[med-svn] r18350 - in trunk/packages/R/r-bioc-genomicranges/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon Oct 20 06:12:51 UTC 2014
Author: tille
Date: 2014-10-20 06:12:51 +0000 (Mon, 20 Oct 2014)
New Revision: 18350
Added:
trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/
trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/series
trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch
Modified:
trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test
trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog
trunk/packages/R/r-bioc-genomicranges/trunk/debian/control
trunk/packages/R/r-bioc-genomicranges/trunk/debian/copyright
Log:
New upstream version, leave out test that requires extra database
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test 2014-10-20 05:44:08 UTC (rev 18349)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test 2014-10-20 06:12:51 UTC (rev 18350)
@@ -9,3 +9,8 @@
EOT
in order to confirm its integrity.
+
+Attention: The full test suite requires the database
+ TxDb.Dmelanogaster.UCSC.dm3.ensGene
+which is not packaged for Debian. The according test was dropped
+from the test suite to run it successfully on a plain Debian machine.
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog 2014-10-20 05:44:08 UTC (rev 18349)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog 2014-10-20 06:12:51 UTC (rev 18350)
@@ -1,3 +1,11 @@
+r-bioc-genomicranges (1.18.1-1) experimental; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * Drop test requiring TxDb.Dmelanogaster.UCSC.dm3.ensGene from test suite
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 Oct 2014 08:07:45 +0200
+
r-bioc-genomicranges (1.16.4-2) unstable; urgency=medium
* Add missing r-cran-digest to Recommends + tests/control
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/control 2014-10-20 05:44:08 UTC (rev 18349)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/control 2014-10-20 06:12:51 UTC (rev 18350)
@@ -2,15 +2,14 @@
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
Testsuite: autopkgtest
+Priority: optional
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
- r-bioc-biocgenerics,
- r-bioc-genomeinfodb,
- r-bioc-xvector
-Standards-Version: 3.9.5
+ r-bioc-genomeinfodb (>= 1.2.0),
+ r-bioc-xvector (>= 0.6.0)
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/
Homepage: http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
@@ -20,9 +19,8 @@
Depends: ${R:Depends},
${shlibs:Depends},
${misc:Depends},
- r-bioc-biocgenerics,
- r-bioc-genomeinfodb,
- r-bioc-xvector
+ r-bioc-genomeinfodb (>= 1.2.0),
+ r-bioc-xvector (>= 0.6.0)
Recommends: r-cran-digest
Description: BioConductor representation and manipulation of genomic intervals
The ability to efficiently store genomic annotations and alignments is
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/copyright 2014-10-20 05:44:08 UTC (rev 18349)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/copyright 2014-10-20 06:12:51 UTC (rev 18350)
@@ -4,12 +4,12 @@
Source: http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html
Files: *
-Copyright: © 2006-2013 P. Aboyoun, H. Pages and M. Lawrence
+Copyright: © 2006-2014 P. Aboyoun, H. Pages and M. Lawrence
License: Artistic-2.0
Files: debian/*
-Copyright: 2013 Andreas Tille <tille at debian.org>
+Copyright: 2013-2014 Andreas Tille <tille at debian.org>
License: Artistic-2.0
License: Artistic-2.0
Added: trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/series (rev 0)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/series 2014-10-20 06:12:51 UTC (rev 18350)
@@ -0,0 +1 @@
+skip_test_requiring_not_packaged_db.patch
Added: trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch (rev 0)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch 2014-10-20 06:12:51 UTC (rev 18350)
@@ -0,0 +1,92 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 18 Oct 2014 08:07:45 +0200
+Description: The full test suite requires the database
+ TxDb.Dmelanogaster.UCSC.dm3.ensGene
+ which is not packaged for Debian. The according test was dropped
+ from the test suite to run it successfully on a plain Debian machine.
+
+
+--- a/inst/unitTests/test_mapCoords-methods.R
++++ /dev/null
+@@ -1,81 +0,0 @@
+-library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
+-txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
+-cdsbytx <- cdsBy(txdb, "tx")[1:3]
+-
+-test_mapCoords_output <- function()
+-{
+- cds <- cdsbytx
+- from <- GRanges("chr2L", IRanges(c(7500, 8400, 9000),
+- width = 200, names = LETTERS[1:3]))
+- x <- mapCoords(from, cds)
+- checkTrue(length(x) == 3L)
+- checkIdentical(names(x), c("B", "B", "C"))
+- checkIdentical(names(mcols(x)), c("queryHits", "subjectHits"))
+- checkTrue(all(width(x) == 200L))
+-
+- x <- mapCoords(from, cds, elt.hits=TRUE)
+- checkTrue("eltHits" %in% names(mcols(x)))
+-
+- x <- mapCoords(from, cds, elt.loc=TRUE)
+- checkTrue("eltLoc" %in% names(mcols(x)))
+-}
+-
+-test_mapCoords_outerlist_vs_listelt <- function()
+-{
+- cds <- cdsbytx
+- from <- GRanges("chr2L", IRanges(c(7500, 8400, 9000), width = 200))
+- strand(from) <- "+"
+- x <- mapCoords(from, cds, elt.loc=TRUE)
+- checkIdentical(start(x), c(645L, 609L, 1167L))
+- checkIdentical(start(mcols(x)$eltLoc), c(208L, 172L, 333L))
+-
+- from <- GRanges("chr2L", IRanges(c(8200, 9000), width = 200))
+- strand(from) <- "-"
+- strand(cds) <- "-"
+- x <- mapCoords(from, cds, elt.loc=TRUE)
+- checkIdentical(start(x), c(212L, 800L, 78L))
+- checkIdentical(start(mcols(x)$eltLoc), c(212L, 191L, 78L))
+-}
+-
+-test_mapCoords_range_order_pos <- function()
+-{
+- from <- GRanges("chrA", IRanges(43522349, width=1), strand="+")
+- ## Strand '+' smallest range first
+- grl <- GRangesList(GRanges("chrA",
+- IRanges(c(43522244, 43528406),
+- c(43524145, 43528644)), strand="+"))
+- x <- mapCoords(from, grl)
+- checkTrue(start(x) == 106L)
+-
+- ## Strand '+' largest range first
+- grl <- GRangesList(GRanges("chrA",
+- IRanges(c(43528406, 43522244),
+- c(43528644, 43524145)), strand="+"))
+- x <- mapCoords(from, grl)
+- checkTrue(start(x) == 106L)
+-}
+-
+-test_mapCoords_range_order_neg <- function()
+-{
+- from <- GRanges("chrA", IRanges(43522349, width=1), strand="-")
+-
+- ## Strand '-' smallest range first
+- grl <- GRangesList(GRanges("chrA",
+- IRanges(c(43522244, 43528406),
+- c(43524145, 43528644)), strand="-"))
+- x <- mapCoords(from, grl, elt.loc = TRUE)
+- checkTrue(start(x) == 2036L)
+- checkTrue(start(mcols(x)$eltLoc) == 1797L)
+-
+- ## Strand '-' largest range first
+- grl <- GRangesList(GRanges("chrA",
+- IRanges(c(43528406, 43522244),
+- c(43528644, 43524145)), strand="-"))
+- x <- mapCoords(from, grl, elt.loc = TRUE)
+- checkTrue(start(x) == 2036L)
+- checkTrue(start(mcols(x)$eltLoc) == 1797L)
+-
+- ## ignore.strand
+- x <- mapCoords(from, grl, ignore.strand=TRUE)
+- checkTrue(all(start(x) == 106L))
+-}
More information about the debian-med-commit
mailing list