debian/0000755000000000000000000000000012257415572007200 5ustar debian/README.test0000644000000000000000000000043612214301143011016 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(biomaRt)’ in order to confirm its integrity. debian/source/0000755000000000000000000000000012214301143010455 5ustar debian/source/format0000644000000000000000000000001412214301143011663 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000002312214301143010023 0ustar debian/README.test debian/README.source0000644000000000000000000000051612257415517011360 0ustar Explanation for binary files inside source package according to http://lists.debian.org/debian-devel/2013/09/msg00332.html Files: build/vignette.rds As explained in man/getSequence.Rd this is a small data set as example how to use the getSequence function. -- Andreas Tille Wed, 04 Sep 2013 15:15:31 +0200 debian/copyright0000644000000000000000000001237412257412410011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: biomaRt Upstream-Contact: Steffen Durinck Source: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html Files: * Copyright: © 2006-2013 Steffen Durinck , Wolfgang Huber 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/upstream0000644000000000000000000000167712257414627010776 0ustar Reference: - Author: Steffen Durinck and Paul T. Spellman and Ewan Birney and Wolfgang Huber Title: "Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt" Journal: Nature Protocols Year: 2009 Volume: 4 Number: 8 Pages: 1184--1191 DOI: 10.1038/nprot.2009.97 PMID: 19617889 URL: http://www.nature.com/nprot/journal/v4/n8/full/nprot.2009.97.html - Author: Steffen Durinck and Yves Moreau and Arek Kasprzyk and Sean Davis and Bart De Moor and Alvis Brazma and Wolfgang Huber Title: "BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis" Journal: Bioinformatics Year: 2005 Volume: 21 Number: 16 Pages: 3439--3440 DOI: 10.1093/bioinformatics/bti525 PMID: 16082012 URL: http://bioinformatics.oxfordjournals.org/content/21/16/3439 eprint: http://bioinformatics.oxfordjournals.org/content/21/16/3439.full.pdf+html debian/rules0000755000000000000000000000011512214301143010232 0ustar #!/usr/bin/make -f debRreposname=bioc include /usr/share/R/debian/r-cran.mk debian/watch0000644000000000000000000000024612214301143010210 0ustar version=3 opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \ http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html .*/biomaRt_([\d\.]+)\.tar\.gz debian/changelog0000644000000000000000000000023612257413366011052 0ustar r-bioc-biomart (2.18.0-1) unstable; urgency=low * Initial release (closes: #733278) -- Andreas Tille Sat, 28 Dec 2013 00:52:10 +0100 debian/compat0000644000000000000000000000000212214301143010353 0ustar 9 debian/control0000644000000000000000000000326012257412222010571 0ustar Source: r-bioc-biomart Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-bioc-biobase, r-cran-xml, r-cran-rcurl Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biomart/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biomart/trunk/ Homepage: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html Package: r-bioc-biomart Architecture: all Depends: ${R:Depends}, ${misc:Depends}, r-bioc-biobase, r-cran-xml, r-cran-rcurl Description: GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.