debian/0000755000000000000000000000000012245321154007165 5ustar debian/control0000644000000000000000000000241612245170126010574 0ustar Source: r-bioc-genomicranges Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-bioc-biocgenerics, r-bioc-iranges, r-bioc-xvector Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ Homepage: http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html Package: r-bioc-genomicranges Architecture: any Depends: ${R:Depends}, ${shlibs:Depends}, ${misc:Depends}, r-bioc-biocgenerics, r-bioc-iranges, r-bioc-xvector Description: BioConductor representation and manipulation of genomic intervals The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. debian/README.source0000644000000000000000000000335712230171612011350 0ustar Explanation for binary files inside source package according to http://lists.debian.org/debian-devel/2013/09/msg00332.html Here is an extract of the response from upstream about Files: GenomicRanges/inst/doc/precomputed_results/*.rda the full response can be read in the log of the ITP bug #721801. From: Hervé Pagès The objects in precomputed_results can be generated by running the code in the OverlapEncodings.Rnw vignette. However running this code takes a long time and would make 'R CMD check' take too much time to complete, making the maintenance of the package very impractical. . So the trick is to have some of the more time-consuming code chunks in the vignette set to eval=FALSE, and to load the precomputed results instead. The loading is performed in a hidden code chunk and it also performs some sanity checks to verify that the precomputed object that was just loaded is in sync with other objects generated earlier in the vignette. From: Martin Morgan For precomputed_results above, it looks like these could be generated by a script, but the specific results depend on a web service query and the web service changes from time to time. So the script will become out-of-date, creating data that are no longer consistent with the illustrative puruposes of the vignette. Also, the time cost of generating data is not consistent with our (nightly) build process; we will not generate this data on the fly, and it would be a mistake for your release process to generate data different from the data used in our release. These (expense of computation, consistency of external data sources) are typical reasons. -- Andreas Tille Fri, 18 Oct 2013 10:34:02 +0200 debian/rules0000755000000000000000000000011512214301142010231 0ustar #!/usr/bin/make -f debRreposname=bioc include /usr/share/R/debian/r-cran.mk debian/watch0000644000000000000000000000026212214301142010205 0ustar version=3 opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \ http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html .*/GenomicRanges_([\d\.]+)\.tar\.gz debian/copyright0000644000000000000000000001234612226255435011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: GenomicRanges Upstream-Contact: Bioconductor Package Maintainer Source: http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html Files: * Copyright: © 2006-2013 P. Aboyoun, H. Pages and M. Lawrence License: Artistic-2.0 Files: debian/* Copyright: 2013 Andreas Tille License: Artistic-2.0 License: Artistic-2.0 The "Artistic License" . Preamble . 1. You may make and give away verbatim copies of the source form of the Standard Version of this Package without restriction, provided that you duplicate all of the original copyright notices and associated disclaimers. . 2. You may apply bug fixes, portability fixes and other modifications derived from the Public Domain or from the Copyright Holder. A Package modified in such a way shall still be considered the Standard Version. . 3. 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THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. debian/source/0000755000000000000000000000000012214301142010454 5ustar debian/source/format0000644000000000000000000000001412214301142011662 0ustar 3.0 (quilt) debian/README.test0000644000000000000000000000044412214301142011014 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(GenomicRanges)’ in order to confirm its integrity. debian/changelog0000644000000000000000000000066512245321154011046 0ustar r-bioc-genomicranges (1.14.3-1) unstable; urgency=low * New upstream version Closes: #730574 * Build-Depends: r-bioc-xvector -- Andreas Tille Tue, 26 Nov 2013 19:52:13 +0100 r-bioc-genomicranges (1.12.4-1) unstable; urgency=low * Initial release (closes: #721801) * Added README.source to document binary files in source tarball -- Andreas Tille Fri, 18 Oct 2013 10:40:04 +0200 debian/compat0000644000000000000000000000000212214301142010352 0ustar 9 debian/docs0000644000000000000000000000002312214301143010023 0ustar debian/README.test