[med-svn] [opensurgsim] 01/01: Fix Vcs fields via `cme fix dpkg-control`
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository opensurgsim.
commit 041045f6d9d8049799925f3f4acf81c1623013bc
Author: Andreas Tille
Date: Sat Aug 1 07:34:49 2015 +0200
Fix Vcs fields via `cme fix dpkg-control`
---
debian/changelog | 4
debian/control | 26 +++---
2 files changed, 19 insertions(+), 11 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index a8db95b..0759a0b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,10 @@
opensurgsim (0.6.0-2) experimental; urgency=low
+ [ Paul Novotny ]
* Updates for yaml-cpp 0.5.2
+
+ [ Andreas Tille ]
+ * Fix Vcs fields via `cme fix dpkg-control`
-- Paul Novotny Fri, 31 Jul 2015 20:31:29 -0400
diff --git a/debian/control b/debian/control
index f1bd5ee..64eac69 100644
--- a/debian/control
+++ b/debian/control
@@ -1,8 +1,8 @@
Source: opensurgsim
-Section: science
-Priority: optional
Maintainer: Debian Med Packaging Team
Uploaders: Paul Novotny
+Section: science
+Priority: optional
Build-Depends: debhelper (>= 9),
dh-linktree,
libboost-chrono-dev,
@@ -19,14 +19,15 @@ Build-Depends: debhelper (>= 9),
libopenscenegraph-dev,
libyaml-cpp-dev (>= 0.5.2)
Standards-Version: 3.9.6
-Homepage: http://www.opensurgsim.org/
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/opensurgsim.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/opensurgsim.git
Vcs-Git: git://anonscm.debian.org/debian-med/opensurgsim.git
+Homepage: http://www.opensurgsim.org/
Package: libopensurgsim
-Section: libs
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Section: libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: Free platform for surgical simulation - runtime
OpenSurgSim is C++ toolkit for developing real-time surgical simulations. It
lets you build simulators using the included building blocks, such as input
@@ -37,9 +38,10 @@ Description: Free platform for surgical simulation - runtime
applications.
Package: libopensurgsim-dev
-Section: libdevel
Architecture: any
-Depends: ${misc:Depends}, libopensurgsim (= ${binary:Version})
+Section: libdevel
+Depends: ${misc:Depends},
+ libopensurgsim (= ${binary:Version})
Description: Free platform for surgical simulation - development
OpenSurgSim is C++ toolkit for developing real-time surgical simulations. It
lets you build simulators using the included building blocks, such as input
@@ -50,10 +52,12 @@ Description: Free platform for surgical simulation -
development
own OpenSurgSim applications.
Package: opensurgsim-doc
-Section: doc
Architecture: all
-Depends: ${misc:Depends}, libjs-mathjax
-Suggests: libopensurgsim-dev, libopensurgsim
+Section: doc
+Depends: ${misc:Depends},
+ libjs-mathjax
+Suggests: libopensurgsim-dev,
+ libopensurgsim
Description: Free platform for surgical simulation - documentation
OpenSurgSim is C++ toolkit for developing real-time surgical simulations. It
lets you build simulators using the included building blocks, such as input
--
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/srv/git.debian.org/git/debian-med/opensurgsim.git
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[med-svn] [opensurgsim] branch master updated (da6aa98 -> 041045f)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch master in repository opensurgsim. from da6aa98 Updated changelog for 0.6.0-2 new 041045f Fix Vcs fields via `cme fix dpkg-control` 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 | 4 debian/control | 26 +++--- 2 files changed, 19 insertions(+), 11 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/opensurgsim.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] r19810 - trunk/packages/python-sqlsoup/tags
Author: tille Date: 2015-08-01 04:57:52 + (Sat, 01 Aug 2015) New Revision: 19810 Added: trunk/packages/python-sqlsoup/tags/0.9.0+dfsg-2.1/ Log: Tagged 0.9.0+dfsg-2.1 ___ 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] r19809 - trunk/packages/python-sqlsoup/trunk/debian
Author: tille Date: 2015-08-01 04:57:22 + (Sat, 01 Aug 2015) New Revision: 19809 Modified: trunk/packages/python-sqlsoup/trunk/debian/changelog trunk/packages/python-sqlsoup/trunk/debian/control Log: Commit Non-maintainer upload Modified: trunk/packages/python-sqlsoup/trunk/debian/changelog === --- trunk/packages/python-sqlsoup/trunk/debian/changelog2015-07-31 21:01:04 UTC (rev 19808) +++ trunk/packages/python-sqlsoup/trunk/debian/changelog2015-08-01 04:57:22 UTC (rev 19809) @@ -1,3 +1,11 @@ +python-sqlsoup (0.9.0+dfsg-2.1) unstable; urgency=medium + + * Non-maintainer upload. + * Rebuild against sqlalchemy (Closes: #793510) + * Add explicit build-dep on dh-python + + -- Scott Kitterman Fri, 31 Jul 2015 20:34:54 -0400 + python-sqlsoup (0.9.0+dfsg-2) unstable; urgency=medium * Rebuild against SQLAlchemy 0.9 Modified: trunk/packages/python-sqlsoup/trunk/debian/control === --- trunk/packages/python-sqlsoup/trunk/debian/control 2015-07-31 21:01:04 UTC (rev 19808) +++ trunk/packages/python-sqlsoup/trunk/debian/control 2015-08-01 04:57:22 UTC (rev 19809) @@ -5,6 +5,7 @@ Section: python Priority: optional Build-Depends: debhelper (>= 9), + dh-python, python | python-all | python-dev | python-all-dev, python-setuptools, python-sqlalchemy ___ 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] [opensurgsim] 01/01: Updated changelog for 0.6.0-2
This is an automated email from the git hooks/post-receive script. paulnovo-guest pushed a commit to branch master in repository opensurgsim. commit da6aa98e4c649cd88178e5a8c578bf02ffd9d635 Author: Paul Novotny Date: Fri Jul 31 20:37:56 2015 -0400 Updated changelog for 0.6.0-2 --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index dfacb9f..a8db95b 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +opensurgsim (0.6.0-2) experimental; urgency=low + + * Updates for yaml-cpp 0.5.2 + + -- Paul Novotny Fri, 31 Jul 2015 20:31:29 -0400 + opensurgsim (0.6.0-1) experimental; urgency=low * Initial release (Closes: #775753) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/opensurgsim.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] [opensurgsim] branch master updated (3dd87d0 -> da6aa98)
This is an automated email from the git hooks/post-receive script. paulnovo-guest pushed a change to branch master in repository opensurgsim. from 3dd87d0 Increase yaml-cpp version to 0.5.2 new da6aa98 Updated changelog for 0.6.0-2 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 | 6 ++ 1 file changed, 6 insertions(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/opensurgsim.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] r19808 - trunk/packages/R/r-bioc-genefilter/trunk/debian
Author: tille Date: 2015-07-31 21:01:04 + (Fri, 31 Jul 2015) New Revision: 19808 Modified: trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog trunk/packages/R/r-bioc-genefilter/trunk/debian/control Log: Upload to unstable Modified: trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog === --- trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog 2015-07-31 20:13:48 UTC (rev 19807) +++ trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog 2015-07-31 21:01:04 UTC (rev 19808) @@ -1,6 +1,5 @@ -r-bioc-genefilter (1.50.0-1) UNRELEASED; urgency=medium +r-bioc-genefilter (1.50.0-1) unstable; urgency=medium - * Initial release (closes: #???). + * Initial release (closes: #794279) - -- Andreas Tille Tue, 05 Aug 2014 15:40:57 +0200 - + -- Andreas Tille Fri, 31 Jul 2015 22:15:11 +0200 Modified: trunk/packages/R/r-bioc-genefilter/trunk/debian/control === --- trunk/packages/R/r-bioc-genefilter/trunk/debian/control 2015-07-31 20:13:48 UTC (rev 19807) +++ trunk/packages/R/r-bioc-genefilter/trunk/debian/control 2015-07-31 21:01:04 UTC (rev 19808) @@ -9,7 +9,7 @@ r-bioc-annotationdbi, r-bioc-annotate, r-cran-survival -Standards-Version: 3.9.5 +Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genefilter/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genefilter/trunk/ Homepage: http://bioconductor.org/packages/release/bioc/html/genefilter.html ___ 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] r19807 - trunk/packages/R/r-bioc-genefilter/trunk/debian
Author: tille Date: 2015-07-31 20:13:48 + (Fri, 31 Jul 2015) New Revision: 19807 Modified: trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog Log: r-bioc-annotate arrived in unstable Modified: trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog === --- trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog 2015-07-31 20:11:50 UTC (rev 19806) +++ trunk/packages/R/r-bioc-genefilter/trunk/debian/changelog 2015-07-31 20:13:48 UTC (rev 19807) @@ -1,7 +1,6 @@ r-bioc-genefilter (1.50.0-1) UNRELEASED; urgency=medium * Initial release (closes: #???). - Needs: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-annotate/trunk/ -- Andreas Tille Tue, 05 Aug 2014 15:40:57 +0200 ___ 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] r19806 - in trunk/packages/R/r-bioc-annotate: . tags
Author: tille Date: 2015-07-31 20:11:50 + (Fri, 31 Jul 2015) New Revision: 19806 Added: trunk/packages/R/r-bioc-annotate/tags/ trunk/packages/R/r-bioc-annotate/tags/1.46.1+dfsg-1/ Log: Tagged 1.46.1+dfsg-1 ___ 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] [khmer] 01/01: fix copyright files statement; clean up overrides
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit 8b604e05260a0bd7d7bb15e713efa36c2db76f2d
Author: Michael R. Crusoe
Date: Fri Jul 31 07:12:22 2015 -0700
fix copyright files statement; clean up overrides
fix liboxli SO version
fix misc paths
---
debian/copyright | 2 +-
debian/doc-base | 4 ++--
debian/khmer-common.lintian-overrides | 1 +
debian/khmer.lintian-overrides| 22
debian/liboxli-dev.install| 2 --
debian/liboxli1.install | 3 ++-
debian/lintian-overrides | 14 -
debian/patches/install-prefix | 39 +++
debian/rules | 2 +-
9 files changed, 68 insertions(+), 21 deletions(-)
diff --git a/debian/copyright b/debian/copyright
index ae0177b..46a71ee 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -32,7 +32,7 @@ Copyright: (c) 2002, Paul Mensonides
2002, The Trustees of Indiana University
License: boost-1.0
-Files: third-party/smhasher
+Files: third-party/smhasher/*
Copyright: none.
License: public-domain
Quoting from the file header: "MurmurHash3 was written by Austin Appleby,
diff --git a/debian/doc-base b/debian/doc-base
index 11809af..5d2678f 100644
--- a/debian/doc-base
+++ b/debian/doc-base
@@ -13,5 +13,5 @@ Abstract: in-memory DNA sequence kmer counting, filtering &
graph traversal
Section: Science/Biology
Format: html
-Files: /usr/share/doc/khmer/html/*
-Index: /usr/share/doc/khmer/html/index.html
+Files: /usr/share/doc/khmer-common/html/*
+Index: /usr/share/doc/khmer-common/html/index.html
diff --git a/debian/khmer-common.lintian-overrides
b/debian/khmer-common.lintian-overrides
new file mode 100644
index 000..5686645
--- /dev/null
+++ b/debian/khmer-common.lintian-overrides
@@ -0,0 +1 @@
+khmer-common: extra-license-file
usr/share/doc/khmer-common/html/_sources/LICENSE.txt
diff --git a/debian/khmer.lintian-overrides b/debian/khmer.lintian-overrides
new file mode 100644
index 000..2b3b18f
--- /dev/null
+++ b/debian/khmer.lintian-overrides
@@ -0,0 +1,22 @@
+# These files are unchanged files from upstream tarball. There is no problem
for a reproducible build
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz
+khmer: gzip-file-is-not-multi-arch-same-safe
usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz
+
+# The test data are provided in different compression methods intentionally to
test different compression methods
+# Since they are small anyway there is no reason to work around this
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.bz2
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.bz2
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.bz2
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.bz2
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz
+khmer: duplicated-compressed-file
usr/lib/python3/dist-packages/khmer/tests/test-data/test-empty.fa.bz2
diff --git a/debian/liboxli-dev.install b/debian/liboxli-dev.install
index 786b4d4..78e99a1 100755
--- a/debian/liboxli-dev.install
+++ b/debian/liboxli-dev.install
@@ -1,6 +1,4 @@
#!/usr/bin/dh-exec
-lib/liboxli.so usr/lib/${DEB_HOST_MULTIARCH}
-lib/liboxli.so.2usr/lib/${DEB_HOST_MULTIARCH}
lib/liboxli.a usr/lib/${DEB_HOST_MULTIARCH}
lib/oxli.pc usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig
# NB: we install the he
[med-svn] [khmer] branch master updated (282f3fd -> 8b604e0)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch master in repository khmer. from 282f3fd clean up d/changelog, drop patch, fix tests & install new 8b604e0 fix copyright files statement; clean up overrides 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/copyright | 2 +- debian/doc-base | 4 ++-- debian/khmer-common.lintian-overrides | 1 + debian/khmer.lintian-overrides| 22 debian/liboxli-dev.install| 2 -- debian/liboxli1.install | 3 ++- debian/lintian-overrides | 14 - debian/patches/install-prefix | 39 +++ debian/rules | 2 +- 9 files changed, 68 insertions(+), 21 deletions(-) create mode 100644 debian/khmer-common.lintian-overrides create mode 100644 debian/khmer.lintian-overrides delete mode 100644 debian/lintian-overrides -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.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] r19805 - trunk/packages/rostlab/profphd/tags
Author: tille Date: 2015-07-31 17:36:08 + (Fri, 31 Jul 2015) New Revision: 19805 Added: trunk/packages/rostlab/profphd/tags/1.0.42-1/ Log: Tagged 1.0.42-1 ___ 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] r19804 - trunk/packages/rostlab/profphd/trunk/debian
Author: tille Date: 2015-07-31 17:35:00 + (Fri, 31 Jul 2015) New Revision: 19804 Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog Log: Upload to unstable Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog === --- trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 17:29:13 UTC (rev 19803) +++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 17:35:00 UTC (rev 19804) @@ -1,4 +1,4 @@ -profphd (1.0.42-1) UNRELEASED; urgency=medium +profphd (1.0.42-1) unstable; urgency=medium * Moved debian/upstream to debian/upstream/metapackages * remove redundant stuff from d/watch @@ -8,7 +8,7 @@ * cme fix dpkg-control * DEP5 fix - -- Andreas Tille Fri, 31 Jul 2015 18:53:46 +0200 + -- Andreas Tille Fri, 31 Jul 2015 19:29:28 +0200 profphd (1.0.40-1) unstable; urgency=low ___ 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] r19803 - trunk/packages/rostlab/profphd/trunk/debian
Author: tille Date: 2015-07-31 17:29:13 + (Fri, 31 Jul 2015) New Revision: 19803 Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog trunk/packages/rostlab/profphd/trunk/debian/copyright Log: DEP5 fix Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog === --- trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 17:28:17 UTC (rev 19802) +++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 17:29:13 UTC (rev 19803) @@ -6,6 +6,7 @@ * Priority: optional * short dh instead of cdbs * cme fix dpkg-control + * DEP5 fix -- Andreas Tille Fri, 31 Jul 2015 18:53:46 +0200 Modified: trunk/packages/rostlab/profphd/trunk/debian/copyright === --- trunk/packages/rostlab/profphd/trunk/debian/copyright 2015-07-31 17:28:17 UTC (rev 19802) +++ trunk/packages/rostlab/profphd/trunk/debian/copyright 2015-07-31 17:29:13 UTC (rev 19803) @@ -3,15 +3,6 @@ Upstream-Contact: Laszlo Kajan Source: ftp://rostlab.org/profphd/ -Files: src/prof/embl/scr/ctime.pl src/prof/embl/scr/lib/ctime.pl -Copyright: 1988 Waldemar Kebsch - March 1990, Feb 1991 Marion Hakanson , Oregon Graduate Institute of Science and Technology -License: GPL-1+ or Artistic - -Files: debian/* -Copyright: 2009 Laszlo Kajan -License: GPL-2+ - Files: * Copyright: 1998 B. Rost EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE) @@ -23,7 +14,16 @@ 2009-2013 L. Kajan Laszlo Kajan Technical University Munich (Munich, DE) License: GPL-2+ +Files: src/prof/embl/scr/ctime.pl src/prof/embl/scr/lib/ctime.pl +Copyright: 1988 Waldemar Kebsch + March 1990, Feb 1991 Marion Hakanson , Oregon Graduate Institute of Science and Technology +License: GPL-1+ or Artistic + +Files: debian/* +Copyright: 2009 Laszlo Kajan 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 ___ 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] r19802 - trunk/packages/rostlab/profphd/trunk/debian
Author: tille
Date: 2015-07-31 17:28:17 + (Fri, 31 Jul 2015)
New Revision: 19802
Modified:
trunk/packages/rostlab/profphd/trunk/debian/changelog
trunk/packages/rostlab/profphd/trunk/debian/control
Log:
cme fix dpkg-control
Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog
===
--- trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31
17:27:48 UTC (rev 19801)
+++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31
17:28:17 UTC (rev 19802)
@@ -5,6 +5,7 @@
* debhelper 9
* Priority: optional
* short dh instead of cdbs
+ * cme fix dpkg-control
-- Andreas Tille Fri, 31 Jul 2015 18:53:46 +0200
Modified: trunk/packages/rostlab/profphd/trunk/debian/control
===
--- trunk/packages/rostlab/profphd/trunk/debian/control 2015-07-31 17:27:48 UTC
(rev 19801)
+++ trunk/packages/rostlab/profphd/trunk/debian/control 2015-07-31 17:28:17 UTC
(rev 19802)
@@ -7,7 +7,7 @@
Build-Depends: debhelper (>= 9),
perl,
rsync
-Standards-Version: 3.9.4
+Standards-Version: 3.9.6
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/profphd/trunk/
Vcs-Svn:
svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/profphd/trunk/
Homepage: http://predictprotein.org/
@@ -16,7 +16,7 @@
Architecture: all
Depends: ${perl:Depends},
${misc:Depends},
- librg-utils-perl (>= 1.0.16),
+ librg-utils-perl,
profnet-prof,
profphd-utils,
profphd-net
@@ -43,4 +43,3 @@
* Transmembrane helix prediction has an expected per-residue accuracy of
about 95%. The number of false positives, i.e., transmembrane helices
predicted in globular proteins, is about 2%.
-
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[med-svn] r19801 - trunk/packages/rostlab/profphd/trunk/debian
Author: tille Date: 2015-07-31 17:27:48 + (Fri, 31 Jul 2015) New Revision: 19801 Removed: trunk/packages/rostlab/profphd/trunk/debian/patches/ Log: Remove unused patch ___ 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] r19800 - trunk/packages/rostlab/profphd/trunk/debian
Author: tille
Date: 2015-07-31 17:26:24 + (Fri, 31 Jul 2015)
New Revision: 19800
Removed:
trunk/packages/rostlab/profphd/trunk/debian/profphd.install
Modified:
trunk/packages/rostlab/profphd/trunk/debian/changelog
trunk/packages/rostlab/profphd/trunk/debian/control
trunk/packages/rostlab/profphd/trunk/debian/rules
Log:
Use short dh instead of cdbs
Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog
===
--- trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31
17:03:57 UTC (rev 19799)
+++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31
17:26:24 UTC (rev 19800)
@@ -4,6 +4,7 @@
* remove redundant stuff from d/watch
* debhelper 9
* Priority: optional
+ * short dh instead of cdbs
-- Andreas Tille Fri, 31 Jul 2015 18:53:46 +0200
Modified: trunk/packages/rostlab/profphd/trunk/debian/control
===
--- trunk/packages/rostlab/profphd/trunk/debian/control 2015-07-31 17:03:57 UTC
(rev 19799)
+++ trunk/packages/rostlab/profphd/trunk/debian/control 2015-07-31 17:26:24 UTC
(rev 19800)
@@ -4,8 +4,7 @@
Andreas Tille
Section: science
Priority: optional
-Build-Depends: cdbs,
- debhelper (>= 9),
+Build-Depends: debhelper (>= 9),
perl,
rsync
Standards-Version: 3.9.4
Deleted: trunk/packages/rostlab/profphd/trunk/debian/profphd.install
===
--- trunk/packages/rostlab/profphd/trunk/debian/profphd.install 2015-07-31
17:03:57 UTC (rev 19799)
+++ trunk/packages/rostlab/profphd/trunk/debian/profphd.install 2015-07-31
17:26:24 UTC (rev 19800)
@@ -1 +0,0 @@
-usr/*
Modified: trunk/packages/rostlab/profphd/trunk/debian/rules
===
--- trunk/packages/rostlab/profphd/trunk/debian/rules 2015-07-31 17:03:57 UTC
(rev 19799)
+++ trunk/packages/rostlab/profphd/trunk/debian/rules 2015-07-31 17:26:24 UTC
(rev 19800)
@@ -1,12 +1,13 @@
#!/usr/bin/make -f
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/makefile.mk
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-# Add here any variable or target overrides you need.
-DEB_MAKE_BUILD_TARGET = prefix=/usr all
-DEB_MAKE_INSTALL_TARGET = prefix=/usr DESTDIR=$(CURDIR)/debian/tmp/ install
+%:
+ dh $@
+override_dh_auto_install:
+ make prefix=/usr DESTDIR=$(CURDIR)/debian/$(DEBPKGNAME)/ install
+
get-orig-source:
mkdir -p ../tarballs
uscan --verbose --force-download --destdir=../tarballs
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[med-svn] [r-bioc-limma] 02/04: pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch pristine-tar in repository r-bioc-limma. commit 8cc56871c47f6551d9afcd29767bbfcfb166a2fc Author: Andreas Tille Date: Fri Jul 31 18:55:09 2015 +0200 pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz --- r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta | Bin 0 -> 6346 bytes r-bioc-limma_3.24.14+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta new file mode 100644 index 000..8d1d34d Binary files /dev/null and b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta differ diff --git a/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.id b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.id new file mode 100644 index 000..11022c8 --- /dev/null +++ b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.id @@ -0,0 +1 @@ +3d2f522481e4c42869c3fb42c2554f2508a7219f -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 10/11: New upstream version
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit 0ff44a6bea010c18fc426248c8ebd98aa191b541 Author: Andreas Tille Date: Fri Jul 31 18:56:23 2015 +0200 New upstream version --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 1f581bc..2fc4cf5 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +r-bioc-limma (3.24.14+dfsg-1) UNRELEASED; urgency=medium + + * New upstream version + + -- Andreas Tille Fri, 31 Jul 2015 18:56:07 +0200 + r-bioc-limma (3.24.13+dfsg-1) unstable; urgency=medium * New upstream version -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] branch upstream updated (140fe49 -> 1411fa9)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch upstream in repository r-bioc-limma. from 140fe49 Imported Upstream version 3.22.1+dfsg new 802f308 Imported Upstream version 3.24.13+dfsg new 3fc04a1 Imported Upstream version 3.24.14+dfsg new 7a403fe Imported Upstream version 3.24.14+dfsg new 1411fa9 Imported Upstream version 3.24.14+dfsg The 4 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: DESCRIPTION | 15 +- NAMESPACE | 18 +- R/alias2Symbol.R | 28 ++- R/arrayWeights.R | 7 +- R/auROC.R | 55 + R/background-normexp.R| 6 +- R/classes.R | 2 +- R/dups.R | 8 +- R/fitFDistRobustly.R | 6 +- R/genas.R | 19 +- R/geneset-camera.R| 52 +++-- R/geneset-fry.R | 138 R/geneset-ids2indices.R | 14 ++ R/geneset-roast.R | 16 +- R/geneset-romer.R | 435 +++--- R/goana.R | 221 +++ R/kegga.R | 277 R/lmfit.R | 39 ++-- R/loessFit.R | 10 +- R/neqc.R | 22 +- R/norm.R | 24 ++- R/plot.R | 64 -- R/plotMD.R| 116 ++ R/plotMDS.R | 80 --- R/plotWithHighlights.R| 56 ++--- R/plotdensities.R | 40 ++-- R/plots-ma.R | 18 +- R/predFCm.R | 80 +++ R/read.idat.R | 24 ++- R/roc.R | 20 -- R/sepchannel.R| 6 +- R/squeezeVar.R| 4 +- R/subsetting.R| 16 +- R/toptable.R | 3 +- R/venn.R | 73 +-- R/voom.R | 6 +- R/write.R | 17 +- build/vignette.rds| Bin 230 -> 231 bytes inst/CITATION | 25 ++- inst/NEWS.Rd | 113 ++ inst/doc/changelog.txt| 315 +-- inst/doc/intro.pdf| Bin 46191 -> 46191 bytes man/01Introduction.Rd | 20 +- man/02classes.Rd | 15 ++ man/03reading.Rd | 14 ++ man/04Background.Rd | 15 ++ man/05Normalization.Rd| 15 ++ man/06linearmodels.Rd | 18 ++ man/07SingleChannel.Rd| 15 ++ man/08Tests.Rd| 14 ++ man/09Diagnostics.Rd | 36 +++- man/10GeneSetTests.Rd | 34 ++- man/11RNAseq.Rd | 32 ++- man/EList.Rd | 1 + man/TestResults.Rd| 5 +- man/arrayWeights.Rd | 2 +- man/arrayWeightsQuick.Rd | 2 +- man/asmalist.Rd | 4 +- man/auROC.Rd | 14 +- man/backgroundcorrect.Rd | 4 +- man/barcodeplot.Rd| 25 ++- man/camera.Rd | 8 +- man/decideTests.Rd| 7 +- man/diffSplice.Rd | 4 +- man/ebayes.Rd | 8 +- man/genas.Rd | 10 + man/getEAWP.Rd| 2 +- man/goana.MArrayLM.Rd | 89 man/goana.Rd | 111 -- man/imageplot.Rd | 2 +- man/lmFit.Rd | 7 +- man/malist.Rd | 2 +- man/mdplot.Rd | 40 ++-- man/modifyWeights.Rd | 2 +- man/normalizeRobustSpline.Rd | 14 +- man/normalizeWithinArrays.Rd | 2 +- man/normalizebetweenarrays.Rd | 2 +- man/normexpfit.Rd | 6 +- man/normexpsignal.Rd | 6 +- man/plot.Rd | 94 man/plotDensities.Rd | 12 +- man/plotExons.Rd | 2 +- man/plotMD.Rd | 133 man/plotMDS.Rd| 34 +-- man/plotSplice.Rd | 5 +- man/plotWithHighlights.Rd | 96 + man/plotma.Rd | 49 +++-- man/plotma3by2.Rd | 2 + man/predFCm.Rd| 59 +++--- man/propTrueNull.Rd | 7 +- man/rankSumTestwithCorrelation.Rd | 5 +- man/read.idat.Rd | 9 +- man/read.ma
[med-svn] [r-bioc-limma] annotated tag upstream/3.24.13+dfsg created (now a6152f0)
This is an automated email from the git hooks/post-receive script. tille pushed a change to annotated tag upstream/3.24.13+dfsg in repository r-bioc-limma. at a6152f0 (tag) tagging 802f30859a7f383b1faddcac7eb85088d13cc9a1 (commit) replaces upstream/3.22.1+dfsg tagged by Andreas Tille on Sun Jul 19 18:14:11 2015 +0200 - Log - Upstream version 3.24.13+dfsg Andreas Tille (1): Imported Upstream version 3.24.13+dfsg --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 03/04: pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch pristine-tar in repository r-bioc-limma. commit 979c856c2187ee81dbbddb45f374d5336a11b4b6 Author: Andreas Tille Date: Fri Jul 31 18:55:42 2015 +0200 pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz --- r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta | Bin 6346 -> 6326 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta index 8d1d34d..adfe9c0 100644 Binary files a/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta and b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta differ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 11/11: New upstream version uploaded to unstable
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit 9e8d649d70c13c9d48c69c684b98c08c0ffbd5c8 Author: Andreas Tille Date: Fri Jul 31 19:08:01 2015 +0200 New upstream version uploaded to unstable --- debian/changelog | 4 ++-- debian/patches/do_not_attempt_GO.db_test.patch | Bin 3895 -> 9604 bytes 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index 2fc4cf5..38fcd4c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,8 @@ -r-bioc-limma (3.24.14+dfsg-1) UNRELEASED; urgency=medium +r-bioc-limma (3.24.14+dfsg-1) unstable; urgency=medium * New upstream version - -- Andreas Tille Fri, 31 Jul 2015 18:56:07 +0200 + -- Andreas Tille Fri, 31 Jul 2015 19:07:56 +0200 r-bioc-limma (3.24.13+dfsg-1) unstable; urgency=medium diff --git a/debian/patches/do_not_attempt_GO.db_test.patch b/debian/patches/do_not_attempt_GO.db_test.patch index 1113ca4..f5e6ee7 100644 Binary files a/debian/patches/do_not_attempt_GO.db_test.patch and b/debian/patches/do_not_attempt_GO.db_test.patch differ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] tag debian/3.24.14+dfsg-1 created (now 9e8d649)
This is an automated email from the git hooks/post-receive script. tille pushed a change to tag debian/3.24.14+dfsg-1 in repository r-bioc-limma. at 9e8d649 (commit) No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 04/04: pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch pristine-tar in repository r-bioc-limma. commit 57df0a8d9beb229f5afa650c0f9b4df28c7c07ff Author: Andreas Tille Date: Fri Jul 31 18:55:56 2015 +0200 pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz --- r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta | Bin 6326 -> 6276 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta index adfe9c0..05c8ac1 100644 Binary files a/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta and b/r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta differ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] annotated tag upstream/3.24.14+dfsg created (now 09e6475)
This is an automated email from the git hooks/post-receive script. tille pushed a change to annotated tag upstream/3.24.14+dfsg in repository r-bioc-limma. at 09e6475 (tag) tagging 1411fa95a8884e2f5eadb33419afb511f13e205d (commit) replaces upstream/3.24.13+dfsg tagged by Andreas Tille on Fri Jul 31 18:55:56 2015 +0200 - Log - Upstream version 3.24.14+dfsg Andreas Tille (3): Imported Upstream version 3.24.14+dfsg Imported Upstream version 3.24.14+dfsg Imported Upstream version 3.24.14+dfsg --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 08/11: Imported Upstream version 3.24.14+dfsg
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit 1411fa95a8884e2f5eadb33419afb511f13e205d Author: Andreas Tille Date: Fri Jul 31 18:55:55 2015 +0200 Imported Upstream version 3.24.14+dfsg -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 07/11: Imported Upstream version 3.24.14+dfsg
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit 7a403fe57105033d754dacea90d87ee06f9e4537 Author: Andreas Tille Date: Fri Jul 31 18:55:41 2015 +0200 Imported Upstream version 3.24.14+dfsg -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 09/11: Merge tag 'upstream/3.24.14+dfsg'
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit a0d92f6e10f38dc0c16779090747a0cd0e55875b Merge: 3702393 1411fa9 Author: Andreas Tille Date: Fri Jul 31 18:55:56 2015 +0200 Merge tag 'upstream/3.24.14+dfsg' Upstream version 3.24.14+dfsg DESCRIPTION | 6 +- R/geneset-camera.R | 43 --- R/geneset-roast.R | 4 +- R/goana.R | 2 +- R/lmfit.R | 4 +- R/subsetting.R | 16 +++- inst/doc/changelog.txt | 18 + inst/doc/intro.pdf | Bin 46191 -> 46191 bytes man/10GeneSetTests.Rd | 2 +- man/TestResults.Rd | 5 +- man/camera.Rd | 8 +- man/roast.Rd| 2 +- man/summary.Rd | 2 +- tests/limma-Tests.Rout.save | 184 +--- vignettes/intro.Rnw | 49 15 files changed, 136 insertions(+), 209 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 01/04: pristine-tar data for r-bioc-limma_3.24.13+dfsg.orig.tar.xz
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch pristine-tar in repository r-bioc-limma. commit 59f310a8d60012f76d8853d607f8afff67555141 Author: Andreas Tille Date: Sun Jul 19 18:14:11 2015 +0200 pristine-tar data for r-bioc-limma_3.24.13+dfsg.orig.tar.xz --- r-bioc-limma_3.24.13+dfsg.orig.tar.xz.delta | Bin 0 -> 6285 bytes r-bioc-limma_3.24.13+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/r-bioc-limma_3.24.13+dfsg.orig.tar.xz.delta b/r-bioc-limma_3.24.13+dfsg.orig.tar.xz.delta new file mode 100644 index 000..771e5df Binary files /dev/null and b/r-bioc-limma_3.24.13+dfsg.orig.tar.xz.delta differ diff --git a/r-bioc-limma_3.24.13+dfsg.orig.tar.xz.id b/r-bioc-limma_3.24.13+dfsg.orig.tar.xz.id new file mode 100644 index 000..2f5524b --- /dev/null +++ b/r-bioc-limma_3.24.13+dfsg.orig.tar.xz.id @@ -0,0 +1 @@ +f8714c23ae164b1617758033af4dd2f9576ab68a -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] branch pristine-tar updated (c91355e -> 57df0a8)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch pristine-tar in repository r-bioc-limma. from c91355e pristine-tar data for r-bioc-limma_3.22.1+dfsg.orig.tar.xz new 59f310a pristine-tar data for r-bioc-limma_3.24.13+dfsg.orig.tar.xz new 8cc5687 pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz new 979c856 pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz new 57df0a8 pristine-tar data for r-bioc-limma_3.24.14+dfsg.orig.tar.xz The 4 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: r-bioc-limma_3.24.13+dfsg.orig.tar.xz.delta | Bin 0 -> 6285 bytes r-bioc-limma_3.24.13+dfsg.orig.tar.xz.id| 1 + r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta | Bin 0 -> 6276 bytes r-bioc-limma_3.24.14+dfsg.orig.tar.xz.id| 1 + 4 files changed, 2 insertions(+) create mode 100644 r-bioc-limma_3.24.13+dfsg.orig.tar.xz.delta create mode 100644 r-bioc-limma_3.24.13+dfsg.orig.tar.xz.id create mode 100644 r-bioc-limma_3.24.14+dfsg.orig.tar.xz.delta create mode 100644 r-bioc-limma_3.24.14+dfsg.orig.tar.xz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 04/11: Merge tag 'upstream/3.24.13+dfsg'
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit 8e8ae7024aab7a0a47fb98e58e95c33dce707ac9 Merge: 871896f 802f308 Author: Andreas Tille Date: Sun Jul 19 18:14:11 2015 +0200 Merge tag 'upstream/3.24.13+dfsg' Upstream version 3.24.13+dfsg DESCRIPTION | 15 +- NAMESPACE | 18 +- R/alias2Symbol.R | 28 ++- R/arrayWeights.R | 7 +- R/auROC.R | 55 + R/background-normexp.R| 6 +- R/classes.R | 2 +- R/dups.R | 8 +- R/fitFDistRobustly.R | 6 +- R/genas.R | 19 +- R/geneset-camera.R| 11 +- R/geneset-fry.R | 138 R/geneset-ids2indices.R | 14 ++ R/geneset-roast.R | 14 +- R/geneset-romer.R | 435 +++--- R/goana.R | 221 +++ R/kegga.R | 277 R/lmfit.R | 35 +-- R/loessFit.R | 10 +- R/neqc.R | 22 +- R/norm.R | 24 ++- R/plot.R | 64 -- R/plotMD.R| 116 ++ R/plotMDS.R | 80 --- R/plotWithHighlights.R| 56 ++--- R/plotdensities.R | 40 ++-- R/plots-ma.R | 18 +- R/predFCm.R | 80 +++ R/read.idat.R | 24 ++- R/roc.R | 20 -- R/sepchannel.R| 6 +- R/squeezeVar.R| 4 +- R/toptable.R | 3 +- R/venn.R | 73 +-- R/voom.R | 6 +- R/write.R | 17 +- build/vignette.rds| Bin 230 -> 231 bytes inst/CITATION | 25 ++- inst/NEWS.Rd | 113 ++ inst/doc/changelog.txt| 297 -- inst/doc/intro.pdf| Bin 46191 -> 46191 bytes man/01Introduction.Rd | 20 +- man/02classes.Rd | 15 ++ man/03reading.Rd | 14 ++ man/04Background.Rd | 15 ++ man/05Normalization.Rd| 15 ++ man/06linearmodels.Rd | 18 ++ man/07SingleChannel.Rd| 15 ++ man/08Tests.Rd| 14 ++ man/09Diagnostics.Rd | 36 +++- man/10GeneSetTests.Rd | 34 ++- man/11RNAseq.Rd | 32 ++- man/EList.Rd | 1 + man/arrayWeights.Rd | 2 +- man/arrayWeightsQuick.Rd | 2 +- man/asmalist.Rd | 4 +- man/auROC.Rd | 14 +- man/backgroundcorrect.Rd | 4 +- man/barcodeplot.Rd| 25 ++- man/decideTests.Rd| 7 +- man/diffSplice.Rd | 4 +- man/ebayes.Rd | 8 +- man/genas.Rd | 10 + man/getEAWP.Rd| 2 +- man/goana.MArrayLM.Rd | 89 man/goana.Rd | 111 -- man/imageplot.Rd | 2 +- man/lmFit.Rd | 7 +- man/malist.Rd | 2 +- man/mdplot.Rd | 40 ++-- man/modifyWeights.Rd | 2 +- man/normalizeRobustSpline.Rd | 14 +- man/normalizeWithinArrays.Rd | 2 +- man/normalizebetweenarrays.Rd | 2 +- man/normexpfit.Rd | 6 +- man/normexpsignal.Rd | 6 +- man/plot.Rd | 94 man/plotDensities.Rd | 12 +- man/plotExons.Rd | 2 +- man/plotMD.Rd | 133 man/plotMDS.Rd| 34 +-- man/plotSplice.Rd | 5 +- man/plotWithHighlights.Rd | 96 + man/plotma.Rd | 49 +++-- man/plotma3by2.Rd | 2 + man/predFCm.Rd| 59 +++--- man/propTrueNull.Rd | 7 +- man/rankSumTestwithCorrelation.Rd | 5 +- man/read.idat.Rd | 9 +- man/read.maimages.Rd | 7 + man/readGPRHeader.Rd | 8 +- man/readImaGeneHeader.Rd | 2 +- man/readgal.Rd| 2 +- man/rglist.Rd | 2 +- man/roast.Rd | 29 ++- man/romer.Rd | 34 +-- man/topGO.Rd | 24 ++- man/topSplice.Rd | 4 +- man/toptable.Rd | 8 + man/venn.Rd | 9 +- man/voom.Rd
[med-svn] [r-bioc-limma] 02/11: New upstream version
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit 871896f0e3659790ea9ca5ff5d8de7dd0a5337f7 Author: Andreas Tille Date: Sun Jul 19 18:13:59 2015 +0200 New upstream version --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 66dcdcd..45f9de4 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +r-bioc-limma (3.24.13+dfsg-1) UNRELEASED; urgency=medium + + * New upstream version + + -- Andreas Tille Sun, 19 Jul 2015 18:02:56 +0200 + r-bioc-limma (3.22.1+dfsg-1) unstable; urgency=medium * New upstream version -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 01/11: Add repacksuffix
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit cf3e216d257a09498d08c065ce6d107547764af3 Author: Andreas Tille Date: Sun Jul 19 18:01:22 2015 +0200 Add repacksuffix --- debian/watch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/watch b/debian/watch index d882018..f5c6562 100644 --- a/debian/watch +++ b/debian/watch @@ -1,6 +1,6 @@ version=3 # This tracks the current stable version of bioconductor -opts=uversionmangle=s|$|+dfsg|,downloadurlmangle=s/\.\./packages\/release\/bioc/ \ +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,downloadurlmangle=s/\.\./packages\/release\/bioc/" \ http://www.bioconductor.org/packages/release/bioc/html/limma.html \ ../src/contrib/limma_(.*).tar.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] [r-bioc-limma] 06/11: Imported Upstream version 3.24.14+dfsg
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-limma.
commit 3fc04a1ff915b4601de908ebfa54fd2c5e4eca74
Author: Andreas Tille
Date: Fri Jul 31 18:55:08 2015 +0200
Imported Upstream version 3.24.14+dfsg
---
DESCRIPTION | 6 +-
R/geneset-camera.R | 43 ---
R/geneset-roast.R | 4 +-
R/goana.R | 2 +-
R/lmfit.R | 4 +-
R/subsetting.R | 16 +++-
inst/doc/changelog.txt | 18 +
inst/doc/intro.pdf | Bin 46191 -> 46191 bytes
man/10GeneSetTests.Rd | 2 +-
man/TestResults.Rd | 5 +-
man/camera.Rd | 8 +-
man/roast.Rd| 2 +-
man/summary.Rd | 2 +-
tests/limma-Tests.Rout.save | 184 +---
vignettes/intro.Rnw | 49
15 files changed, 136 insertions(+), 209 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index b7fe377..17e28c2 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: limma
-Version: 3.24.13
-Date: 2015-07-07
+Version: 3.24.14
+Date: 2015-07-20
Title: Linear Models for Microarray Data
Description: Data analysis, linear models and differential expression for
microarray data.
Author: Gordon Smyth [cre,aut], Matthew Ritchie [ctb], Jeremy Silver [ctb],
James Wettenhall [ctb], Natalie Thorne [ctb], Davis McCarthy [ctb], Di Wu
[ctb], Yifang Hu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Alicia Oshlack
[ctb], Carolyn de Graaf [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb],
Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb], Aaron Lun [ctb]
@@ -20,4 +20,4 @@ biocViews: ExonArray, GeneExpression, Transcription,
MultipleComparison, Normalization, Preprocessing,
QualityControl
NeedsCompilation: yes
-Packaged: 2015-07-09 01:26:56 UTC; biocbuild
+Packaged: 2015-07-21 01:24:42 UTC; biocbuild
diff --git a/R/geneset-camera.R b/R/geneset-camera.R
index 7cd0e7d..248d513 100644
--- a/R/geneset-camera.R
+++ b/R/geneset-camera.R
@@ -21,10 +21,10 @@ interGeneCorrelation <- function(y, design)
camera <- function(y,...) UseMethod("camera")
-camera.default <-
function(y,index,design=NULL,contrast=ncol(design),weights=NULL,use.ranks=FALSE,allow.neg.cor=TRUE,trend.var=FALSE,sort=TRUE,...)
+camera.default <-
function(y,index,design=NULL,contrast=ncol(design),weights=NULL,use.ranks=FALSE,allow.neg.cor=TRUE,inter.gene.cor=NULL,trend.var=FALSE,sort=TRUE,...)
# Competitive gene set test allowing for correlation between genes
# Gordon Smyth and Di Wu
-# Created 2007. Last modified 23 June 2015
+# Created 2007. Last modified 20 July 2015
{
# Issue warning if extra arguments found
dots <- names(list(...))
@@ -51,14 +51,24 @@ camera.default <-
function(y,index,design=NULL,contrast=ncol(design),weights=NUL
if(nrow(design) != n) stop("row dimension of design matrix must match
column dimension of data")
ne <- nonEstimable(design)
if(!is.null(ne)) cat("Coefficients not estimable:",paste(ne,collapse="
"),"\n")
-
p <- ncol(design)
df.residual <- n-p
- df.camera <- min(df.residual,G-2)
# Check weights
if(is.null(weights)) weights <- y$weights
+# Check inter.gene.cor
+ fixed.cor <- !is.null(inter.gene.cor)
+
+# Set for camera tests
+ if(fixed.cor)
+ if(use.ranks)
+ df.camera <- Inf
+ else
+ df.camera <- G-2
+ else
+ df.camera <- min(df.residual,G-2)
+
# Reduce to numeric expression matrix
y <- y$exprs
@@ -124,8 +134,12 @@ camera.default <-
function(y,index,design=NULL,contrast=ncol(design),weights=NUL
if(trend.var) A <- rowMeans(y) else A <- NULL
sv <- squeezeVar(sigma2,df=df.residual,covariate=A)
modt <- unscaledt / sqrt(sv$var.post)
- df.total <- min(df.residual+sv$df.prior, G*df.residual)
- Stat <- zscoreT(modt, df=df.total)
+ if(use.ranks)
+ Stat <- modt
+ else {
+ df.total <- min(df.residual+sv$df.prior, G*df.residual)
+ Stat <- zscoreT(modt, df=df.total, approx=TRUE)
+ }
# Global statistics
meanStat <- mean(Stat)
@@ -139,13 +153,18 @@ camera.default <-
function(y,index,design=NULL,contrast=ncol(design),weights=NUL
StatInSet <- Stat[iset]
m <- length(StatInSet)
m2 <- G-m
- if(m>1) {
- Uset <- U[iset,,drop=FALSE]
- vif <- m * mean(colMeans(Uset)^2)
- correlation <- (vif-1)/(m-1)
+ if(fixed.cor) {
+ correlation <- inter.gene.cor
+ vif <- 1+(m-1)*correlation
} else {
- vif <- 1
-
[med-svn] [r-bioc-limma] branch master updated (1cf2f22 -> 9e8d649)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch master in repository r-bioc-limma. from 1cf2f22 New upstream version new cf3e216 Add repacksuffix new 871896f New upstream version new 802f308 Imported Upstream version 3.24.13+dfsg new 8e8ae70 Merge tag 'upstream/3.24.13+dfsg' new 3702393 Upload to unstable new 3fc04a1 Imported Upstream version 3.24.14+dfsg new 7a403fe Imported Upstream version 3.24.14+dfsg new 1411fa9 Imported Upstream version 3.24.14+dfsg new a0d92f6 Merge tag 'upstream/3.24.14+dfsg' new 0ff44a6 New upstream version new 9e8d649 New upstream version uploaded to unstable The 11 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: DESCRIPTION | 15 +- NAMESPACE | 18 +- R/alias2Symbol.R| 28 +- R/arrayWeights.R| 7 +- R/auROC.R | 55 +++ R/background-normexp.R | 6 +- R/classes.R | 2 +- R/dups.R| 8 +- R/fitFDistRobustly.R| 6 +- R/genas.R | 19 +- R/geneset-camera.R | 52 ++- R/geneset-fry.R | 138 R/geneset-ids2indices.R | 14 + R/geneset-roast.R | 16 +- R/geneset-romer.R | 435 +--- R/goana.R | 221 +++- R/kegga.R | 277 +++ R/lmfit.R | 39 ++- R/loessFit.R| 10 +- R/neqc.R| 22 +- R/norm.R| 24 +- R/plot.R| 64 R/plotMD.R | 116 +++ R/plotMDS.R | 80 +++-- R/plotWithHighlights.R | 56 +-- R/plotdensities.R | 40 ++- R/plots-ma.R| 18 +- R/predFCm.R | 80 +++-- R/read.idat.R | 24 +- R/roc.R | 20 -- R/sepchannel.R | 6 +- R/squeezeVar.R | 4 +- R/subsetting.R | 16 +- R/toptable.R| 3 +- R/venn.R| 73 +++- R/voom.R| 6 +- R/write.R | 17 +- build/vignette.rds | Bin 230 -> 231 bytes debian/changelog| 12 + debian/patches/do_not_attempt_GO.db_test.patch | Bin 4605 -> 9604 bytes debian/patches/do_not_attempt_locfit_test.patch | 12 +- debian/watch| 2 +- inst/CITATION | 25 +- inst/NEWS.Rd| 113 ++ inst/doc/changelog.txt | 315 +++-- inst/doc/intro.pdf | Bin 46191 -> 46191 bytes man/01Introduction.Rd | 20 +- man/02classes.Rd| 15 + man/03reading.Rd| 14 + man/04Background.Rd | 15 + man/05Normalization.Rd | 15 + man/06linearmodels.Rd | 18 + man/07SingleChannel.Rd | 15 + man/08Tests.Rd | 14 + man/09Diagnostics.Rd| 36 +- man/10GeneSetTests.Rd | 34 +- man/11RNAseq.Rd | 32 +- man/EList.Rd| 1 + man/TestResults.Rd | 5 +- man/arrayWeights.Rd | 2 +- man/arrayWeightsQuick.Rd| 2 +- man/asmalist.Rd | 4 +- man/auROC.Rd| 14 +- man/backgroundcorrect.Rd| 4 +- man/barcodeplot.Rd | 25 +- man/camera.Rd | 8 +- man/decideTests.Rd
[med-svn] [r-bioc-limma] 05/11: Upload to unstable
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma. commit 3702393f439f7796f5771fc0ed6cf61790504e3e Author: Andreas Tille Date: Sun Jul 19 21:08:54 2015 +0200 Upload to unstable --- debian/changelog| 4 ++-- debian/patches/do_not_attempt_GO.db_test.patch | Bin 4605 -> 3895 bytes debian/patches/do_not_attempt_locfit_test.patch | 12 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/debian/changelog b/debian/changelog index 45f9de4..1f581bc 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,8 @@ -r-bioc-limma (3.24.13+dfsg-1) UNRELEASED; urgency=medium +r-bioc-limma (3.24.13+dfsg-1) unstable; urgency=medium * New upstream version - -- Andreas Tille Sun, 19 Jul 2015 18:02:56 +0200 + -- Andreas Tille Sun, 19 Jul 2015 18:14:45 +0200 r-bioc-limma (3.22.1+dfsg-1) unstable; urgency=medium diff --git a/debian/patches/do_not_attempt_GO.db_test.patch b/debian/patches/do_not_attempt_GO.db_test.patch index 47334e8..1113ca4 100644 Binary files a/debian/patches/do_not_attempt_GO.db_test.patch and b/debian/patches/do_not_attempt_GO.db_test.patch differ diff --git a/debian/patches/do_not_attempt_locfit_test.patch b/debian/patches/do_not_attempt_locfit_test.patch index 498fe39..5ef71eb 100644 --- a/debian/patches/do_not_attempt_locfit_test.patch +++ b/debian/patches/do_not_attempt_locfit_test.patch @@ -7,9 +7,9 @@ Description: r-cran-locfit has a non-free license and thus can not be packaged to create a local package and remove this patch from series. r-bioc-limma.orig/tests/limma-Tests.R -+++ r-bioc-limma/tests/limma-Tests.R -@@ -48,19 +48,6 @@ +--- a/tests/limma-Tests.R b/tests/limma-Tests.R +@@ -48,19 +48,6 @@ w[1:50] <- 0.5 out <- loessFit(y,x,weights=w,method="weightedLowess") f2 <- quantile(out$fitted) r2 <- quantile(out$residual) @@ -29,9 +29,9 @@ Description: r-cran-locfit has a non-free license and thus can not be packaged ### normalizeWithinArrays r-bioc-limma.orig/tests/limma-Tests.Rout.save -+++ r-bioc-limma/tests/limma-Tests.Rout.save -@@ -594,32 +594,6 @@ +--- a/tests/limma-Tests.Rout.save b/tests/limma-Tests.Rout.save +@@ -594,32 +594,6 @@ $G > out <- loessFit(y,x,weights=w,method="weightedLowess") > f2 <- quantile(out$fitted) > r2 <- quantile(out$residual) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.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] r19799 - trunk/packages/rostlab/profphd/trunk/debian
Author: tille Date: 2015-07-31 17:03:57 + (Fri, 31 Jul 2015) New Revision: 19799 Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog trunk/packages/rostlab/profphd/trunk/debian/compat trunk/packages/rostlab/profphd/trunk/debian/control trunk/packages/rostlab/profphd/trunk/debian/watch Log: debhelper 9, priority optional Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog === --- trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 16:54:20 UTC (rev 19798) +++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 17:03:57 UTC (rev 19799) @@ -1,6 +1,9 @@ -profphd (1.0.40-2) UNRELEASED; urgency=medium +profphd (1.0.42-1) UNRELEASED; urgency=medium * Moved debian/upstream to debian/upstream/metapackages + * remove redundant stuff from d/watch + * debhelper 9 + * Priority: optional -- Andreas Tille Fri, 31 Jul 2015 18:53:46 +0200 Modified: trunk/packages/rostlab/profphd/trunk/debian/compat === --- trunk/packages/rostlab/profphd/trunk/debian/compat 2015-07-31 16:54:20 UTC (rev 19798) +++ trunk/packages/rostlab/profphd/trunk/debian/compat 2015-07-31 17:03:57 UTC (rev 19799) @@ -1 +1 @@ -7 +9 Modified: trunk/packages/rostlab/profphd/trunk/debian/control === --- trunk/packages/rostlab/profphd/trunk/debian/control 2015-07-31 16:54:20 UTC (rev 19798) +++ trunk/packages/rostlab/profphd/trunk/debian/control 2015-07-31 17:03:57 UTC (rev 19799) @@ -3,9 +3,9 @@ Uploaders: Laszlo Kajan , Andreas Tille Section: science -Priority: extra +Priority: optional Build-Depends: cdbs, - debhelper (>= 7.0.50~), + debhelper (>= 9), perl, rsync Standards-Version: 3.9.4 Modified: trunk/packages/rostlab/profphd/trunk/debian/watch === --- trunk/packages/rostlab/profphd/trunk/debian/watch 2015-07-31 16:54:20 UTC (rev 19798) +++ trunk/packages/rostlab/profphd/trunk/debian/watch 2015-07-31 17:03:57 UTC (rev 19799) @@ -1,2 +1,2 @@ version=3 -opts=pasv ftp://rostlab.org/profphd/profphd-([0-9.]+)\.tar\.[a-z]z debian uupdate +opts=pasv ftp://rostlab.org/profphd/profphd-([0-9.]+)\.tar\.[a-z]z ___ 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] r19798 - trunk/packages/rostlab/profphd/trunk/debian
Author: tille Date: 2015-07-31 16:54:20 + (Fri, 31 Jul 2015) New Revision: 19798 Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog Log: Moved debian/upstream to debian/upstream/metapackages Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog === --- trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 15:55:29 UTC (rev 19797) +++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2015-07-31 16:54:20 UTC (rev 19798) @@ -1,3 +1,9 @@ +profphd (1.0.40-2) UNRELEASED; urgency=medium + + * Moved debian/upstream to debian/upstream/metapackages + + -- Andreas Tille Fri, 31 Jul 2015 18:53:46 +0200 + profphd (1.0.40-1) unstable; urgency=low [ Laszlo Kajan ] ___ 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] [khmer] branch upstream updated (f38372a -> abe8250)
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository khmer.
from f38372a Imported Upstream version 2.0rc1+dfsg
new abe8250 Imported Upstream version 2.0~rc2+dfsg
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:
.mailmap | 47 ++
.ycm_extra_conf.py | 105
CITATION | 20 +
ChangeLog | 244
MANIFEST.in| 1 +
Makefile | 63 +-
doc/dev/getting-started.rst| 25 +
doc/release-notes/release-1.4.rst | 2 +-
doc/user/install.rst | 5 +-
doc/user/scripts.rst | 3 +
doc/whats-new-2.0.rst | 30 +
jenkins-build.sh | 21 +-
khmer/__init__.py | 113 +++-
khmer/_khmer.cc| 671 ++---
khmer/_version.py | 4 +-
khmer/kfile.py | 35 +-
khmer/khmer_args.py| 19 +-
khmer/thread_utils.py | 2 +-
khmer/utils.py | 12 +-
lib/Makefile | 220 +++
lib/counting.cc| 85 ++-
lib/counting.hh| 23 +-
lib/get_version.py | 1 +
lib/hashbits.cc| 30 +-
lib/hashbits.hh| 6 +
lib/hashtable.cc | 132 ++--
lib/hashtable.hh | 55 +-
lib/hllcounter.cc | 35 +-
lib/hllcounter.hh | 11 +-
lib/ht-diff.cc | 149 -
lib/khmer_exception.hh | 32 +-
lib/kmer_hash.cc | 10 +-
lib/labelhash.cc | 33 +-
lib/labelhash.hh | 16 +-
lib/{khmer.pc.in => oxli.pc.in}| 4 +-
lib/perf_metrics.cc| 35 --
lib/perf_metrics.hh| 75 ---
lib/read_aligner.cc| 235 ++--
lib/read_aligner.hh| 37 +-
lib/read_parsers.cc| 25 +-
lib/read_parsers.hh| 43 +-
lib/subset.cc | 40 +-
lib/subset.hh | 10 +-
lib/test-HashTables.cc | 150 -
lib/test-Parser.cc | 145 -
lib/test-compile.cc| 5 +-
lib/trace_logger.cc| 70 ---
lib/trace_logger.hh| 76 ---
oxli/__init__.py | 6 +-
oxli/build_graph.py| 12 +-
oxli/functions.py | 129 +++-
sandbox/Makefile.read_aligner_training | 26 +
sandbox/README.rst | 4 +-
sandbox/build-sparse-graph.py | 2 +-
sandbox/calc-best-assembly.py | 17 +-
sandbox/collect-reads.py | 9 +-
sandbox/collect-variants.py| 6 +-
sandbox/correct-errors.py | 219 ---
.../trim-low-abund.py => sandbox/correct-reads.py | 246
sandbox/count-kmers-single.py | 103
sandbox/count-kmers.py | 80 +++
sandbox/error-correct-pass2.py | 94 +++
sandbox/estimate_optimal_hash.py | 11 +-
sandbox/extract-single-partition.py| 2 +-
sandbox/optimal_args_hashbits.py | 2 +-
sandbox/readaligner_pairhmm_train.py | 205 +++
sandbox/saturate-by-median.py | 4 +-
sandbox/sweep-files.py | 8 +-
sandbox/sweep-reads.py | 8 +-
scripts/abundance-dist-single.py | 34 +-
scripts/abundance-dist.py | 32 +-
scripts/count-median.py| 36 +-
scripts/count-overlap.p
[med-svn] [khmer] 02/02: clean up d/changelog, drop patch, fix tests & install
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit 282f3fd598e2bff1466e7c42358ccfe1f87ebbd5
Author: Michael R. Crusoe
Date: Fri Jul 31 07:12:22 2015 -0700
clean up d/changelog, drop patch, fix tests & install
---
debian/changelog | 18 +--
debian/control | 6 +-
debian/liboxli1.install| 2 +-
debian/patches/install-prefix | 11 ++
debian/patches/pr-1148-changes | 358 -
debian/patches/series | 2 +-
debian/rules | 11 +-
7 files changed, 24 insertions(+), 384 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 5954430..5983c59 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,19 +1,5 @@
-khmer (2.0rc1+dfsg-1) UNRELEASED; urgency=low
-
- * Updated to 2.0rc1 release
-
- -- Michael R. Crusoe Wed, 08 Jul 2015 20:02:36 -0700
-
-khmer (1.3+dfsg-2) UNRELEASED; urgency=low
-
- * Remove 'module' infix from CPython extension which allows dh_python2 to
-add the multiarch triplet infix without affecting module loading. Removed
-symlink workaround now that it is no longer needed.
-
- -- Michael R. Crusoe Thu, 12 Feb 2015 06:02:36 -0500
-
-khmer (1.3+dfsg-1) unstable; urgency=medium
+khmer (2.0~rc2+dfsg-1) UNRELEASED; urgency=low
* Initial upload (Closes: #777688)
- -- Michael R. Crusoe Tue, 27 Jan 2015 16:07:19 -0500
+ -- Michael R. Crusoe Tue, 27 Jan 2015 16:07:19 -0500
diff --git a/debian/control b/debian/control
index 5e40aca..9b223b3 100644
--- a/debian/control
+++ b/debian/control
@@ -29,7 +29,7 @@ Architecture: any
Multi-Arch: same
Depends: ${misc:Depends},
${shlibs:Depends}
-Description: in-memory DNA sequence kmer counting, filtering & graph traversal
+Description: common files for the khmer project tools
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
produced by the Illumina platform. khmer takes a k-mer-centric approach to
@@ -63,7 +63,7 @@ Depends: khmer-common,
${shlibs:Depends},
${misc:Depends}
Pre-Depends: ${misc:Pre-Depends}
-Description: in-memory DNA sequence kmer counting, filtering & graph traversal
+Description: in-memory DNA sequence analysis library from the khmer project
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
produced by the Illumina platform. khmer takes a k-mer-centric approach to
@@ -79,7 +79,7 @@ Depends: khmer-common,
${shlibs:Depends},
${misc:Depends}
Pre-Depends: ${misc:Pre-Depends}
-Description: in-memory DNA sequence kmer counting, filtering & graph traversal
+Description: in-memory DNA sequence analysis dev library
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
produced by the Illumina platform. khmer takes a k-mer-centric approach to
diff --git a/debian/liboxli1.install b/debian/liboxli1.install
index b0934fa..3bec701 100755
--- a/debian/liboxli1.install
+++ b/debian/liboxli1.install
@@ -1,2 +1,2 @@
#!/usr/bin/dh-exec
-lib/liboxli.so.2.0rc1+dfsg usr/lib/${DEB_HOST_MULTIARCH}
+lib/liboxli.so.2.0~rc2+dfsg usr/lib/${DEB_HOST_MULTIARCH}
diff --git a/debian/patches/install-prefix b/debian/patches/install-prefix
new file mode 100644
index 000..56745d2
--- /dev/null
+++ b/debian/patches/install-prefix
@@ -0,0 +1,11 @@
+--- khmer.orig/lib/Makefile
khmer/lib/Makefile
+@@ -28,7 +28,7 @@
+ # when optimization is turned on).
+ WANT_DEBUGGING=false
+
+-PREFIX=/usr/local
++PREFIX ?= /usr/local
+
+ ### NOTE: No user-serviceable parts below this line! ###
+
diff --git a/debian/patches/pr-1148-changes b/debian/patches/pr-1148-changes
deleted file mode 100644
index 5882288..000
--- a/debian/patches/pr-1148-changes
+++ /dev/null
@@ -1,358 +0,0 @@
khmer.orig/lib/Makefile
-+++ khmer/lib/Makefile
-@@ -1,3 +1,8 @@
-+# Should we use the standard system zlib and libbz2?
-+
-+USE_SYSTEM_ZLIB ?= false
-+USE_SYSTEM_LIBBZ2 ?= false
-+
- # Profile?
- # Set this variable to true if you wish to profile the codes.
- WANT_PROFILING=false
-@@ -29,47 +34,61 @@
- # and are willing to accept the overhead such instrumentation introduces.
- WITH_INTERNAL_METRICS=false
-
--
- PREFIX=/usr/local
-
- ### NOTE: No user-serviceable parts below this line! ###
-
- INCLUDES= -I ../third-party/seqan/core/include/ \
---I ../third-party/zlib/ \
---I ../third-party/bzip2/ \
- -I ../third-party/smhasher/
-
--CXXFLAGS=$(INCLUDES)
--CXX_WARNING_FLAGS=-Wall
--CXX_OPTIMIZATION_FLAGS=-O3
--CXX_SHARED_LIB_FLAGS=-fPIC
--CXXFLAGS+=\
-- $(CXX_WARNING_FLAGS) \
--
[med-svn] [khmer] branch pristine-tar updated (186a59b -> 582c882)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch pristine-tar in repository khmer. from 186a59b pristine-tar data for khmer_2.0rc1+dfsg.orig.tar.xz new 582c882 pristine-tar data for khmer_2.0~rc2+dfsg.orig.tar.xz 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: khmer_2.0~rc2+dfsg.orig.tar.xz.delta | Bin 0 -> 29101 bytes khmer_2.0~rc2+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 khmer_2.0~rc2+dfsg.orig.tar.xz.delta create mode 100644 khmer_2.0~rc2+dfsg.orig.tar.xz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.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] [khmer] branch master updated (41a3403 -> 282f3fd)
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from 41a3403 Squash of 'big-rebase' down to one commit
new 4347c2e Imported Upstream version 2.0~rc2+dfsg
new 282f3fd clean up d/changelog, drop patch, fix tests & install
The 2 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:
.mailmap | 47 ++
.ycm_extra_conf.py | 105
CITATION | 20 +
ChangeLog | 244
MANIFEST.in| 1 +
Makefile | 63 +-
debian/changelog | 18 +-
debian/control | 6 +-
debian/liboxli1.install| 2 +-
debian/patches/install-prefix | 11 +
debian/patches/pr-1148-changes | 358 ---
debian/patches/series | 2 +-
debian/rules | 11 +-
doc/dev/getting-started.rst| 25 +
doc/release-notes/release-1.4.rst | 2 +-
doc/user/install.rst | 5 +-
doc/user/scripts.rst | 3 +
doc/whats-new-2.0.rst | 30 +
jenkins-build.sh | 21 +-
khmer/__init__.py | 113 +++-
khmer/_khmer.cc| 671 ++---
khmer/_version.py | 4 +-
khmer/kfile.py | 35 +-
khmer/khmer_args.py| 19 +-
khmer/thread_utils.py | 2 +-
khmer/utils.py | 12 +-
lib/Makefile | 220 +++
lib/counting.cc| 85 ++-
lib/counting.hh| 23 +-
lib/get_version.py | 1 +
lib/hashbits.cc| 30 +-
lib/hashbits.hh| 6 +
lib/hashtable.cc | 132 ++--
lib/hashtable.hh | 55 +-
lib/hllcounter.cc | 35 +-
lib/hllcounter.hh | 11 +-
lib/ht-diff.cc | 149 -
lib/khmer_exception.hh | 32 +-
lib/kmer_hash.cc | 10 +-
lib/labelhash.cc | 33 +-
lib/labelhash.hh | 16 +-
lib/{khmer.pc.in => oxli.pc.in}| 4 +-
lib/perf_metrics.cc| 35 --
lib/perf_metrics.hh| 75 ---
lib/read_aligner.cc| 235 ++--
lib/read_aligner.hh| 37 +-
lib/read_parsers.cc| 25 +-
lib/read_parsers.hh| 43 +-
lib/subset.cc | 40 +-
lib/subset.hh | 10 +-
lib/test-HashTables.cc | 150 -
lib/test-Parser.cc | 145 -
lib/test-compile.cc| 5 +-
lib/trace_logger.cc| 70 ---
lib/trace_logger.hh| 76 ---
oxli/__init__.py | 6 +-
oxli/build_graph.py| 12 +-
oxli/functions.py | 129 +++-
sandbox/Makefile.read_aligner_training | 26 +
sandbox/README.rst | 4 +-
sandbox/build-sparse-graph.py | 2 +-
sandbox/calc-best-assembly.py | 17 +-
sandbox/collect-reads.py | 9 +-
sandbox/collect-variants.py| 6 +-
sandbox/correct-errors.py | 219 ---
.../trim-low-abund.py => sandbox/correct-reads.py | 246
sandbox/count-kmers-single.py | 103
sandbox/count-kmers.py | 80 +++
sandbox/error-correct-pass2.py | 94 +++
sandbox/estimate_optimal_hash.py | 11 +-
sandbox/extract-single-partition.py| 2 +-
san
[med-svn] [khmer] 01/01: pristine-tar data for khmer_2.0~rc2+dfsg.orig.tar.xz
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch pristine-tar in repository khmer. commit 582c882587fc4d5ad8db87ded222435130f55450 Author: Michael R. Crusoe Date: Fri Jul 31 07:10:11 2015 -0700 pristine-tar data for khmer_2.0~rc2+dfsg.orig.tar.xz --- khmer_2.0~rc2+dfsg.orig.tar.xz.delta | Bin 0 -> 29101 bytes khmer_2.0~rc2+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/khmer_2.0~rc2+dfsg.orig.tar.xz.delta b/khmer_2.0~rc2+dfsg.orig.tar.xz.delta new file mode 100644 index 000..c32f750 Binary files /dev/null and b/khmer_2.0~rc2+dfsg.orig.tar.xz.delta differ diff --git a/khmer_2.0~rc2+dfsg.orig.tar.xz.id b/khmer_2.0~rc2+dfsg.orig.tar.xz.id new file mode 100644 index 000..28649d3 --- /dev/null +++ b/khmer_2.0~rc2+dfsg.orig.tar.xz.id @@ -0,0 +1 @@ +4147c2078519589e89f426e151eee9e07c9f91d1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.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] [khmer] branch daube/libkhmerdev created (now 06ade8d)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch daube/libkhmerdev in repository khmer. at 06ade8d Update changelog with UNRELEASED 2.0-rc1 No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.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] [python-skbio] 02/02: Without testing lintian-overrides should look like this
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository python-skbio. commit 7519348856ba06f87b566a281a77f09855c54534 Author: Andreas Tille Date: Fri Jul 31 18:05:35 2015 +0200 Without testing lintian-overrides should look like this --- debian/lintian-overrides | 5 - debian/python-skbio.lintian-overrides | 2 ++ debian/python3-skbio.lintian-overrides | 2 ++ 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/debian/lintian-overrides b/debian/lintian-overrides deleted file mode 100644 index 9f8e37d..000 --- a/debian/lintian-overrides +++ /dev/null @@ -1,5 +0,0 @@ -python3-skbio binary: package-contains-timestamped-gzip usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.gz -python3-skbio binary: package-contains-timestamped-gzip usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.gz - -python-skbio binary: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/skbio/io/tests/data/big5_file.gz -python-skbio binary: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/skbio/io/tests/data/example_file.gz diff --git a/debian/python-skbio.lintian-overrides b/debian/python-skbio.lintian-overrides new file mode 100644 index 000..41b4c6c --- /dev/null +++ b/debian/python-skbio.lintian-overrides @@ -0,0 +1,2 @@ +python-skbio: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/skbio/io/tests/data/big5_file.gz +python-skbio: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/skbio/io/tests/data/example_file.gz diff --git a/debian/python3-skbio.lintian-overrides b/debian/python3-skbio.lintian-overrides new file mode 100644 index 000..8021c8a --- /dev/null +++ b/debian/python3-skbio.lintian-overrides @@ -0,0 +1,2 @@ +python3-skbio: package-contains-timestamped-gzip usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.gz +python3-skbio: package-contains-timestamped-gzip usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.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] [python-skbio] branch master updated (89d16ab -> 7519348)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch master in repository python-skbio. from 89d16ab Add upstream gzips to linitan overrides new 7ba9dfe Make versioned build-depends from python-numpy effective by also specifying epoch new 7519348 Without testing lintian-overrides should look like this The 2 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/control | 4 ++-- debian/lintian-overrides | 5 - debian/python-skbio.lintian-overrides | 2 ++ debian/python3-skbio.lintian-overrides | 2 ++ 4 files changed, 6 insertions(+), 7 deletions(-) delete mode 100644 debian/lintian-overrides create mode 100644 debian/python-skbio.lintian-overrides create mode 100644 debian/python3-skbio.lintian-overrides -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.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] [python-skbio] 01/02: Make versioned build-depends from python-numpy effective by also specifying epoch
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository python-skbio. commit 7ba9dfe46ea9be306fe43769f29e7f2eff5a975a Author: Andreas Tille Date: Fri Jul 31 18:05:00 2015 +0200 Make versioned build-depends from python-numpy effective by also specifying epoch --- debian/control | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/control b/debian/control index 4ca71c1..5dcd583 100644 --- a/debian/control +++ b/debian/control @@ -13,8 +13,8 @@ Build-Depends: debhelper (>= 9), python3-dev, python-setuptools, python3-setuptools, - python-numpy (>= 1.9.2), - python3-numpy (>= 1.9.2), + python-numpy (>= 1:1.9.2), + python3-numpy (>= 1:1.9.2), python-natsort, python3-natsort, python-pandas, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.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] r19797 - trunk/packages/R/r-bioc-annotate/trunk/debian
Author: tille Date: 2015-07-31 15:55:29 + (Fri, 31 Jul 2015) New Revision: 19797 Modified: trunk/packages/R/r-bioc-annotate/trunk/debian/changelog trunk/packages/R/r-bioc-annotate/trunk/debian/copyright trunk/packages/R/r-bioc-annotate/trunk/debian/watch Log: Exclude *.ps without source Modified: trunk/packages/R/r-bioc-annotate/trunk/debian/changelog === --- trunk/packages/R/r-bioc-annotate/trunk/debian/changelog 2015-07-31 15:29:49 UTC (rev 19796) +++ trunk/packages/R/r-bioc-annotate/trunk/debian/changelog 2015-07-31 15:55:29 UTC (rev 19797) @@ -1,4 +1,4 @@ -r-bioc-annotate (1.46.1-1) unstable; urgency=medium +r-bioc-annotate (1.46.1+dfsg-1) unstable; urgency=medium * Initial release (closes: #784873). Modified: trunk/packages/R/r-bioc-annotate/trunk/debian/copyright === --- trunk/packages/R/r-bioc-annotate/trunk/debian/copyright 2015-07-31 15:29:49 UTC (rev 19796) +++ trunk/packages/R/r-bioc-annotate/trunk/debian/copyright 2015-07-31 15:55:29 UTC (rev 19797) @@ -2,6 +2,7 @@ Upstream-Name: annotate Upstream-Contact: Bioconductor Package Maintainer Source: http://bioconductor.org/packages/release/bioc/html/annotate.html +Files-Excluded: vignettes/HOWTOigenes.ps Files: * Copyright: © 2006-2014 R. Gentleman Modified: trunk/packages/R/r-bioc-annotate/trunk/debian/watch === --- trunk/packages/R/r-bioc-annotate/trunk/debian/watch 2015-07-31 15:29:49 UTC (rev 19796) +++ trunk/packages/R/r-bioc-annotate/trunk/debian/watch 2015-07-31 15:55:29 UTC (rev 19797) @@ -1,3 +1,4 @@ version=3 -opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \ + +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,downloadurlmangle=s/\.\./packages\/release\/bioc/" \ http://www.bioconductor.org/packages/release/bioc/html/annotate.html .*/annotate_([\d\.]+)\.tar\.gz ___ 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] [hyphy] tag debian/jessie/2.2.5+dfsg-1_bpo8+1 created (now 488aaeb)
This is an automated email from the git hooks/post-receive script. tille pushed a change to tag debian/jessie/2.2.5+dfsg-1_bpo8+1 in repository hyphy. at 488aaeb (commit) No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hyphy.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] [hyphy] branch debian/jessie created (now 488aaeb)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch debian/jessie in repository hyphy. at 488aaeb Backport to Jessie This branch includes the following new commits: new 488aaeb Backport to Jessie 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hyphy.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] [hyphy] 01/01: Backport to Jessie
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch debian/jessie in repository hyphy. commit 488aaeb288b1c8aac8575caa6564fb9c3b574316 Author: Andreas Tille Date: Fri Jul 31 16:47:58 2015 +0200 Backport to Jessie --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index d03862f..94de561 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +hyphy (2.2.5+dfsg-1~bpo8+1) jessie-backports; urgency=medium + + * Backport to Jessie + + -- Andreas Tille Fri, 31 Jul 2015 16:46:29 +0200 + hyphy (2.2.5+dfsg-2) unstable; urgency=medium * Versioned Build-Depends: cmake (>= 3.0) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hyphy.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] r19796 - trunk/packages/logol/trunk/debian
Author: ebourg-guest Date: 2015-07-31 15:29:49 + (Fri, 31 Jul 2015) New Revision: 19796 Modified: trunk/packages/logol/trunk/debian/control Log: Depend on libmail-java instead of libgnumail-java (more) Modified: trunk/packages/logol/trunk/debian/control === --- trunk/packages/logol/trunk/debian/control 2015-07-31 15:29:16 UTC (rev 19795) +++ trunk/packages/logol/trunk/debian/control 2015-07-31 15:29:49 UTC (rev 19796) @@ -25,7 +25,7 @@ libbiojava-java, antlr3, libcommons-cli-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-lang-java, libcommons-logging-java, libxalan2-java, - libxerces2-java, libgnumail-java, liblog4j1.2-java, + libxerces2-java, libmail-java, liblog4j1.2-java, cassiopee, logol-bin #libdrmaa-java removed from Jessie, to be reintroduced. Suggests: ruby-cassiopee (>=0.1.12) ___ 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] r19795 - in trunk/packages/logol/trunk/debian: . patches
Author: ebourg-guest Date: 2015-07-31 15:29:16 + (Fri, 31 Jul 2015) New Revision: 19795 Modified: trunk/packages/logol/trunk/debian/changelog trunk/packages/logol/trunk/debian/control trunk/packages/logol/trunk/debian/logol.links trunk/packages/logol/trunk/debian/patches/fixLibPath Log: Depend on libmail-java instead of libgnumail-java Modified: trunk/packages/logol/trunk/debian/changelog === --- trunk/packages/logol/trunk/debian/changelog 2015-07-31 15:01:09 UTC (rev 19794) +++ trunk/packages/logol/trunk/debian/changelog 2015-07-31 15:29:16 UTC (rev 19795) @@ -1,3 +1,10 @@ +logol (1.7.2-3) UNRELEASED; urgency=medium + + * Team upload. + * Depend on libmail-java instead of libgnumail-java + + -- Emmanuel Bourg Fri, 31 Jul 2015 17:17:23 +0200 + logol (1.7.2-2) unstable; urgency=medium * d/patches/fix_swipl72: Fix swipl v7.x compatibility (Closes: #790136). Modified: trunk/packages/logol/trunk/debian/control === --- trunk/packages/logol/trunk/debian/control 2015-07-31 15:01:09 UTC (rev 19794) +++ trunk/packages/logol/trunk/debian/control 2015-07-31 15:29:16 UTC (rev 19795) @@ -10,7 +10,7 @@ libbiojava-java, antlr3, libcommons-cli-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-lang-java, libcommons-logging-java, libxalan2-java, - libxerces2-java, junit4, libgnumail-java, + libxerces2-java, junit4, libmail-java, liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht, libncursesw5-dev, ant-optional, cassiopee, ruby-cassiopee Modified: trunk/packages/logol/trunk/debian/logol.links === --- trunk/packages/logol/trunk/debian/logol.links 2015-07-31 15:01:09 UTC (rev 19794) +++ trunk/packages/logol/trunk/debian/logol.links 2015-07-31 15:29:16 UTC (rev 19795) @@ -14,6 +14,6 @@ usr/share/java/xalan2.jar usr/share/logol/lib/xalan.jar usr/share/java/xercesImpl.jar usr/share/logol/lib/xercesImpl.jar usr/share/java/xml-apis.jar usr/share/logol/lib/xml-apis.jar -usr/share/java/gnumail.jar usr/share/logol/lib/mail.jar +usr/share/java/javax.mail.jar usr/share/logol/lib/mail.jar usr/share/java/log4j-1.2.jar usr/share/logol/lib/log4j-1.2.jar usr/share/java/serializer.jar usr/share/logol/lib/serializer.jar Modified: trunk/packages/logol/trunk/debian/patches/fixLibPath === --- trunk/packages/logol/trunk/debian/patches/fixLibPath2015-07-31 15:01:09 UTC (rev 19794) +++ trunk/packages/logol/trunk/debian/patches/fixLibPath2015-07-31 15:29:16 UTC (rev 19795) @@ -39,7 +39,7 @@ + + + -+ ++ + + + @@ -51,7 +51,7 @@ -+ ++ ___ 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] r19794 - trunk/packages/R/r-bioc-annotate/trunk/debian
Author: tille Date: 2015-07-31 15:01:09 + (Fri, 31 Jul 2015) New Revision: 19794 Added: trunk/packages/R/r-bioc-annotate/trunk/debian/README.source Log: Add README.source describing rda files Added: trunk/packages/R/r-bioc-annotate/trunk/debian/README.source === --- trunk/packages/R/r-bioc-annotate/trunk/debian/README.source (rev 0) +++ trunk/packages/R/r-bioc-annotate/trunk/debian/README.source 2015-07-31 15:01:09 UTC (rev 19794) @@ -0,0 +1,36 @@ +Explanation for binary files inside source package according to + http://lists.debian.org/debian-devel/2013/09/msg00332.html + +Files: data/hgu95All.rda +Documentation: man/hgu95All.Rd + -> sample data in the form of environments for the Affymetrix U95A chip. + +Files: data/hgByChroms.rda +Documentation: man/hgByChroms.Rd + -> dataset to show the human genome base pair locations per chromosome + by Cheng Li of the Dana-Farber Cancer Institute + +Files: data/hgu95AProbLocs.rda +Documentation: man/hgu95AProbLocs.Rd + -> chromLocation instance hgu95AProbLocs, an example of a chromLocation object + gives chromosome locations for Affy U95 probes + +Files: data/hgCLengths.rda +Documentation: man/hgCLengths.Rd + -> dataset which contains the lengths (in base pairs) of the human chromosomes + UCSC Human Genome Project + +Files: data/hgu95Achrom.rda +Documentation: man/hgu95Achrom.Rd + -> Annotation data for the Affymetrix HGU95A GeneChip + +Files: data/hgu95Achroloc.rda +Documentation: man/hgu95Achroloc.Rd + -> Annotation data for the Affymetrix HGU95A GeneChip + +Files: data/hgu95Asym.rda +Documentation: man/hgu95Asym.Rd + -> Annotation data for the Affymetrix HGU95A GeneChip + + -- Andreas Tille Sun, 12 Jul 2015 07:29:08 +0200 + ___ 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] [khmer] branch master updated (a7c2d16 -> 41a3403)
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from a7c2d16 Rename liboxli2=>liboxli1, python3 deps in d/ctrl
new 41a3403 Squash of 'big-rebase' down to one commit
The 1 revisions listed above as "new" are entirely new to this
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listed as "adds" were already present in the repository and have only
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Summary of changes:
.gitignore |3 +
CITATION |2 +-
ChangeLog | 354 +-
Doxyfile.in|2 +-
Makefile | 34 +-
README.rst | 15 +-
debian/control | 48 +-
debian/copyright | 44 +
debian/khmer-common.install|1 +
.../{liboxli1.postinst => khmer-common.postinst} |1 +
debian/{liboxli1.postrm => khmer-common.postrm}|2 +-
debian/khmer.install |0
debian/liboxli-dev.install |4 +-
debian/liboxli1.install|3 +-
debian/patches/get_version |3 +-
debian/patches/pr-1148-changes | 358 ++
debian/patches/series |2 +
debian/patches/setup-py-py3|8 +
debian/rules | 17 +-
debian/upstream/metadata | 10 +-
doc/conf.py|2 +-
doc/dev/binary-file-formats.rst| 115 +
doc/dev/development.rst|6 +-
doc/dev/for-khmer-developers.rst |4 +-
doc/dev/getting-started.rst| 29 +-
doc/dev/hackathon.rst | 12 +-
doc/dev/index.rst |1 +
doc/dev/release.rst| 20 +-
doc/dev/scripts-and-sandbox.rst|2 +-
doc/index.rst |5 +-
doc/release-notes/release-1.0.1.md | 12 +-
doc/release-notes/release-1.0.1.rst| 14 +-
doc/release-notes/release-1.0.md | 12 +-
doc/release-notes/release-1.0.rst | 16 +-
doc/release-notes/release-1.1.md | 14 +-
doc/release-notes/release-1.1.rst | 14 +-
doc/release-notes/release-1.2.md | 14 +-
doc/release-notes/release-1.2.rst | 14 +-
doc/release-notes/release-1.3.md |2 +-
doc/release-notes/release-1.3.rst |2 +-
doc/release-notes/release-1.4.md |4 +-
doc/release-notes/release-1.4.rst |4 +-
doc/roadmap.rst|2 +-
doc/run-corn-50m.sh|4 +-
doc/user/choosing-table-sizes.rst | 74 +-
doc/user/examples.rst |4 +-
doc/user/getting-help.rst |2 +-
doc/user/guide.rst |2 +-
doc/user/known-issues.rst | 14 +-
doc/user/scripts.rst | 12 +-
doc/whats-new-2.0.rst | 29 +
examples/stamps/do.sh |4 +-
jenkins-build.sh |2 +-
khmer/__init__.py | 120 +-
khmer/{_khmermodule.cc => _khmer.cc} | 3792 ++--
khmer/_version.py | 11 +-
khmer/kfile.py | 72 +-
khmer/khmer_args.py| 175 +-
khmer/thread_utils.py | 66 +-
khmer/utils.py | 46 +-
lib/.check_openmp.cc |2 +-
lib/Makefile |2 +-
lib/counting.cc| 70 +-
lib/counting.hh|2 +-
lib/get_version.py |3 +-
lib/graphtest.cc |4 +-
lib/hashbits.cc| 35 +-
lib/hashbits.hh| 11 +-
lib/hashtable.cc | 119 +-
lib/hashtable.hh | 26 +-
lib/hllcounter.cc | 13 +-
lib/hllcounter.hh |2 +-
l
[med-svn] [Debian Wiki] Update of "DebianMed/MoM" by AndreasTille
Dear Wiki user, You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification. The "DebianMed/MoM" page has been changed by AndreasTille: https://wiki.debian.org/DebianMed/MoM?action=diff&rev1=70&rev2=71 Comment: Mai+July MoM projects ended with upload ||02.2015 ||AndreasTille||Paul Novotny ||opensurgsim ||git://git.debian.org/git/debian-med/opensurgsim.git ||yes || || ||03.2015 ||AndreasTille||Yves Martelli ||dwvexplorer ||git://git.debian.org/git/debian-med/dwv-orthanc-plugin.git |||| || ||04.2015 ||AndreasTille||Malihe Asemani||manila ||git://git.debian.org/git/openstack/cinder.git |||| || - ||05.2015 ||AndreasTille||Afif Elghraoui||kmer-tools ||git://git.debian.org/git/debian-med/kmer-tools.git |||| || + ||05.2015 ||AndreasTille||Afif Elghraoui||kmer-tools ||git://git.debian.org/git/debian-med/kmer-tools.git ||yes || || ||06.2015 ||AndreasTille||Alba Crespi ||r-cran-fastmatch||git://git.debian.org/git/debian-med/r-cran-fastmatch.git ||yes || || - ||07.2015 ||AndreasTille||Julien Lamy ||dcmtk++ ||git://git.debian.org/git/debian-med/dcmtk++.git |||| || + ||07.2015 ||AndreasTille||Julien Lamy ||dcmtk++ ||git://git.debian.org/git/debian-med/dcmtk++.git ||yes || || == Students in the queue == * Christoph Gille (Strap - svn://svn.debian.org/debian-med/trunk/packages/strap/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] [blasr] branch master updated (5d2d2e3 -> 5430650)
This is an automated email from the git hooks/post-receive script. tille pushed a change to branch master in repository blasr. from 5d2d2e3 Add missing licenses new 5430650 Upload to unstable 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 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.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] [blasr] 01/01: Upload to unstable
This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository blasr. commit 54306500a3280bdcae3c3ed964cec596110df182 Author: Andreas Tille Date: Fri Jul 31 09:51:22 2015 +0200 Upload to unstable --- debian/changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 7f24d68..a19571d 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -blasr (0~20150724+git3ca7fe8-1) UNRELEASED; urgency=low +blasr (0~20150724+git3ca7fe8-1) unstable; urgency=low * Initial release (Closes: #793763) * Statically link native libraries and dynamically link external ones -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.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] [python-skbio] branch master updated (c15a580 -> 89d16ab)
This is an automated email from the git hooks/post-receive script. daube-guest pushed a change to branch master in repository python-skbio. from c15a580 Merge tag 'upstream/0.4.0' new 89d16ab Add upstream gzips to linitan overrides 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/lintian-overrides | 5 + 1 file changed, 5 insertions(+) create mode 100644 debian/lintian-overrides -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.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] [python-skbio] 01/01: Add upstream gzips to linitan overrides
This is an automated email from the git hooks/post-receive script. daube-guest pushed a commit to branch master in repository python-skbio. commit 89d16abf57e2d5766f5e92e10bdbceaca5fc0cc3 Author: Kevin Murray Date: Fri Jul 31 17:09:12 2015 +1000 Add upstream gzips to linitan overrides --- debian/lintian-overrides | 5 + 1 file changed, 5 insertions(+) diff --git a/debian/lintian-overrides b/debian/lintian-overrides new file mode 100644 index 000..9f8e37d --- /dev/null +++ b/debian/lintian-overrides @@ -0,0 +1,5 @@ +python3-skbio binary: package-contains-timestamped-gzip usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.gz +python3-skbio binary: package-contains-timestamped-gzip usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.gz + +python-skbio binary: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/skbio/io/tests/data/big5_file.gz +python-skbio binary: package-contains-timestamped-gzip usr/lib/python2.7/dist-packages/skbio/io/tests/data/example_file.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.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
