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commit 57b8b9de371cb92381bef03fc8c31c24af6ba25e Author: Graham Inggs <[email protected]> Date: Mon May 15 14:37:54 2017 +0000 Initial packaging --- debian/README.source | 16 ++++++++ debian/changelog | 5 +++ debian/compat | 1 + debian/control | 20 ++++++++++ debian/copyright | 106 +++++++++++++++++++++++++++++++++++++++++++++++++++ debian/rules | 4 ++ debian/source/format | 1 + debian/watch | 3 ++ 8 files changed, 156 insertions(+) diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..4ad890c --- /dev/null +++ b/debian/README.source @@ -0,0 +1,16 @@ +This package contains three mapping objects: + +* data/speciesMap.rda: A data frame with columns 'tax_id', 'genus', and + 'species'. Used to retrieve taxonomy ID by species and returns list of + available species. + +* data/validTaxIds.rda: An integer vector of valid taxonomy IDs created + from 'speciesMap'. Used internally for quick taxonomy ID look ups. + +* data/specData.rds: A data frame with columns 'taxon' and 'species'. + Used internally to retrieve species by taxonomy ID. + + +Scripts to generate these files are in inst/scripts. +All originate from the public taxonomy dump at +ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..17bd319 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +r-bioc-genomeinfodbdata (0.99.0-1) unstable; urgency=medium + + * Initial release (Closes: #862550) + + -- Graham Inggs <[email protected]> Mon, 15 May 2017 16:12:39 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..f599e28 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +10 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..032a012 --- /dev/null +++ b/debian/control @@ -0,0 +1,20 @@ +Source: r-bioc-genomeinfodbdata +Section: gnu-r +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Graham Inggs <[email protected]> +Build-Depends: debhelper (>= 10), dh-r, r-base-dev +Standards-Version: 3.9.8 +Homepage: https://bioconductor.org/packages/GenomeInfoDbData/ +Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomeinfodbdata/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomeinfodbdata/trunk/ + +Package: r-bioc-genomeinfodbdata +Architecture: all +Depends: ${R:Depends}, ${misc:Depends}, ${shlibs:Depends} +Recommends: ${R:Recommends} +Suggests: ${R:Suggests} +Description: BioConductor species and taxonomy ID look up tables + This package contains files for mapping between NCBI taxonomy ID and species. + . + It is used by functions in the r-bioc-genomeinfodb package. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..b7e6571 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,106 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: GenomeInfoDbData +Upstream-Contact: Bioconductor Maintainer <[email protected]> +Source: https://bioconductor.org/packages/GenomeInfoDbData/ + +Files: * +Copyright: 2006-2017 Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès +License: Artistic-2.0 + +Files: debian/* +Copyright: 2017 Graham Inggs <[email protected]> +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. diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..68d9a36 --- /dev/null +++ b/debian/rules @@ -0,0 +1,4 @@ +#!/usr/bin/make -f + +%: + dh $@ --buildsystem R diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..9248da7 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=4 +opts=downloadurlmangle=s?^(.*)\.\.?https:$1packages/release/data/annotation? \ +http://www.bioconductor.org/packages/release/data/annotation/html/GenomeInfoDbData.html .*/GenomeInfoDbData_(.*).tar.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-genomeinfodbdata.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
