[med-svn] [r-cran-treespace] 02/02: Initial debian/ packaging
Andreas Tille
tille at debian.org
Thu Sep 14 17:22:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-treespace.
commit 61104a413377146aa51b1a039cf88a701e6c0709
Author: Andreas Tille <tille at debian.org>
Date: Thu Sep 14 19:21:33 2017 +0200
Initial debian/ packaging
---
debian/README.Debian | 5 +++++
debian/README.source | 32 ++++++++++++++++++++++++++++++++
debian/README.test | 8 ++++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 40 ++++++++++++++++++++++++++++++++++++++++
debian/copyright | 32 ++++++++++++++++++++++++++++++++
debian/docs | 3 +++
debian/rules | 5 +++++
debian/source/format | 1 +
debian/tests/control | 5 +++++
debian/tests/run-unit-test | 17 +++++++++++++++++
debian/watch | 2 ++
13 files changed, 156 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..bf05174
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,5 @@
+The package treescape is discontinued and the old homepage
+
+ https://cran.r-project.org/package=treescape
+
+suggests using r-cran-treespace instead.
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..beff60a
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,32 @@
+Explanation for binary files inside source package according to
+ http://lists.debian.org/debian-devel/2013/09/msg00332.html
+
+Files: data/DengueBEASTMCC.RData
+Documented: man/DengueBEASTMCC.Rd
+ Dengue fever BEAST MCC tree
+ http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214
+
+Files: data/DengueSeqs.RData
+Documented: man/DengueSeqs.Rd
+ Dengue fever sequences
+ http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214
+
+Files: data/DengueTrees.RData
+Documented: man/DengueTrees.Rd
+ BEAST analysis of Dengue fever
+ http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214
+
+Files: data/fluTrees.RData
+Documented: man/fluTrees.Rd
+ BEAST analysis of seasonal influenza (A/H3N2)
+ http://beast.bio.ed.ac.uk/tutorials
+
+Files: data/woodmiceTrees.RData
+Documented: man/woodmiceTrees.Rd
+ Bootstrap trees from woodmouse dataset
+ A set of 15 sequences of the mitochondrial gene cytochrome b of the
+ woodmouse (Apodemus sylvaticus) which is a subset of the data analysed by
+ Michaux et al. (2003). The full data set is available through GenBank
+ (accession numbers AJ511877 to AJ511987)
+
+ -- Andreas Tille <tille at debian.org> Fri, 08 Sep 2017 11:32:19 +0200
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..57396d7
--- /dev/null
+++ b/debian/README.test
@@ -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.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6569a04
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-cran-treespace (1.0.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (closes: #xxxxxx)
+
+ -- Andreas Tille <tille at debian.org> Fri, 08 Sep 2017 11:32:19 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..51d2e15
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,40 @@
+Source: r-cran-treespace
+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 (>= 10),
+ dh-r,
+ r-base-dev,
+ r-cran-ape,
+ r-cran-ade4,
+ r-cran-adegenet,
+ r-cran-adegraphics,
+ r-cran-adephylo,
+ r-cran-combinat,
+ r-cran-distory,
+ r-cran-fields,
+ r-cran-htmlwidgets,
+ r-cran-mass,
+ r-cran-phangorn,
+ r-cran-rcpp,
+ r-cran-rlumshiny,
+ r-cran-scatterd3,
+ r-cran-shiny,
+ r-cran-shinybs
+Standards-Version: 4.1.0
+Vcs-Browser: https://anonscm.debian.org/git/debian-med/r-cran-treespace.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/r-cran-treespace.git
+Homepage: https://cran.r-project.org/package=treespace
+
+Package: r-cran-treespace
+Architecture: any
+Depends: ${R:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
+Description: Statistical Exploration of Landscapes of Phylogenetic Trees
+ Tools for the exploration of distributions of phylogenetic trees.
+ This package includes a shiny interface which can be started from R using
+ 'treespaceServer()'.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7af461a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,32 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: treespace
+Upstream-Contact: Thibaut Jombart <thibautjombart at gmail.com>
+Source: https://cran.r-project.org/package=treespace
+
+Files: *
+Copyright: 2015-2016 Thibaut Jombart and Michelle Kendall
+License: MIT
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..970f5e0
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+debian/tests/run-unit-test
+debian/README.test
+tests
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..529c38a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+
+%:
+ dh $@ --buildsystem R
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..a62fb6e
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,5 @@
+Tests: run-unit-test
+Depends: @, r-cran-testthat,
+Restrictions: allow-stderr
+
+
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..4432f10
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,17 @@
+#!/bin/sh -e
+
+pkgname=treespace
+debname=r-cran-treespace
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${debname}-test.XXXXXX`
+ trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/$debname/tests/* $ADTTMP
+gunzip -r *
+for testfile in *.R; do
+ echo "BEGIN TEST $testfile"
+ LC_ALL=C R --no-save < $testfile
+done
+
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..08c1ec2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=4
+https://cran.r-project.org/src/contrib/treespace_([-\d.]*)\.tar\.gz
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