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[PATCH] import: Update Bioconductor release to 3.5.

From: Roel Janssen
Subject: [PATCH] import: Update Bioconductor release to 3.5.
Date: Wed, 26 Apr 2017 11:13:33 +0200
User-agent: mu4e 0.9.18; emacs 25.1.1

Attachment: 0001-import-Update-Bioconductor-release-to-3.5.patch
Description: Text Data

Attachment: 0001-gnu-Add-r-bookdown.patch
Description: Text Data

Attachment: 0001-gnu-Add-r-delayedarray.patch
Description: Text Data

Attachment: 0001-gnu-Add-r-genomeinfodbdata.patch
Description: Text Data

Dear Guix,

With this patch, I would like to open the mass-update of Bioconductor

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

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