debian/0000755000000000000000000000000012260074201007160 5ustar debian/watch0000644000000000000000000000025412214301143010207 0ustar version=3 opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \ http://www.bioconductor.org/packages/release/bioc/html/biovizBase.html .*/biovizBase_([\d\.]+)\.tar\.gz debian/copyright0000644000000000000000000001230612260073243011122 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: biovizBase Upstream-Contact: Tengfei Yin Source: http://bioconductor.org/packages/release/bioc/html/biovizBase.html Files: * Copyright: © 2006-2013 Tengfei Yin, Michael Lawrence, Dianne Cook 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. 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/README.test0000644000000000000000000000044112214301143011012 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(biovizBase)’ in order to confirm its integrity. debian/changelog0000644000000000000000000000024112260074201011027 0ustar r-bioc-biovizbase (1.10.7-1) unstable; urgency=low * Initial release (closes: #733527) -- Andreas Tille Sun, 29 Dec 2013 18:56:22 +0100 debian/README.source0000644000000000000000000000467312260067414011361 0ustar Explanation for binary files inside source package according to http://lists.debian.org/debian-devel/2013/09/msg00332.html Files: inst/extdata/SRR027894subRBM17.bam* The documentation inst/doc/intro.Rnw says: Sample raw data is from SRA(Short Read Archive), Accession: SRR027894 and subset the gene at chr10:6118023-6137427, which within gene RBM17. contains junction reads. Files: data/crc1.GeRL.rda As explained in man/crc1.GeRL.Rd this is a data set of a CRC-1 mutation and structural rearrangment and described in . Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, Jing R, Parkin M, Pugh T, Verhaak RG, Stransky N, Boutin AT, Barretina J, Solit DB, Vakiani E, Shao W, Mishina Y, Warmuth M, Jimenez J, Chiang DY, Signoretti S, Kaelin WG, Spardy N, Hahn WC, Hoshida Y, Ogino S, Depinho RA, Chin L, Garraway LA, Fuchs CS, Baselga J, Tabernero J, Gabriel S, Lander ES, Getz G, Meyerson M. "Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion." Nat Genet. 2011 Sep 4;43(10):964-8. doi: 10.1038/ng.936. Files: data/darned_hg19_subset500.rda As explained in man/darned_hg19_subset500.Rd this data set provides a subset(500 sites only) of hg19 RNA editing sites, and originally from DARNED (http://darned.ucc.ie/) for the hg19 assembly. Files: data/genesymbol.rda As explained in man/genesymbol.Rd this data set provides gene symbols in human with position and starnd information, stored as GRanges object. . These data can be obtained for example from http://www.genecards.org/cgi-bin/carddisp.pl?gene=RBM17 Files: data/hg19Ideogram.rda As explained in man/hg19Ideogram.Rd this data set provides hg19 genome information without cytoband information. . These human genome data can be obtained for instance from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ Files: data/hg19IdeogramCyto.rda As explained in man/hg19IdeogramCyto.Rd this data set provides hg19 genome information with cytoband information. . These human genome data can be obtained for instance from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ Files: build/vignette.rds As explained in inst/doc/intro.Rnw this vignette demonstrates some color schemes and different utilities functions using simple examples and data sets. -- Andreas Tille Sun, 29 Dec 2013 18:56:22 +0100 debian/source/0000755000000000000000000000000012214301143010455 5ustar debian/source/format0000644000000000000000000000001412214301143011663 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212214301143010353 0ustar 9 debian/rules0000755000000000000000000000011512214301143010232 0ustar #!/usr/bin/make -f debRreposname=bioc include /usr/share/R/debian/r-cran.mk debian/control0000644000000000000000000000304012260063027010564 0ustar Source: r-bioc-biovizbase Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-dichromat, r-cran-hmisc, r-cran-rcolorbrewer, r-cran-scales, r-bioc-biobase, r-bioc-iranges, r-bioc-biostrings, r-bioc-genomicranges, r-bioc-genomicfeatures Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biovizbase/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biovizbase/trunk/ Homepage: http://bioconductor.org/packages/release/bioc/html/biovizBase.html Package: r-bioc-biovizbase Architecture: any Depends: ${R:Depends}, ${misc:Depends}, ${shlibs:Depends}, r-cran-dichromat, r-cran-hmisc, r-cran-rcolorbrewer, r-cran-scales, r-bioc-biobase, r-bioc-iranges, r-bioc-biostrings, r-bioc-genomicranges, r-bioc-genomicfeatures Description: GNU R basic graphic utilities for visualization of genomic data The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency. debian/docs0000644000000000000000000000002312214301143010023 0ustar debian/README.test