes.")
     (license license:artistic2.0)))
 
+(define-public r-xvector
+  (package
+    (name "r-xvector")
+    (version "0.30.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "XVector" version))
+              (sha256
+               (base32
+                "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
+    (properties
+     `((upstream-name . "XVector")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-zlib
+           (lambda _
+             (substitute* "DESCRIPTION"
+               (("zlibbioc, ") ""))
+             (substitute* "NAMESPACE"
+               (("import\\(zlibbioc\\)") ""))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/XVector")
+    (synopsis "Representation and manpulation of external sequences")
+    (description
+     "This package provides memory efficient S4 classes for storing sequences
+\"externally\" (behind an R external pointer, or on disk).")
+    (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 eb466868d1..51301a9603 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7695,311 +7695,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-limma
-  (package
-    (name "r-limma")
-    (version "3.46.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "limma" version))
-              (sha256
-               (base32
-                "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
-    (build-system r-build-system)
-    (home-page "http://bioinf.wehi.edu.au/limma")
-    (synopsis "Package for linear models for microarray and RNA-seq data")
-    (description "This package can be used for the analysis of gene expression
-studies, especially the use of linear models for analysing designed experiments
-and the assessment of differential expression.  The analysis methods apply to
-different technologies, including microarrays, RNA-seq, and quantitative PCR.")
-    (license license:gpl2+)))
-
-(define-public r-xvector
-  (package
-    (name "r-xvector")
-    (version "0.30.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "XVector" version))
-              (sha256
-               (base32
-                "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
-    (properties
-     `((upstream-name . "XVector")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-zlib
-           (lambda _
-             (substitute* "DESCRIPTION"
-               (("zlibbioc, ") ""))
-             (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/XVector")
-    (synopsis "Representation and manpulation of external sequences")
-    (description
-     "This package provides memory efficient S4 classes for storing sequences
-\"externally\" (behind an R external pointer, or on disk).")
-    (license license:artistic2.0)))
-
-(define-public r-genomicranges
-  (package
-    (name "r-genomicranges")
-    (version "1.42.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicRanges" version))
-              (sha256
-               (base32
-                "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
-    (properties
-     `((upstream-name . "GenomicRanges")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/GenomicRanges")
-    (synopsis "Representation and manipulation of genomic intervals")
-    (description
-     "This package provides tools to efficiently represent and manipulate
-genomic annotations and alignments is playing a central role when it comes to
-analyzing high-throughput sequencing data (a.k.a. NGS data).  The
-GenomicRanges package defines general purpose containers for storing and
-manipulating genomic intervals and variables defined along a genome.")
-    (license license:artistic2.0)))
-
-(define-public r-biobase
-  (package
-    (name "r-biobase")
-    (version "2.50.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Biobase" version))
-              (sha256
-               (base32
-                "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
-    (properties
-     `((upstream-name . "Biobase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)))
-    (home-page "https://bioconductor.org/packages/Biobase")
-    (synopsis "Base functions for Bioconductor")
-    (description
-     "This package provides functions that are needed by many other packages
-on Bioconductor or which replace R functions.")
-    (license license:artistic2.0)))
-
-(define-public r-annotationdbi
-  (package
-    (name "r-annotationdbi")
-    (version "1.52.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "AnnotationDbi" version))
-              (sha256
-               (base32
-                "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
-    (properties
-     `((upstream-name . "AnnotationDbi")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-dbi" ,r-dbi)
-       ("r-iranges" ,r-iranges)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/AnnotationDbi")
-    (synopsis "Annotation database interface")
-    (description
-     "This package provides user interface and database connection code for
-annotation data packages using SQLite data storage.")
-    (license license:artistic2.0)))
-
-(define-public r-biomart
-  (package
-    (name "r-biomart")
-    (version "2.46.3")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "biomaRt" version))
-              (sha256
-               (base32
-                "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
-    (properties
-     `((upstream-name . "biomaRt")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-httr" ,r-httr)
-       ("r-openssl" ,r-openssl)
-       ("r-progress" ,r-progress)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-stringr" ,r-stringr)
-       ("r-xml" ,r-xml)
-       ("r-xml2" ,r-xml2)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/biomaRt")
-    (synopsis "Interface to BioMart databases")
-    (description
-     "biomaRt provides an interface to a growing collection of databases
-implementing the @url{BioMart software suite, http://www.biomart.org}.  The
-package enables retrieval of large amounts of data in a uniform way without
-the need to know the underlying database schemas or write complex SQL queries.
-Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
-Wormbase and dbSNP mapped to Ensembl.  These major databases give biomaRt
-users direct access to a diverse set of data and enable a wide range of
-powerful online queries from gene annotation to database mining.")
-    (license license:artistic2.0)))
-
-(define-public r-biocparallel
-  (package
-    (name "r-biocparallel")
-    (version "1.24.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BiocParallel" version))
-              (sha256
-               (base32
-                "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
-    (properties
-     `((upstream-name . "BiocParallel")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-futile-logger" ,r-futile-logger)
-       ("r-snow" ,r-snow)
-       ("r-bh" ,r-bh)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/BiocParallel")
-    (synopsis "Bioconductor facilities for parallel evaluation")
-    (description
-     "This package provides modified versions and novel implementation of
-functions for parallel evaluation, tailored to use with Bioconductor
-objects.")
-    (license (list license:gpl2+ license:gpl3+))))
-
-(define-public r-biostrings
-  (package
-    (name "r-biostrings")
-    (version "2.58.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Biostrings" version))
-              (sha256
-               (base32
-                "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
-    (properties
-     `((upstream-name . "Biostrings")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-crayon" ,r-crayon)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/Biostrings")
-    (synopsis "String objects and algorithms for biological sequences")
-    (description
-     "This package provides memory efficient string containers, string
-matching algorithms, and other utilities, for fast manipulation of large
-biological sequences or sets of sequences.")
-    (license license:artistic2.0)))
-
-(define-public r-rsamtools
-  (package
-    (name "r-rsamtools")
-    (version "2.6.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "Rsamtools" version))
-              (sha256
-               (base32
-                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
-    (properties
-     `((upstream-name . "Rsamtools")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-zlib
-           (lambda _
-             (substitute* "DESCRIPTION"
-               (("zlibbioc, ") ""))
-             (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bitops" ,r-bitops)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
-    (synopsis "Interface to samtools, bcftools, and tabix")
-    (description
-     "This package provides an interface to the @code{samtools},
-@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
-Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
-tab-delimited (tabix) files.")
-    (license license:expat)))
-
-(define-public r-delayedarray
-  (package
-    (name "r-delayedarray")
-    (version "0.16.2")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "DelayedArray" version))
-              (sha256
-               (base32
-                "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0"))))
-    (properties
-     `((upstream-name . "DelayedArray")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixgenerics" ,r-matrixgenerics)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/DelayedArray")
-    (synopsis "Delayed operations on array-like objects")
-    (description
-     "Wrapping an array-like object (typically an on-disk object) in a
-@code{DelayedArray} object allows one to perform common array operations on it
-without loading the object in memory.  In order to reduce memory usage and
-optimize performance, operations on the object are either delayed or executed
-using a block processing mechanism.  Note that this also works on in-memory
-array-like objects like @code{DataFrame} objects (typically with Rle columns),
-@code{Matrix} objects, and ordinary arrays and data frames.")
-    (license license:artistic2.0)))
-
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-- 
2.30.1
Z
Z
zimoun wrote on 17 Mar 2021 21:15
Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).
(name . Ricardo Wurmus)(address . rekado@elephly.net)
86o8fhv8od.fsf@gmail.com
Hi Ricardo,

On Tue, 16 Mar 2021 at 23:04, Ricardo Wurmus <rekado@elephly.net> wrote:

Toggle quote (2 lines)
> I meant the same guix-patches issue number; separate commits.

Done in v2. I have double-checked but who knows. :-)


Thanks,
simon
R
R
Ricardo Wurmus wrote on 31 Mar 2021 21:29
Re: [PATCH v2 1/3] gnu: r-bisquerna: Move to (gnu packages bioconductor).
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 47171-done@debbugs.gnu.org)
871rbv3yvm.fsf@elephly.net
Thanks for this new patch set. I applied it and ran “make
as-derivation” without problems.

I pushed these three commits to the master branch.

--
Ricardo
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