[r-cran-coin] 01/01: Added debian/ directory
Jonathon Love
jon at thon.cc
Thu Sep 10 14:40:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
jonathon-guest pushed a commit to branch master
in repository r-cran-coin.
commit f834b27caaaeb0a5f6efa2e06c56f98d135cf626
Author: Jonathon Love <jon at thon.cc>
Date: Thu Sep 10 16:39:12 2015 +0200
Added debian/ directory
---
debian/README.source | 168 +++++++++++++++++++++++++++++++++++++++++++++
debian/README.test | 9 +++
debian/changelog | 6 ++
debian/compat | 1 +
debian/control | 30 ++++++++
debian/copyright | 34 +++++++++
debian/docs | 3 +
debian/rules | 4 ++
debian/source/format | 1 +
debian/tests/control | 3 +
debian/tests/run-unit-test | 20 ++++++
debian/watch | 3 +
12 files changed, 282 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..5b9813b
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,168 @@
+Explanation for binary files inside source package according to
+ http://lists.debian.org/debian-devel/2013/09/msg00332.html
+
+This package contains many example data sets
+
+Files: data/alpha.rda
+Documentation: man/alpha.Rd
+ Example data set:
+ Levels of expressed alpha synuclein mRNA in three groups of allele lengths of
+ NACP-REP1.
+ Various studies have linked alcohol dependence phenotypes to chromosome 4.
+ One candidate gene is NACP (non-amyloid component of plaques), coding for
+ alpha synuclein. \enc{Bönsch}{Boensch} \emph{et al.} (2005) found longer
+ alleles of NACP-REP1 in alcohol-dependent patients compared with healthy
+ controls and reported that the allele lengths show some association with
+ levels of expressed alpha synuclein mRNA.
+
+Files: data/alzheimer.rda
+Documentation: man/alzheimer.Rd
+ Example data set:
+ A case-control study of smoking and Alzheimer's disease.
+ Subjects with Alzheimer's disease are compared to two different control groups
+ with respect to smoking history. The data are given in Salib and Hillier
+ (1997, Tab. 4).
+
+
+Files: data/asat.rda
+Documentation: man/asat.Rd
+ Example data set:
+ Measurements of the liver enzyme aspartate aminotransferase (ASAT) for a new
+ compound and a control group of 34 female Wistar rats.
+ The aim of this toxicological study is the proof of safety for the new
+ compound. The data were originally given in Hothorn (1992) and later
+ reproduced by Hauschke, Kieser and Hothorn (1999).
+
+
+Files: data/CWD.rda
+Documentation: man/CWD.Rd
+ Example data set:
+ Carbon flux on six pieces of wood.
+ Coarse woody debris (CWD, dead wood greater than 10 cm in diameter) is
+ a large stock of carbon in tropical forests, yet the flux of carbon
+ out of this pool, via respiration, is poorly resolved (Chambers,
+ Schimel and Nobre, 2001). The heterotrophic process involved in CWD
+ respiration should respond to reductions in moisture availability,
+ which occurs during dry season (Chambers, Schimel and Nobre, 2001).
+
+
+Files: data/glioma.rda
+Documentation: man/glioma.Rd
+ Example data set:
+ A non-randomized pilot study on malignant glioma patients with pretargeted
+ adjuvant radioimmunotherapy using yttrium-90-biotin.
+ The primary endpoint of this small pilot study is survival. Since the
+ survival times are tied, the classical asymptotic logrank test may be
+ inadequate in this setup. Therefore, a permutation test using Monte Carlo
+ resampling was computed in the original paper. The data are taken from Tables
+ 1 and 2 of Grana \emph{et al.} (2002).
+
+
+Files: data/GTSG.rda
+Documentation: man/GTSG.Rd
+ Example data set:
+ A randomized clinical trial in gastric cancer.
+ A clinical trial comparing chemotherapy alone versus a combination of
+ chemotherapy and radiation therapy in the treatment of locally advanced,
+ nonresectable gastric carcinoma.
+
+
+Files: data/hohnloser.rda
+Documentation: man/hohnloser.Rd
+ Example data set:
+ Left ventricular ejection fraction in patients with malignant ventricular
+ tachyarrhythmias including recurrence-free month and censoring.
+ The data was used by Lausen and Schumacher (1992) to illustrate the use of
+ maximally selected statistics.
+
+
+Files: data/jobsatisfaction.rda
+Documentation: man/jobsatisfaction.Rd
+ Example data set:
+ Income and job satisfaction by gender.
+ The data are given in Agresti (2002, p. 288, Tab. 7.8).
+
+
+Files: data/malformations.rda
+Documentation: man/malformations.Rd
+ Example data set:
+ A subset of data from a study on the relationship between maternal alcohol
+ consumption and congenital malformations.
+ Data from a prospective study undertaken to determine whether moderate or
+ light drinking during the first trimester of pregnancy increases the risk for
+ congenital malformations (Mills and Graubard, 1987). The subset given here
+ concerns only sex organ malformation (Mills and Graubard, 1987, Tab. 4).
+ Graubard and Korn (1987) used this data set to illustrate that different
+ choices of scores for ordinal variables can lead to conflicting conclusions.
+
+
+Files: data/mercuryfish.rda
+Documentation: man/mercuryfish.Rd
+ Example data set:
+ The mercury level in blood, the proportion of cells with abnormalities, and
+ the proportion of cells with chromosome aberrations in consumers of
+ mercury-contaminated fish and a control group.
+ Control subjects (\code{"control"}) and subjects who ate contaminated fish for
+ more than three years (\code{"exposed"}) are under study.
+
+
+Files: data/neuropathy.rda
+Documentation: man/neuropathy.Rd
+ Example data set:
+ The logarithm of the ratio of pain scores measured at baseline and after four
+ weeks in a control group and a treatment group.
+
+
+Files: data/ocarcinoma.rda
+Documentation: man/ocarcinoma.Rd
+ Example data set:
+ Survival times of 35 women suffering from ovarian carcinoma at stadium II and
+ IIA.
+ Data from Fleming \emph{et al.} (1980) and Fleming, Green and Harrington
+ (1984). Reanalysed in Schumacher and Schulgen (2002).
+
+
+Files: data/photocar.rda
+Documentation: man/photocar.Rd
+ Example data set:
+ Survival time, time to first tumor, and total number of tumors in three groups
+ of animals in a photococarcinogenicity study.
+
+
+Files: data/rotarod.rda
+Documentation: man/rotarod.Rd
+ Example data set:
+ The endurance time of 24 rats in two groups on a rotating cylinder.
+ The rats were randomly assigned to receive a fixed oral dose of a centrally
+ acting muscle relaxant (\code{"treatment"}) or a saline solvent
+ (\code{"control"}). The animals were placed on a rotating cylinder and the
+ endurance time of each rat, i.e., the length of time each rat remained on the
+ cylinder, was measured up to a maximum of 300 seconds.
+ This dataset is the basis of a comparison of 11 different software
+ implementations of the Wilcoxon-Mann-Whitney test presented in Bergmann,
+ Ludbrook and Spooren (2000).
+
+Files: data/treepipit.rda
+Documentation: man/treepipit.Rd
+ Example data set:
+ Data on the population density of tree pipits, Anthus trivialis, in
+ Franconian oak forests including variables describing the forest ecosystem.
+ This study is based on fieldwork conducted in three lowland oak forests in the
+ Franconian region of northern Bavaria close to Uffenheim, Germany. Diurnal
+ breeding birds were sampled five times, from March to June 2002, using a
+ quantitative grid mapping. Each grid was a one-hectare square. In total, 86
+ sample sites were established in 9 stands. All individuals were counted in
+ time intervals of 7 min/grid during slow walks along the middle of the grid
+ with a stop in the centre. Environmental factors were measured for each
+ grid.
+
+
+Files: data/vision.rda
+Documentation: man/vision.Rd
+ Example data set:
+ Assessment of unaided distance vision of women in Britain.
+ Paired ordered categorical data from case-records of eye-testing of 7477 women
+ aged 30--39 years employed by Royal Ordnance Factories in Britain during
+ 1943--46, as given by Stuart (1953).
+
+
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..ab9ca74
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package you can do
+
+ sh run-unit-test
+
+in this directory.
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..9c0defd
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+r-cran-coin (1.1-0-1) unstable; urgency=low
+
+ * Initial release. (Closes: #797818)
+
+ -- Jonathon Love <jon at thon.cc> Thu, 10 Sep 2015 16:09:23 +0200
+
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..6691054
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: r-cran-coin
+Maintainer: Debian Science Maintainers <debian-science-maintainers at lists.alioth.debian.org>
+Uploaders: Jonathon Love <jon at thon.cc>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cdbs,
+ r-base-dev,
+ r-cran-modeltools,
+ r-cran-mvtnorm (>= 1.0-3),
+ r-cran-multcomp
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-science/packages/r-cran-coin.git
+Vcs-Git: git://anonscm.debian.org/debian-science/packages/r-cran-coin.git
+Homepage: http://coin.r-forge.r-project.org/
+
+Package: r-cran-coin
+Architecture: any
+Depends: ${R:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends},
+ r-base,
+ r-cran-modeltools,
+ r-cran-mvtnorm (>= 1.0-3),
+ r-cran-multcomp
+Description: GNU R package providing conditional inference procedures
+ The r-cran-coin package is a GNU R package providing conditional
+ inference procedures for the general independence problem including two-
+ sample, K-sample (non-parametric ANOVA), correlation, censored, ordered
+ and multivariate problems.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d1ddf4a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,34 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: coin
+Upstream-Contact: Torsten Hothorn <torsten.hothorn at r-project.org>
+Source: https://cran.r-project.org/web/packages/coin
+
+Files: *
+Copyright: 2005-2015 Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel, Henric Winell, Achim Zeileis
+License: GPL-2
+
+Files: debian/*
+Copyright: 2015 Jonathon Love <jon at thon.cc>
+License: GPL-2
+
+License: GPL-2
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation;
+ version 2.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..3adf0d6
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+debian/README.test
+debian/tests/run-unit-test
+tests
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..935f37f
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+include /usr/share/R/debian/r-cran.mk
+
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..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..180e391
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,20 @@
+#!/bin/sh -e
+
+pkg=r-cran-coin
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+gunzip -r *.gz
+for runtest in `ls *.R` ; do
+ LC_ALL=C R --no-save < $runtest >/dev/null
+ if [ ! $? ] ; then
+ echo "Test ${runtest} failed"
+ exit 1
+ else
+ echo "Test ${runtest} passed"
+ fi
+done
+rm -rf $ADTTMP/*
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..0ff2716
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+http://cran.r-project.org/src/contrib/coin_([\d\.-]*).tar.gz
+
--
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