debian/0000755000000000000000000000000012146363730007173 5ustar debian/watch0000644000000000000000000000020611267757356010240 0ustar version=3 http://mccammon.ucsd.edu/~bgrant/bio3d/download/download.html \ http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_(.+)\.tar\.gz debian/rules0000755000000000000000000000012112131442540010234 0ustar #!/usr/bin/make -f debRreposname := other include /usr/share/R/debian/r-cran.mk debian/README.Debian0000644000000000000000000000121511536160576011240 0ustar ... and I always thought that R would not be good for protein structure analysis. This fine work has completely escaped my routine scanning, albeit being properly published in bioinformatics. Let this Debian packaging help its dissemination a bit. When using the package, please cite Bio3D: An R package for the comparative analysis of protein structures. Grant, Rodrigues, ElSawy, McCammon, Caves, (2006) Bioinformatics 22, 2695-2696 in your publications. Concerning the packaging, it is is organised via the Debian-Med portal at http://debian-med.alioth.debian.org. -- Steffen Moeller Sat, 26 Jul 2008 19:19:11 +0200 debian/copyright0000644000000000000000000000247512131446503011130 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Bio3D Upstream-Contact: Barry Grant Source: http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.1-5.tar.gz Files: * Copyright: Barry Grant License: GPL-2+ Files: debian/* Copyright: © 2008 Steffen Moeller © 2009–2011 Charles Plessy © 2010–2012 Andreas Tille License: GPL-2+ License: GPL-2+ 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. . On a Debian GNU/Linux system, the GPL license version 2 is included in the file ‘/usr/share/common-licenses/GPL-2’. debian/upstream0000644000000000000000000000126112131446336010754 0ustar Contact: Barry Grant Gallery: http://thegrantlab.org/bio3d/gallery/gallery.html Homepage: http://thegrantlab.org/bio3d/ Name: Bio3D Reference: author: Grant, Barry J. and Rodrigues, Ana P. C. and ElSawy, Karim M. and McCammon, J. Andrew and Caves, Leo S. D. title: > Bio3d: an R package for the comparative analysis of protein structures journal: Bioinformatics volume: 22 number: 21 pages: 2695-2696 doi: 10.1093/bioinformatics/btl461 PMID: 16940322 year: 2006 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/21/2695 eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/21/2695.pdf Wiki: http://bio3d.pbworks.com/ debian/source/0000755000000000000000000000000012132153554010467 5ustar debian/source/format0000644000000000000000000000001411473462523011703 0ustar 3.0 (quilt) debian/README.test0000644000000000000000000000055511536160576011043 0ustar Notes on how this package is tested. ──────────────────────────────────── After building on the maintainer's computer, this package was locally installed and the library loaded into R in order to confirm its integrity. -- Charles Plessy Thu, 25 Mar 2010 13:57:34 +0900 debian/compat0000644000000000000000000000000212131441474010365 0ustar 9 debian/control0000644000000000000000000000260512131446336010577 0ustar Source: r-other-bio3d Section: gnu-r Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 9), cdbs, r-base-dev (>= 2.14.2~20120222) Standards-Version: 3.9.4 Homepage: http://thegrantlab.org/bio3d/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-other-bio3d/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-other-bio3d/trunk/ Package: r-other-bio3d Architecture: all Depends: ${misc:Depends}, ${R:Depends} Suggests: r-cran-ncdf, r-cran-bigmemory, r-cran-rocr, mafft Description: GNU R package for biological structure analysis The bio3d package contains utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform atom summaries, atom selection, re-orientation, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, and principal component analysis (PCA). In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. debian/changelog0000644000000000000000000001030412146363730011043 0ustar r-other-bio3d (1.1-5-1build1) saucy; urgency=low * Rebuild against R 3.0.0. -- Colin Watson Mon, 20 May 2013 10:07:36 +0100 r-other-bio3d (1.1-5-1) unstable; urgency=low * New upstream version * New homepage. * Remove copyright statement for trivial makefile. * Conforms to Policy version 3.9.4. * Using Debhelper 9. * Deleted obsolete DM-Upload-Allowed field. * Normalised VCS URLs following Lintian's standards. -- Charles Plessy Sat, 13 Apr 2013 12:55:21 +0900 r-other-bio3d (1.1-4-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Build-Depends: r-base-dev (>= 2.14.2~20120222) which is supporting R:Depends substitution variable * debian/rules: Remove R:Depends substitution variable which is now included in /usr/share/R/debian/r-cran.mk * debian/upstream: removed duplicated entry doi and moved pmid to references * debian/copyright: Fixed DEP5 issues using cme fix dpkg-copyright and some additional information -- Andreas Tille Thu, 19 Apr 2012 09:31:56 +0200 r-other-bio3d (1.1-3-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect compliance with Policy 3.9.2. (debian/control, no changes needed) * Corrected Vcs-* URLs (debian/control). -- Charles Plessy Fri, 24 Jun 2011 14:40:42 +0900 r-other-bio3d (1.1-2-1) unstable; urgency=low * New upstream release. * Reformatted debian/copyright following DEP-5. * Moved test instructions from README.Debian to README.test. * Use Debhelper 8 (debian/control, debian/compat). -- Charles Plessy Thu, 10 Mar 2011 23:22:05 +0900 r-other-bio3d (1.1-0-1) unstable; urgency=low * New upstream version * Added myself to uploaders * Standards-Version: 3.9.1 (no changes needed) * debian/copyright: more generic source location * debian/rules: fix cut-n-pasto in header comments * debian/source/format: 3.0 (quilt) -- Andreas Tille Thu, 25 Nov 2010 14:07:10 +0100 r-other-bio3d (1.0-8-1) unstable; urgency=low * New upstream release (Closes: #577386). * Added a tilde to the R:Depends substvar to also accept pre-release versions (debian/rules). * Allow upload by Debian Maintainers (debian/control). * Suggests r-cran-bigmemory, that is not yet available (debian/control). -- Charles Plessy Tue, 13 Apr 2010 08:19:29 +0900 r-other-bio3d (1.0-7-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version (debian/control) to reflect compliance with Policy 3.8.4. * Depend on a version equal or superior than the R upstream release that was used to build this package, using a R:Depends substvar (debian/control, debian/rules). * Added notes to explain how this package is tested (debian/README.Debian). -- Charles Plessy Thu, 25 Mar 2010 14:02:42 +0900 r-other-bio3d (1.0-6-1) unstable; urgency=low * New upstream release. * Mended debian/watch thanks to Yan Morin (Closes: #551414). * Conforms to Policy 3.8.3: - Changed section to gnu-r (debian/control). - Added VCS fields (debian/control). - Incremented Standards-Version (debian/control). * Switched to Debhelper 7 (debian/control, debian/compat). * Depend on ${misc:Depends}, not on ${shlibs:Depends} (debian/compat). * Added myself to Uploaders (debian/control). * Added various upstream informations in debian/upstream-metadata.yaml. * Deleted debian/files, not needed. * Converted debian/copyright to experimental machine-readable format. -- Charles Plessy Thu, 22 Oct 2009 13:07:32 +0900 r-other-bio3d (1.0-5-1.1) unstable; urgency=low * Non-maintainer upload * debian/control: Removed myself from uploaders as - Steffen never asked me whether I wanted to be included - Steffen never removed me despited repeated requests to do so -- Dirk Eddelbuettel Sat, 29 Nov 2008 13:28:02 -0600 r-other-bio3d (1.0-5-1) unstable; urgency=low * Initial release (closes: #492499). -- Steffen Moeller Sat, 26 Jul 2008 19:08:08 +0200