debian/0000755000000000000000000000000012247104622007166 5ustar debian/control0000644000000000000000000000321112246727647010607 0ustar Source: r-bioc-shortread Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter, Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-shortread/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-shortread/trunk/ Homepage: http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html Package: r-bioc-shortread Architecture: any Depends: ${R:Depends}, ${misc:Depends}, ${shlibs:Depends}, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter Description: GNU R classes and methods for high-throughput short-read sequencing data This BioConductor module is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. debian/rules0000755000000000000000000000011512235745041010246 0ustar #!/usr/bin/make -f debRreposname=bioc include /usr/share/R/debian/r-cran.mk debian/watch0000644000000000000000000000025212235745056010227 0ustar version=3 opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \ http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html .*/ShortRead_([\d\.]+)\.tar\.gz debian/upstream0000644000000000000000000000104112235752571010756 0ustar Reference: Author: Martin Morgan and Simon Anders and Michael Lawrence and Patrick Aboyoun and Hervé Pagès and Robert Gentleman Title: "ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data" Journal: Bioinformatics Year: 2009 Volume: 25 Number: 19 Pages: 2607-2608 DOI: 10.1093/bioinformatics/btp450 PMID: 19654119 URL: http://bioinformatics.oxfordjournals.org/content/25/19/2607 eprint: http://bioinformatics.oxfordjournals.org/content/25/19/2607.full.pdf+html debian/copyright0000644000000000000000000001427112247104622011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ShortRead Upstream-Contact: Bioconductor Package Maintainer Source: http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html Files: * Copyright: © 2006-2013 Martin Morgan, Michael Lawrence, Simon Anders License: Artistic-2.0 Files: src/const.h src/maqmap_m.h Copyright: Li Hang License: GPLv2 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; either version 2 of the License, or (at your option) any later version. . 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 program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. . You can find the text of GNU General Public License version 2.0 at /usr/share/common-licenses/GPL-2. Comment: The files are adapted from maq which is also packaged for Debian. 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. You may otherwise modify your copy of this Package in any way, provided that you insert a prominent notice in each changed file stating how and when you changed that file, and provided that you do at least ONE of the following: . a) place your modifications in the Public Domain or otherwise make them Freely Available, such as by posting said modifications to Usenet or an equivalent medium, or placing the modifications on a major archive site such as uunet.uu.net, or by allowing the Copyright Holder to include your modifications in the Standard Version of the Package. . b) use the modified Package only within your corporation or organization. . c) rename any non-standard executables so the names do not conflict with standard executables, which must also be provided, and provide a separate manual page for each non-standard executable that clearly documents how it differs from the Standard Version. . d) make other distribution arrangements with the Copyright Holder. . 4. You may distribute the programs of this Package in object code or executable form, provided that you do at least ONE of the following: . a) distribute a Standard Version of the executables and library files, together with instructions (in the manual page or equivalent) on where to get the Standard Version. . b) accompany the distribution with the machine-readable source of the Package with your modifications. . c) give non-standard executables non-standard names, and clearly document the differences in manual pages (or equivalent), together with instructions on where to get the Standard Version. . d) make other distribution arrangements with the Copyright Holder. . 5. You may charge a reasonable copying fee for any distribution of this Package. You may charge any fee you choose for support of this Package. You may not charge a fee for this Package itself. However, you may distribute this Package in aggregate with other (possibly commercial) programs as part of a larger (possibly commercial) software distribution provided that you do not advertise this Package as a product of your own. You may embed this Package's interpreter within an executable of yours (by linking); this shall be construed as a mere form of aggregation, provided that the complete Standard Version of the interpreter is so embedded. . 6. The scripts and library files supplied as input to or produced as output from the programs of this Package do not automatically fall under the copyright of this Package, but belong to whoever generated them, and may be sold commercially, and may be aggregated with this Package. If such scripts or library files are aggregated with this Package via the so-called "undump" or "unexec" methods of producing a binary executable image, then distribution of such an image shall neither be construed as a distribution of this Package nor shall it fall under the restrictions of Paragraphs 3 and 4, provided that you do not represent such an executable image as a Standard Version of this Package. . 7. C subroutines (or comparably compiled subroutines in other languages) supplied by you and linked into this Package in order to emulate subroutines and variables of the language defined by this Package shall not be considered part of this Package, but are the equivalent of input as in Paragraph 6, provided these subroutines do not change the language in any way that would cause it to fail the regression tests for the language. . 8. Aggregation of this Package with a commercial distribution is always permitted provided that the use of this Package is embedded; that is, when no overt attempt is made to make this Package's interfaces visible to the end user of the commercial distribution. Such use shall not be construed as a distribution of this Package. . 9. The name of the Copyright Holder may not be used to endorse or promote products derived from this software without specific prior written permission. . 10. 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/0000755000000000000000000000000012211574407010471 5ustar debian/source/format0000644000000000000000000000001411743742137011705 0ustar 3.0 (quilt) debian/README.test0000644000000000000000000000044012235746225011032 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(ShortRead)’ in order to confirm its integrity. debian/changelog0000644000000000000000000000024012246722105011035 0ustar r-bioc-shortread (1.20.0-1) unstable; urgency=low * Initial release (closes: #731085) -- Andreas Tille Mon, 04 Nov 2013 17:24:35 +0100 debian/patches/0000755000000000000000000000000012235746327010630 5ustar debian/patches/use_debian_packaged_zlib.patch0000644000000000000000000000200712246724523016601 0ustar /home/tillea/debian-maintain/repack/r-bioc-rsamtools/debian/patches/use_debian_packaged_zlib.patch 827/874 94% Author: Andreas Tille LastChanged: Sun, 01 Dec 2013 09:45:58 +0100 Description: If the systems includes zlib natively there is no point in requiring the import of zlibbioc --- a/DESCRIPTION +++ b/DESCRIPTION @@ -13,7 +13,7 @@ LazyLoad: yes Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.19.34), GenomicRanges (>= 1.13.43), Biostrings (>= 2.29.18), lattice, Rsamtools (>= 1.13.1) -Imports: Biobase, hwriter, zlibbioc, latticeExtra +Imports: Biobase, hwriter, latticeExtra Enhances: Rmpi, parallel Suggests: biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi LinkingTo: IRanges, XVector, Biostrings --- a/NAMESPACE +++ b/NAMESPACE @@ -1,7 +1,5 @@ useDynLib(ShortRead, .registration=TRUE) -import(zlibbioc) - import(methods) importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, debian/patches/series0000644000000000000000000000003712235746265012046 0ustar use_debian_packaged_zlib.patch debian/compat0000644000000000000000000000000212205374244010367 0ustar 9 debian/docs0000644000000000000000000000002312214301143010023 0ustar debian/README.test