From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: [PATCH] import: Update Bioconductor release to 3.5. Date: Wed, 26 Apr 2017 11:13:33 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34253) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1d3J13-0005hM-EK for guix-devel@gnu.org; Wed, 26 Apr 2017 05:13:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1d3J10-0004uR-5K for guix-devel@gnu.org; Wed, 26 Apr 2017 05:13:41 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:51828) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1d3J0z-0004uL-VR for guix-devel@gnu.org; Wed, 26 Apr 2017 05:13:38 -0400 Received: from [143.121.198.177] (port=52152 helo=cog147) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1d3J0z-0006rZ-Dd for guix-devel@gnu.org; Wed, 26 Apr 2017 05:13:37 -0400 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0001-import-Update-Bioconductor-release-to-3.5.patch >From de9f486828827b1d024cad4918eed3ed96202cc0 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0001-gnu-Add-r-bookdown.patch >From cf66fb44a3a8c706b69adbc49fc76d8aaeb47975 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0001-gnu-Add-r-delayedarray.patch >From f661fce758f3f051f4f951c4c7384c69268169d9 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0001-gnu-Add-r-genomeinfodbdata.patch >From d4313b287e05efcf54f87160d6e34ea60bfbadf6 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --=-=-= Content-Type: text/plain 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 --=-=-=--