[med-svn] r15833 - in trunk/packages/R: . r-bioc-org.sc.sgd.db r-bioc-org.sc.sgd.db/trunk r-bioc-org.sc.sgd.db/trunk/debian r-bioc-org.sc.sgd.db/trunk/debian/source
Author: tille
Date: 2014-01-19 13:09:29 + (Sun, 19 Jan 2014)
New Revision: 15833
Added:
trunk/packages/R/r-bioc-org.sc.sgd.db/
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/README.test
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/changelog
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/compat
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/control
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/copyright
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/rules
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/source/
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/source/format
trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/watch
Log:
Add another database to enable testing of annotationdbi
Added: trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/README.test
===
--- trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/README.test
(rev 0)
+++ trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/README.test
2014-01-19 13:09:29 UTC (rev 15833)
@@ -0,0 +1,5 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by loading it into R with the command
+‘library(org.Sc.sgd.db)’ in order to confirm its integrity.
Added: trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/changelog
===
--- trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/changelog
(rev 0)
+++ trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/changelog
2014-01-19 13:09:29 UTC (rev 15833)
@@ -0,0 +1,5 @@
+r-bioc-org.sc.sgd.db (2.10.1-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+
+ -- Andreas Tille ti...@debian.org Thu, 16 Jan 2014 14:13:14 +0100
Added: trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/compat
===
--- trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/compat
(rev 0)
+++ trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/compat 2014-01-19
13:09:29 UTC (rev 15833)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/control
===
--- trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/control
(rev 0)
+++ trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/control 2014-01-19
13:09:29 UTC (rev 15833)
@@ -0,0 +1,23 @@
+Source: r-bioc-org.sc.sgd.db
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Andreas Tille ti...@debian.org
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (= 9),
+ cdbs,
+ r-base-dev,
+ r-bioc-annotationdbi
+Standards-Version: 3.9.5
+Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/
+Vcs-Svn:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/
+Homepage:
http://bioconductor.org/packages/release/data/annotation/html/org.Sc.sgd.db.html
+
+Package: r-bioc-org.sc.sgd.db
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-bioc-annotationdbi
+Description: Genome wide annotation for Yeast
+ This package is part of BioConductor and provides Genome wide
+ annotation for Yeast, primarily based on mapping using ORF identifiers
+ from SGD.
Added: trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/copyright
===
--- trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/copyright
(rev 0)
+++ trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/debian/copyright
2014-01-19 13:09:29 UTC (rev 15833)
@@ -0,0 +1,134 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: org.Sc.sgd.db
+Upstream-Contact: Bioconductor Package Maintainer
maintai...@bioconductor.org
+Source:
http://bioconductor.org/packages/release/data/annotation/html/org.Sc.sgd.db.html
+
+Files: *
+Copyright: © 2006-2013 Marc Carlson
+License: Artistic-2.0
+
+Files: debian/*
+Copyright: 2014 Andreas Tille ti...@debian.org
+License: Artistic-2.0
+
+License: Artistic-2.0
+ Permission for Use and Modification Without Distribution
+ .
+ (1) You are permitted to use the Standard Version and create and use
+ Modified Versions for any purpose without restriction, provided that you
+ do not Distribute the Modified Version. Permissions for Redistribution
+ of the Standard Version
+ .
+ (2) You may Distribute verbatim copies of the Source form of the
+ Standard Version of this Package in any medium without restriction,
+ either gratis or for a Distributor Fee, provided
[med-svn] r15834 - trunk/packages/R/r-bioc-annotationdbi/trunk/debian
Author: tille Date: 2014-01-19 13:11:08 + (Sun, 19 Jan 2014) New Revision: 15834 Modified: trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog Log: Add SVN location of another missing database Modified: trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog === --- trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog 2014-01-19 13:09:29 UTC (rev 15833) +++ trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog 2014-01-19 13:11:08 UTC (rev 15834) @@ -11,7 +11,7 @@ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-hom.hs.inp.db/trunk/ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.tguttatatestingsubset.eg.db/trunk/ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.at.tair.db/trunk/ - http://www.bioconductor.org/packages/release/data/annotation/html/org.Sc.sgd.db.html + svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/ -- Andreas Tille ti...@debian.org Thu, 16 Jan 2014 14:07:52 +0100 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r15835 - trunk/packages/R/r-bioc-annotationdbi/trunk/debian
Author: tille Date: 2014-01-19 13:46:08 + (Sun, 19 Jan 2014) New Revision: 15835 Modified: trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog Log: I think now all BioC databases needed to run annotationdbi test are packaged but there are two remaining failures. I'm not sure whether bloating the Debian archive with large size packages just for testing a package is worth the effort - it needs to be discussed on list. Modified: trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog === --- trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog 2014-01-19 13:11:08 UTC (rev 15834) +++ trunk/packages/R/r-bioc-annotationdbi/trunk/debian/changelog 2014-01-19 13:46:08 UTC (rev 15835) @@ -12,6 +12,7 @@ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.tguttatatestingsubset.eg.db/trunk/ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.at.tair.db/trunk/ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/ + svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-go.db/trunk/ -- Andreas Tille ti...@debian.org Thu, 16 Jan 2014 14:07:52 +0100 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r15836 - in trunk/packages/R: . r-bioc-go.db r-bioc-go.db/trunk r-bioc-go.db/trunk/debian r-bioc-go.db/trunk/debian/source
Author: tille
Date: 2014-01-19 13:49:19 + (Sun, 19 Jan 2014)
New Revision: 15836
Added:
trunk/packages/R/r-bioc-go.db/
trunk/packages/R/r-bioc-go.db/trunk/
trunk/packages/R/r-bioc-go.db/trunk/debian/
trunk/packages/R/r-bioc-go.db/trunk/debian/README.test
trunk/packages/R/r-bioc-go.db/trunk/debian/changelog
trunk/packages/R/r-bioc-go.db/trunk/debian/compat
trunk/packages/R/r-bioc-go.db/trunk/debian/control
trunk/packages/R/r-bioc-go.db/trunk/debian/copyright
trunk/packages/R/r-bioc-go.db/trunk/debian/rules
trunk/packages/R/r-bioc-go.db/trunk/debian/source/
trunk/packages/R/r-bioc-go.db/trunk/debian/source/format
trunk/packages/R/r-bioc-go.db/trunk/debian/watch
Log:
Inject packaging for last database needed to test annotationdbi
Added: trunk/packages/R/r-bioc-go.db/trunk/debian/README.test
===
--- trunk/packages/R/r-bioc-go.db/trunk/debian/README.test
(rev 0)
+++ trunk/packages/R/r-bioc-go.db/trunk/debian/README.test 2014-01-19
13:49:19 UTC (rev 15836)
@@ -0,0 +1,5 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by loading it into R with the command
+‘library(GO.db)’ in order to confirm its integrity.
Added: trunk/packages/R/r-bioc-go.db/trunk/debian/changelog
===
--- trunk/packages/R/r-bioc-go.db/trunk/debian/changelog
(rev 0)
+++ trunk/packages/R/r-bioc-go.db/trunk/debian/changelog2014-01-19
13:49:19 UTC (rev 15836)
@@ -0,0 +1,5 @@
+r-bioc-go.db (2.10.1-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+
+ -- Andreas Tille ti...@debian.org Thu, 16 Jan 2014 14:13:14 +0100
Added: trunk/packages/R/r-bioc-go.db/trunk/debian/compat
===
--- trunk/packages/R/r-bioc-go.db/trunk/debian/compat
(rev 0)
+++ trunk/packages/R/r-bioc-go.db/trunk/debian/compat 2014-01-19 13:49:19 UTC
(rev 15836)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-bioc-go.db/trunk/debian/control
===
--- trunk/packages/R/r-bioc-go.db/trunk/debian/control
(rev 0)
+++ trunk/packages/R/r-bioc-go.db/trunk/debian/control 2014-01-19 13:49:19 UTC
(rev 15836)
@@ -0,0 +1,22 @@
+Source: r-bioc-go.db
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Andreas Tille ti...@debian.org
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (= 9),
+ cdbs,
+ r-base-dev,
+ r-bioc-annotationdbi
+Standards-Version: 3.9.5
+Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-go.db/trunk/
+Vcs-Svn:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-go.db/trunk/
+Homepage:
http://bioconductor.org/packages/release/data/annotation/html/GO.db.html
+
+Package: r-bioc-go.db
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-bioc-annotationdbi
+Description: annotation maps describing the entire Gene Ontology
+ This package is part of BioConductor and provides a set of annotation
+ maps describing the entire Gene Ontology assembled using data from GO.
Added: trunk/packages/R/r-bioc-go.db/trunk/debian/copyright
===
--- trunk/packages/R/r-bioc-go.db/trunk/debian/copyright
(rev 0)
+++ trunk/packages/R/r-bioc-go.db/trunk/debian/copyright2014-01-19
13:49:19 UTC (rev 15836)
@@ -0,0 +1,134 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: GO.db
+Upstream-Contact: Bioconductor Package Maintainer
maintai...@bioconductor.org
+Source:
http://bioconductor.org/packages/release/data/annotation/html/GO.db.html
+
+Files: *
+Copyright: © 2006-2013 Marc Carlson
+License: Artistic-2.0
+
+Files: debian/*
+Copyright: 2014 Andreas Tille ti...@debian.org
+License: Artistic-2.0
+
+License: Artistic-2.0
+ Permission for Use and Modification Without Distribution
+ .
+ (1) You are permitted to use the Standard Version and create and use
+ Modified Versions for any purpose without restriction, provided that you
+ do not Distribute the Modified Version. Permissions for Redistribution
+ of the Standard Version
+ .
+ (2) You may Distribute verbatim copies of the Source form of the
+ Standard Version of this Package in any medium without restriction,
+ either gratis or for a Distributor Fee, provided that you duplicate all
+ of the original copyright notices and associated disclaimers. At your
+ discretion, such verbatim copies may or may not include a Compiled form
+ of the Package.
+ .
+ (3) You may apply any bug fixes, portability changes, and other
[med-svn] r15837 - trunk/packages/mgltools/pmv/trunk/debian/patches
Author: alteholz
Date: 2014-01-19 16:20:10 + (Sun, 19 Jan 2014)
New Revision: 15837
Added:
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
Log:
argh, it is still needed to maintain this version
Copied:
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
(from rev 14726,
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch)
===
---
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
(rev 0)
+++
trunk/packages/mgltools/pmv/trunk/debian/patches/indentiationStylesCommands.patch
2014-01-19 16:20:10 UTC (rev 15837)
@@ -0,0 +1,13 @@
+Index: Pmv-1.5.6~rc2+cvs.20111222/Pmv/stylesCommands.py
+===
+--- Pmv-1.5.6~rc2+cvs.20111222.orig/Pmv/stylesCommands.py 2011-10-01
01:36:21.0 +0200
Pmv-1.5.6~rc2+cvs.20111222/Pmv/stylesCommands.py 2011-12-23
21:57:47.0 +0100
+@@ -51,7 +51,7 @@
+ ## self.vf.undo.addEntry((undoCmd), (name))
+
+
+- def setupUndo(self, name):
++def setupUndo(self, name):
+ oldRendering = getRendering(self.vf.GUI.VIEWER)
+ self.undoRenderingStack.append(oldRendering)
+ self.vf.NEWundo.addUndoCall( ([(self.undo, (),{})], name))
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r15839 - in trunk/packages/R: . r-bioc-txdb.hsapiens.ucsc.hg19.knowngene r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian r-bioc-txdb.hsap
Author: tille
Date: 2014-01-19 22:21:56 + (Sun, 19 Jan 2014)
New Revision: 15839
Added:
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/README.test
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/changelog
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/compat
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/control
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/copyright
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/rules
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/source/
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/source/format
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/watch
Log:
Add another database this time for testing r-bioc-genomicfeatures
Added:
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/README.test
===
---
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/README.test
(rev 0)
+++
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/README.test
2014-01-19 22:21:56 UTC (rev 15839)
@@ -0,0 +1,5 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by loading it into R with the command
+‘library(TxDb.Hsapiens.UCSC.hg19.knownGene)’ in order to confirm its integrity.
Added:
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/changelog
===
---
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/changelog
(rev 0)
+++
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/changelog
2014-01-19 22:21:56 UTC (rev 15839)
@@ -0,0 +1,5 @@
+r-bioc-txdb.hsapiens.ucsc.hg19.knowngene (2.10.1-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+
+ -- Andreas Tille ti...@debian.org Thu, 16 Jan 2014 14:13:14 +0100
Added:
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/compat
===
---
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/compat
(rev 0)
+++
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/compat
2014-01-19 22:21:56 UTC (rev 15839)
@@ -0,0 +1 @@
+9
Added:
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/control
===
---
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/control
(rev 0)
+++
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/control
2014-01-19 22:21:56 UTC (rev 15839)
@@ -0,0 +1,24 @@
+Source: r-bioc-txdb.hsapiens.ucsc.hg19.knowngene
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+Uploaders: Andreas Tille ti...@debian.org
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (= 9),
+ cdbs,
+ r-base-dev,
+ r-bioc-annotationdbi,
+ r-bioc-genomicfeatures
+Standards-Version: 3.9.5
+Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/
+Vcs-Svn:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/
+Homepage:
http://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html
+
+Package: r-bioc-txdb.hsapiens.ucsc.hg19.knowngene
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-bioc-annotationdbi,
+ r-bioc-genomicfeatures
+Description: BioConductor Annotation package for TranscriptDb object(s)
+ This package is part of BioConductor and provides exposes an annotation
+ databases generated from UCSC by exposing these as TranscriptDb objects.
Added:
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/copyright
===
---
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/copyright
(rev 0)
+++
trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/debian/copyright
2014-01-19 22:21:56 UTC (rev 15839)
@@ -0,0 +1,134 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: TxDb.Hsapiens.UCSC.hg19.knownGene
+Upstream-Contact: Bioconductor Package Maintainer
[med-svn] r15840 - trunk/packages/R/r-bioc-genomicfeatures/trunk/debian
Author: tille Date: 2014-01-19 22:24:56 + (Sun, 19 Jan 2014) New Revision: 15840 Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test Log: Add hint how to create a package from the needed BioC database Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test === --- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test 2014-01-19 22:21:56 UTC (rev 15839) +++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test 2014-01-19 22:24:56 UTC (rev 15840) @@ -9,3 +9,10 @@ EOT in order to confirm its integrity. + +As it is reported in bug #735548 to successfully run this test you some +BioCOnductor databases as preconditions. If you want to install these +as Debian packages you can use: + + svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/ + ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r15841 - trunk/packages/R/r-bioc-genomicfeatures/trunk/debian
Author: tille Date: 2014-01-19 22:29:39 + (Sun, 19 Jan 2014) New Revision: 15841 Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test Log: A further database will be needed Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test === --- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test 2014-01-19 22:24:56 UTC (rev 15840) +++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test 2014-01-19 22:29:39 UTC (rev 15841) @@ -16,3 +16,8 @@ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/ +A further database + + http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html + +will be needed as well but it is not yet packaged. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [vista] 01/01: Added make rule to compile .m into .o files.
This is an automated email from the git hooks/post-receive script. luisibanez-guest pushed a commit to branch master in repository vista. commit b1ea3a1921040beeb9f62189e04ac92165e66b82 Author: Luis Ibanez luis.iba...@kitware.com Date: Sun Jan 19 17:39:31 2014 -0500 Added make rule to compile .m into .o files. Once the .m routines are installed, we compile them all into the VistA instance /o directory, using a make rule. This new rule invokes the mumps compiler with the environment variable gtm_destdir set to remove the prefix of the local debian build directory. In this way, the resulting .o files can be relocated to their final destination in the destdir/o instance directory, and yet the $TEXT function will be able to locate the source code of the routines. --- debian/changelog | 1 + debian/rules | 40 +++- 2 files changed, 40 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index e061162..6be36e6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -22,5 +22,6 @@ vista-foia (0.20140106-1) UNRELEASED; urgency=low * In control, added xinetd and ssh as dependencies. * In rules, removing .pyc files in clean: target. * Started adding deployment scripts to create instances. + * In rules, added make rule for compiling VistA .m routines into .o files. -- Luis Ibanez luis.iba...@kitware.com Wed, 4 Jul 2012 17:16:45 -0500 diff --git a/debian/rules b/debian/rules index af54dc8..4229c89 100755 --- a/debian/rules +++ b/debian/rules @@ -8,7 +8,8 @@ ARCH=$(shell dpkg-architecture -qDEB_HOST_GNU_CPU) UAPIVER=6.0-003 UAPIDIR=V$(UAPIVER)_$(ARCH) -VISTAINSTANCEDIR=$(PWD)/debian/usr/share/vista-foia +LOCALINSTANCEDIR=$(PWD)/debian +VISTAINSTANCEDIR=$(LOCALINSTANCEDIR)/usr/share/vista-foia GTM_INSTALL_DIR=/usr/lib/fis-gtm/$(UAPIDIR) VISTA_GLOBALS_DIR=$(VISTAINSTANCEDIR)/g VISTA_ROUTINES_DIR=$(VISTAINSTANCEDIR)/r @@ -25,6 +26,43 @@ VISTA_TESTING_SOURCE_DIR=$(PWD) %: dh $@ + +# +# Bring in the full list of VistA M routines +# and place them in the vista_m_sources variable +# +include debian/vista_m_routines_list + +# +# Define the default paths for finding .m files and .o files +# +vpath %.m $(VISTA_ROUTINES_DIR) +vpath %.o $(VISTA_OBJECTS_DIR) + +# +# Implicit rule to compile MUMPS files into object files +# +# http://tinco.pair.com/bhaskar/gtm/doc/books/pg/UNIX_manual/ch03s05.html#Compile_from_Shell +# +%.o : %.m + echo $ -o $(VISTA_OBJECTS_DIR)/$(@F) + (export gtmgbldir=$(VISTA_GTM_DATABASE); \ +export gtmroutines=$(VISTA_GTM_ROUTINES); \ +export gtm_dist=$(GTM_INSTALL_DIR); \ +export gtm_destdir=$(LOCALINSTANCEDIR); \ +$(GTM_INSTALL_DIR)/mumps -object=$(VISTA_OBJECTS_DIR)/$(@F) $ ) + +vista_m_sources := $(patsubst %.m,$(VISTA_ROUTINES_DIR)/%.m,$(vista_m_sources_files)) +vista_o_objects_files := $(patsubst %.m,%.o,$(vista_m_sources_files)) + +# +# This list of dependencies will invoke the implicit rule for .m - .o +# +compile_vista_routines: $(vista_o_objects_files) + echo Compiling all M routines + + + override_dh_auto_configure: (export gtmgbldir=$(VISTA_GTM_DATABASE); export gtmroutines=$(VISTA_GTM_ROUTINES); export gtm_dist=$(GTM_INSTALL_DIR); \ cd $(VISTA_TESTING_BINARY_DIR); \ -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/vista.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [vista] branch master updated (bc19c3f - b1ea3a1)
This is an automated email from the git hooks/post-receive script. luisibanez-guest pushed a change to branch master in repository vista. from bc19c3f Build upon vista-foia base install. new b1ea3a1 Added make rule to compile .m into .o files. The 1 revisions listed above as new are entirely new to this repository and will be described in separate emails. The revisions listed as adds were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog | 1 + debian/rules | 40 +++- 2 files changed, 40 insertions(+), 1 deletion(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/vista.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
