[med-svn] [r-bioc-metagenomeseq] 04/09: * New upstream version * Convert to dh-r * Generic BioConductor homepage * Use testthat for autopkgtest since other unittest is empty

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-bioc-metagenomeseq.

commit 29b254dd90fe4affcca495f9b409ce9784e1cdfa
Author: Andreas Tille <tille at debian.org>
Date:   Fri Nov 4 14:14:53 2016 +0000

      * New upstream version
      * Convert to dh-r
      * Generic BioConductor homepage
      * Use testthat for autopkgtest since other unittest is empty
---
 debian/README.test         |  8 +++-----
 debian/changelog           |  9 +++++++++
 debian/control             | 16 +++++-----------
 debian/copyright           |  4 ++--
 debian/docs                |  2 ++
 debian/rules               |  4 ++--
 debian/tests/run-unit-test | 14 +++++++++++---
 7 files changed, 34 insertions(+), 23 deletions(-)

diff --git a/debian/README.test b/debian/README.test
index 98dc1a1..53fb4d7 100644
--- a/debian/README.test
+++ b/debian/README.test
@@ -1,10 +1,8 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-You can run the test suite by doing
+This package can be tested by running the provided test:
 
-R --no-save <<EOT
-BiocGenerics:::testPackage("metagenomeSeq")
-EOT
+   sh ./run-unit-test
 
- -- Andreas Tille <tille at debian.org>  Mon, 16 Jun 2014 16:28:55 +0200
+in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
index 509d1f6..a1fb3d7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+r-bioc-metagenomeseq (1.16.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Convert to dh-r
+  * Generic BioConductor homepage
+  * Use testthat for autopkgtest since other unittest is empty
+
+ -- Andreas Tille <tille at debian.org>  Fri, 04 Nov 2016 14:55:51 +0100
+
 r-bioc-metagenomeseq (1.14.2-1) unstable; urgency=low
 
   * Initial release (closes: #835135)
diff --git a/debian/control b/debian/control
index baa60f8..3ca95d3 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               cdbs,
+               dh-r,
                r-base-dev,
                r-bioc-biobase,
                r-bioc-limma,
@@ -17,20 +17,14 @@ Build-Depends: debhelper (>= 9),
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-metagenomeseq/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-metagenomeseq/trunk/
-Homepage: http://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html
+Homepage: https://bioconductor.org/packages/metagenomeSeq/
 
 Package: r-bioc-metagenomeseq
 Architecture: all
 Depends: ${R:Depends},
-         ${misc:Depends},
-         r-bioc-biobase,
-         r-bioc-limma,
-         r-cran-glmnet,
-         r-cran-rcolorbrewer,
-         r-cran-matrixstats,
-         r-cran-foreach,
-         r-cran-matrix,
-         r-cran-gplots
+         ${misc:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
 Description: GNU R statistical analysis for sparse high-throughput sequencing
  MetagenomeSeq is designed to determine features (be it Operational
  Taxanomic Unit (OTU), species, etc.) that are differentially abundant
diff --git a/debian/copyright b/debian/copyright
index a9aeada..73e629c 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: metagenomeSeq
 Upstream-Contact: Joseph N. Paulson <jpaulson at jimmy.harvard.edu>
-Source: http://www.bioconductor.org/packages/release/bioc/html/metagenomeSeq.html
+Source: https://bioconductor.org/packages/metagenomeSeq/
 
 Files: *
 Copyright: © 2010-2016 Joseph N. Paulson <jpaulson at jimmy.harvard.edu>
diff --git a/debian/docs b/debian/docs
index 50f6656..960011c 100644
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,3 @@
+tests
 debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/rules b/debian/rules
index aeb12b3..68d9a36 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,4 +1,4 @@
 #!/usr/bin/make -f
 
-debRreposname=bioc
-include /usr/share/R/debian/r-cran.mk
+%:
+	dh $@ --buildsystem R
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index 488dbef..ae67c0b 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -1,5 +1,13 @@
 #!/bin/sh -e
 
-LC_ALL=C R --no-save <<EOT
-BiocGenerics:::testPackage("metagenomeSeq")
-EOT
+oname=metagenomeSeq
+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
+find . -name "*.gz" -exec gunzip \{\} \;
+LC_ALL=C R --no-save < testthat.R

-- 
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