Author: plessy Date: 2011-03-10 14:37:42 +0000 (Thu, 10 Mar 2011) New Revision: 6237
Added: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.Debian trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.test trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/changelog trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/compat trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/control trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/copyright Removed: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.Debian trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/changelog trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/compat trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/control trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/copyright Log: [svn-buildpackage] Tagging r-other-bio3d 1.1-2-1 Deleted: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.Debian =================================================================== --- trunk/packages/R/r-other-bio3d/trunk/debian/README.Debian 2011-03-10 13:58:13 UTC (rev 6233) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.Debian 2011-03-10 14:37:42 UTC (rev 6237) @@ -1,26 +0,0 @@ -... 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 <[email protected]> Sat, 26 Jul 2008 19:19:11 +0200 - - -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 <[email protected]> Thu, 25 Mar 2010 13:57:34 +0900 Copied: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.Debian (from rev 6236, trunk/packages/R/r-other-bio3d/trunk/debian/README.Debian) =================================================================== --- trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.Debian (rev 0) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.Debian 2011-03-10 14:37:42 UTC (rev 6237) @@ -0,0 +1,17 @@ +... 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 <[email protected]> Sat, 26 Jul 2008 19:19:11 +0200 Copied: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.test (from rev 6236, trunk/packages/R/r-other-bio3d/trunk/debian/README.test) =================================================================== --- trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.test (rev 0) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/README.test 2011-03-10 14:37:42 UTC (rev 6237) @@ -0,0 +1,7 @@ +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 <[email protected]> Thu, 25 Mar 2010 13:57:34 +0900 Deleted: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/changelog =================================================================== --- trunk/packages/R/r-other-bio3d/trunk/debian/changelog 2011-03-10 13:58:13 UTC (rev 6233) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/changelog 2011-03-10 14:37:42 UTC (rev 6237) @@ -1,65 +0,0 @@ -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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Sat, 29 Nov 2008 13:28:02 -0600 - -r-other-bio3d (1.0-5-1) unstable; urgency=low - - * Initial release (closes: #492499). - - -- Steffen Moeller <[email protected]> Sat, 26 Jul 2008 19:08:08 +0200 Copied: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/changelog (from rev 6236, trunk/packages/R/r-other-bio3d/trunk/debian/changelog) =================================================================== --- trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/changelog (rev 0) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/changelog 2011-03-10 14:37:42 UTC (rev 6237) @@ -0,0 +1,74 @@ +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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Sat, 29 Nov 2008 13:28:02 -0600 + +r-other-bio3d (1.0-5-1) unstable; urgency=low + + * Initial release (closes: #492499). + + -- Steffen Moeller <[email protected]> Sat, 26 Jul 2008 19:08:08 +0200 Deleted: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/compat =================================================================== --- trunk/packages/R/r-other-bio3d/trunk/debian/compat 2011-03-10 13:58:13 UTC (rev 6233) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/compat 2011-03-10 14:37:42 UTC (rev 6237) @@ -1 +0,0 @@ -7 Copied: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/compat (from rev 6236, trunk/packages/R/r-other-bio3d/trunk/debian/compat) =================================================================== --- trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/compat (rev 0) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/compat 2011-03-10 14:37:42 UTC (rev 6237) @@ -0,0 +1 @@ +8 Deleted: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/control =================================================================== --- trunk/packages/R/r-other-bio3d/trunk/debian/control 2011-03-10 13:58:13 UTC (rev 6233) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/control 2011-03-10 14:37:42 UTC (rev 6237) @@ -1,27 +0,0 @@ -Source: r-other-bio3d -Section: gnu-r -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Steffen Moeller <[email protected]>, Charles Plessy <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: debhelper (>> 7), cdbs, r-base-dev -Standards-Version: 3.9.1 -Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-bio3d/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/svn/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. Copied: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/control (from rev 6236, trunk/packages/R/r-other-bio3d/trunk/debian/control) =================================================================== --- trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/control (rev 0) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/control 2011-03-10 14:37:42 UTC (rev 6237) @@ -0,0 +1,27 @@ +Source: r-other-bio3d +Section: gnu-r +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller <[email protected]>, Charles Plessy <[email protected]>, + Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 8), cdbs, r-base-dev +Standards-Version: 3.9.1 +Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-bio3d/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/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. Deleted: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/copyright =================================================================== --- trunk/packages/R/r-other-bio3d/trunk/debian/copyright 2011-03-10 13:58:13 UTC (rev 6233) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/copyright 2011-03-10 14:37:42 UTC (rev 6237) @@ -1,35 +0,0 @@ -Name : Bio3D -Contact : Barry Grant <[email protected]> -Source : http://mccammon.ucsd.edu/~bgrant/bio3d/download/download.html -Copyright : Barry Grant <[email protected]> -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’. - - -Files: debian/* -Copyright: © 2008 Steffen Moeller <[email protected]> - © 2009 Charles Plessy <[email protected]> -License: GPL-2+ - -This package was created by Steffen Moeller <[email protected]>, based on -work for the r-cran-rodbc package of Dirk Eddelbuettel <[email protected]>. - -The package was renamed from its upstream name 'bio3d' to 'r-other-bio3d' -to highlight the fact that is it a package for R and in neither of the -CRAN, OmegaHat or the BioConductor archives. Copied: trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/copyright (from rev 6236, trunk/packages/R/r-other-bio3d/trunk/debian/copyright) =================================================================== --- trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/copyright (rev 0) +++ trunk/packages/R/r-other-bio3d/tags/1.1-2-1/debian/copyright 2011-03-10 14:37:42 UTC (rev 6237) @@ -0,0 +1,33 @@ +Format: DEP-5 +Source: http://mccammon.ucsd.edu/~bgrant/bio3d/download/download.html + +Files: * +Copyright: Barry Grant <[email protected]> +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. +Comment: On a Debian GNU/Linux system, the GPL license version 2 is included + in the file ‘/usr/share/common-licenses/GPL-2’. + +Files: debian/* +Copyright: © 2008 Steffen Moeller <[email protected]> + © 2009–2011 Charles Plessy <[email protected]> +License: GPL-2+ +Comment: This package was created by Steffen Moeller <[email protected]>, + based on work for the r-cran-rodbc package of Dirk Eddelbuettel + <[email protected]>. + . + The package was renamed from its upstream name 'bio3d' to 'r-other-bio3d' + to highlight the fact that is it a package for R and in neither of the + CRAN, OmegaHat or the BioConductor archives. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
