From: Roel Janssen <roel@gnu.org>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] import: Update Bioconductor release to 3.5.
Date: Wed, 26 Apr 2017 11:13:33 +0200 [thread overview]
Message-ID: <rbuvaprilaa.fsf@gnu.org> (raw)
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[-- Attachment #1: 0001-import-Update-Bioconductor-release-to-3.5.patch --]
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From de9f486828827b1d024cad4918eed3ed96202cc0 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 26 Apr 2017 10:30:52 +0200
Subject: [PATCH] import: Update Bioconductor release to 3.5.
* guix/import/cran.scm: Change Bioconductor release to 3.5.
---
guix/import/cran.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 4d36882..be34a75 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -122,11 +122,11 @@ package definition."
(define %cran-url "http://cran.r-project.org/web/packages/")
(define %bioconductor-url "http://bioconductor.org/packages/")
-;; The latest Bioconductor release is 3.4. Bioconductor packages should be
+;; The latest Bioconductor release is 3.5. Bioconductor packages should be
;; updated together.
(define %bioconductor-svn-url
(string-append "https://readonly:readonly@"
- "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/"
+ "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/"
"madman/Rpacks/"))
--
2.7.4
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[-- Attachment #2: 0001-gnu-Add-r-bookdown.patch --]
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From cf66fb44a3a8c706b69adbc49fc76d8aaeb47975 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 26 Apr 2017 10:59:47 +0200
Subject: [PATCH] gnu: Add r-bookdown.
* gnu/packages/bioinformatics.scm (r-bookdown): New variable.
---
gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46e238f..3853a78 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6092,6 +6092,28 @@ categorize packages in a Bioconductor package repository according to keywords,
also known as views, in a controlled vocabulary.")
(license license:artistic2.0)))
+(define-public r-bookdown
+ (package
+ (name "r-bookdown")
+ (version "0.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "bookdown" version))
+ (sha256
+ (base32
+ "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)
+ ("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://github.com/rstudio/bookdown")
+ (synopsis "Authoring books and technical documents with R markdown")
+ (description "This package provides output formats and utilities for
+authoring books and technical documents with R Markdown.")
+ (license license:gpl3)))
+
(define-public r-biocstyle
(package
(name "r-biocstyle")
--
2.7.4
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[-- Attachment #3: 0001-gnu-Add-r-delayedarray.patch --]
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From f661fce758f3f051f4f951c4c7384c69268169d9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 26 Apr 2017 11:02:28 +0200
Subject: [PATCH] gnu: Add r-delayedarray.
* gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46e238f..67e8d0c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6656,6 +6656,36 @@ binary variant call (BCF) and compressed indexed tab-delimited (tabix)
files.")
(license license:expat)))
+(define-public r-delayedarray
+ (package
+ (name "r-delayedarray")
+ (version "0.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DelayedArray" version))
+ (sha256
+ (base32
+ "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r"))))
+ (properties
+ `((upstream-name . "DelayedArray")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)))
+ (home-page "http://bioconductor.org/packages/DelayedArray")
+ (synopsis "Delayed operations on array-like objects")
+ (description
+ "Wrapping an array-like object (typically an on-disk object) in a
+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 DataFrame objects (typically
+with Rle columns), Matrix objects, and ordinary arrays and data frames.")
+ (license license:artistic2.0)))
+
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
--
2.7.4
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[-- Attachment #4: 0001-gnu-Add-r-genomeinfodbdata.patch --]
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From d4313b287e05efcf54f87160d6e34ea60bfbadf6 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 26 Apr 2017 11:01:23 +0200
Subject: [PATCH] gnu: Add r-genomeinfodbdata.
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
---
gnu/packages/bioinformatics.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46e238f..903535a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6307,6 +6307,26 @@ naming and share the same rich and consistent \"Vector API\" as much as
possible.")
(license license:artistic2.0)))
+(define-public r-genomeinfodbdata
+ (package
+ (name "r-genomeinfodbdata")
+ (version "0.99.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomeInfoDbData" version))
+ (sha256
+ (base32
+ "120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25"))))
+ (properties
+ `((upstream-name . "GenomeInfoDbData")))
+ (build-system r-build-system)
+ (home-page "http://bioconductor.org/packages/GenomeInfoDbData")
+ (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
+ (description
+ "This package contains data for mapping between NCBI taxonomy ID and
+species. It is used by functions in the GenomeInfoDb package.")
+ (license license:artistic2.0)))
+
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
--
2.7.4
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Dear Guix,
With this patch, I would like to open the mass-update of Bioconductor
packages.
I built the affected packages after running:
$ guix refresh -t bioconductor -u
Some new packages must be added because of added dependencies to
existing packages:
r-genomeinfodbdata, r-delayedarray, r-bookdown
For these three packages, I attached patches as well.
And these packages would be upgraded:
r-annotate, r-geneplotter, r-genefilter, r-summarizedexperiment,
r-deseq2, r-annotationforge, r-rbgl, r-gseabase, r-category, r-gostats,
r-shortread, r-systempiper, r-grohmm, r-biocgenerics, r-biocinstaller,
r-biocviews, r-biocstyle, r-bioccheck, r-dnacopy, r-s4vectors,
r-iranges, r-genomeinfodb, r-variantannotation, r-limma, r-xvector,
r-genomicranges, r-biobase, r-annotationdbi, r-biomart, r-biocparallel,
r-biostrings, r-rsamtools, r-genomicalignments, r-rtracklayer,
r-genomicfeatureso, r-graph, r-topgo, r-bsgenome, r-impute,
r-seqpattern, r-genomation, r-seqlogo, r-motifrg, r-zlibbioc, r-rhtslib,
r-bamsignals, r-mutationalpatterns, r-tximport, r-rhdf5, r-chipseq,
r-copywriter, r-sva, r-protgenerics, r-mzr, r-affyio, r-affy, r-vsn,
r-mzid, r-pcamethods, r-msnbase, r-msnid, r-preprocesscore
Because these Bioconductor packages strongly depend on each other's
versions, I'd like to update them all in one go (in separate patches
of course..).
May I proceed with this mass-update?
Kind regards,
Roel Janssen
next reply other threads:[~2017-04-26 9:13 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-04-26 9:13 Roel Janssen [this message]
2017-04-27 6:51 ` [PATCH] import: Update Bioconductor release to 3.5 Ricardo Wurmus
2017-04-27 7:44 ` Roel Janssen
2017-04-27 13:14 ` Ricardo Wurmus
2017-04-28 9:11 ` Roel Janssen
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