debian/0000755000000000000000000000000012261057567007201 5ustar debian/watch0000644000000000000000000000024012214301142010201 0ustar version=3 opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \ http://www.bioconductor.org/packages/release/bioc/html/Gviz.html .*/Gviz_([\d\.]+)\.tar\.gz debian/copyright0000644000000000000000000001602712261057343011132 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Gviz Upstream-Contact: Florian Hahne Source: http://bioconductor.org/packages/release/bioc/html/Gviz.html Files: * Copyright: © 2006-2013 Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou License: Artistic-2.0 Files: debian/* Copyright: 2013 Andreas Tille License: Artistic-2.0 License: Artistic-2.0 Permission for Use and Modification Without Distribution . 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UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. debian/README.test0000644000000000000000000000043312260475344011033 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(Gviz)’ in order to confirm its integrity. debian/changelog0000644000000000000000000000023212260553267011045 0ustar r-bioc-gviz (1.6.0-1) unstable; urgency=low * Initial release (closes: #733720) -- Andreas Tille Mon, 30 Dec 2013 23:46:37 +0100 debian/README.source0000644000000000000000000000600112261057567011355 0ustar Explanation for binary files inside source package according to http://lists.debian.org/debian-devel/2013/09/msg00332.html Files: data/biomTrack.rda The documentation inst/doc/Gviz.Rnw describes this file as a minimalistic example how to use the BiomartGeneRegionTrack class of Gviz. Files: data/bmTrack.rda The documentation man/BiomartGeneRegionTrack-class.Rd uses this minimalistic example for several demonstration purposes. Files: data/collapseTrack.rda The documentation inst/doc/Gviz.Rnw describes this file as a minimalistic example how to Gviz tries to avoid unreadable plots by collapsing overlapping ranges Files: data/cpgIslands.rda The documentation inst/doc/Gviz.Rnw describes this file as a minimalistic example containing a run-length encoded vector as sample set of CpG island coordinates to demonstrate the AnnotationTrack function. Files: data/cyp2b10.rda The documentation man/GenomeAxisTrack-class.Rd describes this file as a minimalistic example to demonstrate the GenomeAxisTrack class and methods. Files: data/denseAnnTrack.rda The documentation inst/doc/Gviz.Rnw uses this file as an minimalistic example to demonstrate an \Rclass{AnnotationTrack} object that represents a good portion of a real human chromosome. Files: data/dtHoriz.rda The documentation inst/doc/Gviz.Rnw uses this file as an minimalistic example to demonstrate different plotting types demonstrating different Gviz festures. Files: data/geneDetails.rda The documentation inst/doc/Gviz.Rnw uses this example data to demonstrate details of the DetailsAnnotationTrack} object. Files: data/geneModels.rda The documentation inst/doc/Gviz.Rnw uses this file to demonstrate the track class GeneRegionTrack, which can be created via the constructor function GeneRegionTrack. Files: data/idTrack.rda The documentation man/IdeogramTrack-class.Rd uses this sample data to demonstrate the IdeogramTrack class and methods. Files: data/itrack.rda The documentation inst/doc/Gviz.Rnw uses this as another example data set to demonstrate GenomeAxisTrack class and methods. Files: data/twoGroups.rda The documentation inst/doc/Gviz.Rnw uses this as example data to load a sample from an GRanges object. Files: data/ucscItems.rda The documentation inst/doc/Gviz.Rnw uses this as example data as a genome axis and an IdeogramTrack of the x chromosome. Files: Rplots.pdf This seems to be simply a broken (invalid) pdf file which should be removed from upstream tarball. I'll inform upstream about this Files: inst/extdata/test.bedGraph inst/extdata/test.bam inst/extdata/test.bam.bai These test data are used as examples in the documentation inst/doc/Gviz.Rnw to demonstrate graphing features. Files: build/vignette.rds The documentation inst/doc/Gviz.Rnw is using this simple data file in demonstrations. Files: inst/doc/ucsc1.pdf inst/doc/ucsc2.pdf Screenshots taken by upstream to include into documentation inst/doc/Gviz.Rnw. -- Andreas Tille Sun, 29 Dec 2013 18:56:22 +0100 debian/source/0000755000000000000000000000000012214301142010454 5ustar debian/source/format0000644000000000000000000000001412214301142011662 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212214301142010352 0ustar 9 debian/rules0000755000000000000000000000026312260473760010256 0ustar #!/usr/bin/make -f debRreposname=bioc include /usr/share/R/debian/r-cran.mk install/$(package):: chmod -x debian/$(package)/usr/lib/R/site-library/$(cranNameOrig)/scripts/*.R debian/control0000644000000000000000000000326612260472431010601 0ustar Source: r-bioc-gviz Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-lattice, r-cran-rcolorbrewer, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-iranges, r-bioc-annotationdbi, r-bioc-biostrings, r-bioc-genomicranges, r-bioc-biovizbase Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-gviz/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-gviz/trunk/ Homepage: http://bioconductor.org/packages/release/bioc/html/Gviz.html Package: r-bioc-gviz Architecture: all Depends: ${R:Depends}, ${misc:Depends}, r-cran-lattice, r-cran-rcolorbrewer, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-iranges, r-bioc-annotationdbi, r-bioc-biostrings, r-bioc-genomicranges, r-bioc-biovizbase Description: Plotting data and annotation information along genomic coordinates Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. debian/docs0000644000000000000000000000002312214301143010023 0ustar debian/README.test debian/upstream0000644000000000000000000000070212214301142010736 0ustar Reference: Author: Michael Lawrence and Robert Gentleman and "Vincent Carey Title: "rtracklayer: an R package for interfacing with genome browsers" Journal: Bioinformatics Year: 2009 Volume: 25 Number: 14 Pages: 1841-1842 DOI: 10.1093/bioinformatics/btp328 PMID: 19468054 URL: http://bioinformatics.oxfordjournals.org/content/25/14/1841.abstract eprint: http://bioinformatics.oxfordjournals.org/content/25/14/1841.full.pdf+html