[med-svn] r22693 - in trunk/packages/R: . r-bioc-savr r-bioc-savr/trunk r-bioc-savr/trunk/debian r-bioc-savr/trunk/debian/source r-bioc-savr/trunk/debian/tests
Andreas Tille
tille at moszumanska.debian.org
Thu Aug 18 09:36:38 UTC 2016
Author: tille
Date: 2016-08-18 09:36:37 +0000 (Thu, 18 Aug 2016)
New Revision: 22693
Added:
trunk/packages/R/r-bioc-savr/
trunk/packages/R/r-bioc-savr/trunk/
trunk/packages/R/r-bioc-savr/trunk/debian/
trunk/packages/R/r-bioc-savr/trunk/debian/README.source
trunk/packages/R/r-bioc-savr/trunk/debian/README.test
trunk/packages/R/r-bioc-savr/trunk/debian/changelog
trunk/packages/R/r-bioc-savr/trunk/debian/compat
trunk/packages/R/r-bioc-savr/trunk/debian/control
trunk/packages/R/r-bioc-savr/trunk/debian/copyright
trunk/packages/R/r-bioc-savr/trunk/debian/docs
trunk/packages/R/r-bioc-savr/trunk/debian/rules
trunk/packages/R/r-bioc-savr/trunk/debian/source/
trunk/packages/R/r-bioc-savr/trunk/debian/source/format
trunk/packages/R/r-bioc-savr/trunk/debian/tests/
trunk/packages/R/r-bioc-savr/trunk/debian/tests/control
trunk/packages/R/r-bioc-savr/trunk/debian/tests/run-unit-test
trunk/packages/R/r-bioc-savr/trunk/debian/watch
Log:
Inject r-bioc-savr
Added: trunk/packages/R/r-bioc-savr/trunk/debian/README.source
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/README.source (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/README.source 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,33 @@
+Explanation for binary files inside source package according to
+ http://lists.debian.org/debian-devel/2013/09/msg00332.html
+
+Files: inst/extdata/MiSeq/InterOp/CorrectedIntMetricsOut.bin
+Documentation: inst/doc/savR.Rnw
+ Corrected intensitites
+ .
+ Corrected intensity metrics can be inspected by the correctedIntestites
+ accessor method
+
+Files: inst/extdata/MiSeq/InterOp/ExtractionMetricsOut.bin
+Documentation: inst/doc/savR.Rnw
+ Extraction Metrics
+ .
+ The extraction metrics file contains per-lane/cycle/tile information about
+ per-base FWHM (full width pixel size of clusters at half maximum) and
+ 90th %-ile intensity of signal intensity.
+
+Files: inst/extdata/MiSeq/InterOp/QMetricsOut.bin
+Documentation: inst/doc/savR.Rnw
+ Quality Metrics
+ .
+ The quality metrics file contains per-lane/tile/cycle metrics for the number
+ of clusters with quality at each PHRED value from 1-50.
+
+Files: inst/extdata/MiSeq/InterOp/TileMetricsOut.bin
+Documentation: inst/doc/savR.Rnw
+ Tile Metrics
+ .
+ The tile metrics file contains coded information about per-lane/cycle/tile
+ cluster density, pass-filter clusters, phasing and pre-phasing data.
+
+ -- Andreas Tille <tille at debian.org> Thu, 18 Aug 2016 11:01:11 +0200
Added: trunk/packages/R/r-bioc-savr/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/README.test (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/README.test 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh ./run-unit-test
+
+in order to confirm its integrity.
Added: trunk/packages/R/r-bioc-savr/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/changelog 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,5 @@
+r-bioc-savr (1.10.0-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Thu, 18 Aug 2016 11:01:11 +0200
Added: trunk/packages/R/r-bioc-savr/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/compat (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/compat 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-bioc-savr/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/control 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,30 @@
+Source: r-bioc-savr
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cdbs,
+ r-base-dev,
+ r-cran-ggplot2,
+ r-cran-reshape2,
+ r-cran-scales,
+ r-cran-gridextra,
+ r-cran-xml
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-savr/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-savr/trunk/
+Homepage: http://bioconductor.org/packages/release/bioc/html/savR.html
+
+Package: r-bioc-savr
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-cran-ggplot2,
+ r-cran-reshape2,
+ r-cran-scales,
+ r-cran-gridextra,
+ r-cran-xml
+Description: GNU R parse and analyze Illumina SAV files
+ This BioConductor module enables to parse Illumina Sequence Analysis
+ Viewer (SAV) files, access data, and generate QC plots.
Added: trunk/packages/R/r-bioc-savr/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/copyright 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,675 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: savR
+Upstream-Contact: R. Brent Calder <brent.calder at einstein.yu.edu>
+Source: http://bioconductor.org/packages/release/bioc/html/savR.html
+
+Files: *
+Copyright: 2013-2016 R. Brent Calder <brent.calder at einstein.yu.edu>
+License: AGPL-3
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: AGPL-3
+
+License: AGPL-3
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
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+ 13. Remote Network Interaction; Use with the GNU General Public License.
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+ along with this program. If not, see <http://www.gnu.org/licenses/>.
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+ For more information on this, and how to apply and follow the GNU AGPL, see
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Added: trunk/packages/R/r-bioc-savr/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/docs (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/docs 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,3 @@
+tests
+debian/README.test
+debian/tests/run-unit-test
Added: trunk/packages/R/r-bioc-savr/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/rules 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk
+
+install/$(package)::
+ chmod -x $(debRlib)/$(cranNameOrig)/extdata/MiSeq/InterOp/*.bin
Property changes on: trunk/packages/R/r-bioc-savr/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-bioc-savr/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/source/format (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/source/format 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/R/r-bioc-savr/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/tests/control (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/tests/control 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-testthat
+Restrictions: allow-stderr
Added: trunk/packages/R/r-bioc-savr/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/tests/run-unit-test 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,13 @@
+#!/bin/sh -e
+
+oname=savR
+pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+LC_ALL=C R --no-save < testthat.R
+rm -fr $ADTTMP/*
Added: trunk/packages/R/r-bioc-savr/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-savr/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-bioc-savr/trunk/debian/watch 2016-08-18 09:36:37 UTC (rev 22693)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
+ http://www.bioconductor.org/packages/release/bioc/html/savR.html .*/savR_([\d\.]+)\.tar\.gz
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