[med-svn] [r-bioc-rbgl] 02/02: Initial release (Closes: #834398)
Christopher Hoskin
christopher.hoskin at gmail.com
Thu Sep 1 08:07:16 UTC 2016
This is an automated email from the git hooks/post-receive script.
grinorcole-guest pushed a commit to branch master
in repository r-bioc-rbgl.
commit 115fa415cfbe9c1c85345a0b218e1557859284a3
Author: Christopher Hoskin <christopher.hoskin at gmail.com>
Date: Wed Aug 31 19:06:52 2016 +0100
Initial release (Closes: #834398)
---
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 17 +++
debian/copyright | 259 ++++++++++++++++++++++++++++++++++++++++
debian/lintian-overrides | 2 +
debian/patches/boost-1.61.patch | 30 +++++
debian/patches/series | 1 +
debian/rules | 40 +++++++
debian/source/format | 1 +
debian/tests/control | 3 +
debian/watch | 7 ++
11 files changed, 366 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..606923b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-bioc-rbgl (1.48.1+dfsg-1) unstable; urgency=medium
+
+ * Initial release (Closes: #834398)
+
+ -- Christopher Hoskin <christopher.hoskin at gmail.com> Thu, 04 Aug 2016 19:31:28 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..0a3df30
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,17 @@
+Source: r-bioc-rbgl
+Section: gnu-r
+Priority: optional
+Maintainer: Christopher Hoskin <christopher.hoskin at gmail.com>
+Build-Depends: debhelper (>=9), cdbs, r-base-dev, r-bioc-graph, libboost-dev
+Standards-Version: 3.9.8
+Homepage: http://www.bioconductor.org/packages/release/bioc/html/RBGL.html
+#Vcs-Git: git://anonscm.debian.org/collab-maint/r-bioc-rbgl.git
+#Vcs-Browser: https://anonscm.debian.org/cgit/collab-maint/r-bioc-rbgl.git
+
+Package: r-bioc-rbgl
+Architecture: any
+Depends: ${R:Depends}, ${shlibs:Depends}, ${misc:Depends}, r-bioc-graph
+Description: R interface to the graph algorithms contained in the BOOST library
+ RBGL is part of the BioConductor GNU R suite. It is a fairly extensive and
+ comprehensive interface to the graph algorithms contained in the BOOST C++
+ libraries.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..206ffb3
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,259 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: RBGL
+Source: http://www.bioconductor.org/packages/release/bioc/html/RBGL.html
+Files-Excluded: src/rbgl_trimmed_boost_*.tar.gz configure cleanup src/Makevars inst/dtd
+Comment: Use packaged Boost rather than bundled
+ .
+ GXL DTD has a copyright, but not a license as such.
+ Website http://www.gupro.de/GXL/dtd/dtd.html says:
+ .
+ GXL has been developed to be an open standard. No licensing or other legal
+ arrangements are required for its use, whether commercial and non-commercial.
+ The specification of GXL is copyright by its authors, to allow control of its
+ evolution. The specification can be reproduced and used without charge, but
+ with explicit acknowledgement of its authors.
+ .
+ Not clear that this complies with DFSG (3. Derived Works)
+
+Files: *
+Copyright: 2002-2016 Vince Carey <stvjc at channing.harvard.edu>, Li Long <li.long at isb-sib.ch>, R. Gentleman
+License: Artistic-2.0
+
+Files: debian/*
+Copyright: 2016 Christopher Hoskin <christopher.hoskin at gmail.com>
+License: Artistic-2.0
+
+Files: inst/boostExamples/bfs-example.cpp
+ inst/boostExamples/dfs-example.cpp
+ inst/boostExamples/kruskal-example.cpp
+Copyright: 2001 Jeremy G. Siek, Andrew Lumsdaine, Lie-Quan Lee,
+License: BSL-1.0
+
+Files: inst/boostExamples/connected_components.cpp
+ inst/boostExamples/cycdet.cpp
+ inst/boostExamples/file_dependencies.cpp
+ inst/boostExamples/quick_tour.cpp
+Copyright: 1997-2000 University of Notre Dame.
+License: BSL-1.0
+
+Files: src/fruchterman_reingold.hpp
+Copyright: 2004 The Trustees of Indiana University.
+License: BSL-1.0
+
+
+License: BSL-1.0
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
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+ Copyright (c) 2000-2006, The Perl Foundation.
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+ Modified Version) with other packages and Distribute the
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+ (11) If your Modified Version has been derived from a Modified
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+ (12) This license does not grant you the right to use any trademark,
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+ (13) This license includes the non-exclusive, worldwide,
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+ (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
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+
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
new file mode 100644
index 0000000..a6a0b39
--- /dev/null
+++ b/debian/lintian-overrides
@@ -0,0 +1,2 @@
+#Upstream provides no changelog
+r-bioc-rbgl: no-upstream-changelog
diff --git a/debian/patches/boost-1.61.patch b/debian/patches/boost-1.61.patch
new file mode 100644
index 0000000..4032b28
--- /dev/null
+++ b/debian/patches/boost-1.61.patch
@@ -0,0 +1,30 @@
+Description: Make RBGL compatible with Boost 1.61, don't use bundled copy
+Author: Christopher Hoskin <christopher.hoskin at gmail.com>, Vince Carey <stvjc at channing.harvard.edu>
+Forwarded: not-needed, https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RBGL@120031,
+ https://github.com/Bioconductor-mirror/RBGL/commit/2344cf7daa3f8ebacf9e00aad17c536d9f7c97d0
+Last-Update: 20XX-YY-ZZ
+--- a/src/RBGL.hpp
++++ b/src/RBGL.hpp
+@@ -1,6 +1,12 @@
+ /* RBGL2.h -- R interface to Boost Graph Library header */
+ /* assumes -IboostIncl for RBGL/src */
+
++extern "C" {
++#include <Rdefines.h>
++}
++#undef protect
++#undef cons
++
+ #ifndef RBGL_RBGL_H
+ #define RBGL_RBGL_H
+
+@@ -37,9 +43,6 @@
+ #include <boost/graph/adjacency_list.hpp>
+ #include <boost/graph/visitors.hpp>
+
+-extern "C" {
+-#include <Rdefines.h>
+-}
+
+ template <class DirectedS = boost::directedS, typename WeightT = double>
+ class R_adjacency_list
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..4fe82fb
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+boost-1.61.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..de3d576
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,40 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+#%:
+# dh $@ --with autotools_dev
+
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk
+
+#build:
+# mkdir -p src/rbgl_trimmed_boost_1_49_0
+
+common-install-indep::
+common-install-arch::
+ chmod -x debian/r-bioc-rbgl/usr/lib/R/site-library/RBGL/dot/*.dot
+ chmod -x debian/r-bioc-rbgl/usr/lib/R/site-library/RBGL/XML/simpleExample.gxl
+
+unittests:
+ R -f tests/runTests.R
+
+
+# dh_make generated override targets
+# This is example for Cmake (See https://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+# dh_auto_configure -- # -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+
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..74f7dd4
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Test-Command: R -e "library('RBGL')"
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..7c90e8b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,7 @@
+version=3
+opts=\
+dversionmangle=s/\+(debian|dfsg|ds|deb)(\.\d+)?$//,\
+repacksuffix=+dfsg,\
+downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
+http://www.bioconductor.org/packages/release/bioc/html/RBGL.html .*/RBGL_([\d\.]+)\.tar\.gz
+
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