[med-svn] r23597 - in trunk/packages/R/r-bioc-rsamtools/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2017-01-15 17:17:33 +0000 (Sun, 15 Jan 2017)
New Revision: 23597

Added:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/skip_test_requiring_network.patch
Removed:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides
Modified:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/series
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch
Log:
  * Remove test requiring network connection
  * debhelper 10
  * d/watch: version=4
  * drop unused lintian override


Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2017-01-15 16:56:52 UTC (rev 23596)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2017-01-15 17:17:33 UTC (rev 23597)
@@ -1,3 +1,12 @@
+r-bioc-rsamtools (1.26.1-2) unstable; urgency=medium
+
+  * Remove test requiring network connection
+  * debhelper 10
+  * d/watch: version=4
+  * drop unused lintian override
+
+ -- Andreas Tille <tille at debian.org>  Sun, 15 Jan 2017 17:25:11 +0100
+
 r-bioc-rsamtools (1.26.1-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat	2017-01-15 16:56:52 UTC (rev 23596)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat	2017-01-15 17:17:33 UTC (rev 23597)
@@ -1 +1 @@
-9
+10

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2017-01-15 16:56:52 UTC (rev 23596)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2017-01-15 17:17:33 UTC (rev 23597)
@@ -3,7 +3,7 @@
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
                dh-r,
                r-base-dev,
                r-cran-bitops,

Deleted: trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides	2017-01-15 16:56:52 UTC (rev 23596)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides	2017-01-15 17:17:33 UTC (rev 23597)
@@ -1,2 +0,0 @@
-# Same file as in source tarball is installed in binary - this does not affect reproducible builds
-r-bioc-rsamtools: package-contains-timestamped-gzip usr/lib/R/site-library/Rsamtools/unitTests/cases/ex1.sam.gz

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/series	2017-01-15 16:56:52 UTC (rev 23596)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/series	2017-01-15 17:17:33 UTC (rev 23597)
@@ -1 +1,2 @@
 use_debian_packaged_zlib.patch
+skip_test_requiring_network.patch

Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/skip_test_requiring_network.patch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/skip_test_requiring_network.patch	                        (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/skip_test_requiring_network.patch	2017-01-15 17:17:33 UTC (rev 23597)
@@ -0,0 +1,34 @@
+Description: Remove test requiring network connection
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 15 Jan 2017 17:23:15 +0100
+
+--- a/inst/unitTests/test_utilities.R
++++ /dev/null
+@@ -1,27 +0,0 @@
+-test_catch_samtools <- function()
+-{
+-    fl <- system.file("unitTests", "cases", "ex1_unsort.bam",
+-                      package="Rsamtools")
+-    err <- warn <- FALSE
+-    tryCatch(suppressWarnings(withCallingHandlers({
+-        indexBam(fl)
+-    }, warning=function(msg) {
+-        warn <<- TRUE
+-    })), error=function(msg) {
+-        err <<- TRUE
+-    })
+-    checkTrue(warn)
+-    checkTrue(err)
+-}
+-
+-test_catch_samtools_504 <- function()
+-{
+-    err <- FALSE
+-    tryCatch({
+-        scanBam("http://httpbin.org/status/504")
+-    }, error=function(err) {
+-        txt <- "failed to open BamFile:"
+-        err <<- startsWith(conditionMessage(err), txt)
+-    })
+-    checkTrue(err)
+-}

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch	2017-01-15 16:56:52 UTC (rev 23596)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch	2017-01-15 17:17:33 UTC (rev 23597)
@@ -1,3 +1,3 @@
-version=3
+version=4
 opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
  http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html .*/Rsamtools_([\d\.]+)\.tar\.gz