[med-svn] [pixelmed] 02/12: debhelper 10

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commit 9cb3e3fd41f9817efd95eb6ff4769452b7f6134d
Author: Andreas Tille 
Date:   Fri Sep 15 11:53:50 2017 +0200

debhelper 10
---
 debian/changelog | 1 +
 debian/compat| 2 +-
 debian/control   | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ba9d78f..090bc18 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,7 @@ pixelmed (20150917-2) UNRELEASED; urgency=medium
   * Move packaging from SVN to Git
   * Do not set bootclasspath
 Closes: #874150
+  * debhelper 10
 
  -- Andreas Tille   Fri, 15 Sep 2017 11:15:57 +0200
 
diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index 54b3923..9c0b3cc 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team 

 Section: graphics
 Priority: optional
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 10)
 Build-Depends-Indep: default-jdk,
  javahelper,
  junit4,

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[med-svn] [pixelmed] tag debian/20150917+dfsg-1 created (now 7d1b746)

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at  7d1b746   (commit)
No new revisions were added by this update.

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[med-svn] [pixelmed] branch upstream updated (28d19b1 -> 81e9a7c)

[Andreas Tille]

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  from  28d19b1   New upstream version 20150917
   new  81e9a7c   New upstream version 20150917+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:
 com/pixelmed/display/testmammohome | 1 -
 1 file changed, 1 deletion(-)
 delete mode 12 com/pixelmed/display/testmammohome

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[med-svn] [pixelmed] 08/12: DEP3

[Andreas Tille]

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commit 2dd224bb60103fa415b0d0f8473c428f886d49e1
Author: Andreas Tille 
Date:   Fri Sep 15 12:59:48 2017 +0200

DEP3
---
 debian/patches/imageio.patch   | 4 
 debian/patches/set_java_home.patch | 4 
 2 files changed, 8 insertions(+)

diff --git a/debian/patches/imageio.patch b/debian/patches/imageio.patch
index 686033f..31d87ae 100644
--- a/debian/patches/imageio.patch
+++ b/debian/patches/imageio.patch
@@ -1,3 +1,7 @@
+Author: Andreas Tille
+Last-Update: 2015-10-06 20:02:48
+Description: Add missing import
+
 --- a/com/pixelmed/display/ImageEditUtilities.java
 +++ b/com/pixelmed/display/ImageEditUtilities.java
 @@ -26,6 +26,7 @@ import java.io.File;
diff --git a/debian/patches/set_java_home.patch 
b/debian/patches/set_java_home.patch
index af5ae29..485f7e3 100644
--- a/debian/patches/set_java_home.patch
+++ b/debian/patches/set_java_home.patch
@@ -1,3 +1,7 @@
+Author: Andreas Tille
+Last-Update: 2015-10-06
+Description: Use JAVA_HOME variable instead of calculating it (possibly 
wrongly)
+
 --- a/Makefile.common.mk
 +++ b/Makefile.common.mk
 @@ -61,7 +61,7 @@ JAVACTARGETOPTIONS=-target ${JAVAVERSION

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[med-svn] [pixelmed] 07/12: Drop fixme

[Andreas Tille]

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commit 9a24b095f53e664721fb775412cb52f337e27d36
Author: Andreas Tille 
Date:   Fri Sep 15 12:58:17 2017 +0200

Drop fixme
---
 debian/rules | 1 -
 1 file changed, 1 deletion(-)

diff --git a/debian/rules b/debian/rules
index 4d5d58d..ae29f13 100755
--- a/debian/rules
+++ b/debian/rules
@@ -19,7 +19,6 @@ override_dh_auto_test:
 endif
 
 override_dh_auto_install:
-   # FIXME: isn't there something easier:
cp sample.com.pixelmed.display.DicomImageViewer.properties 
.com.pixelmed.display.DicomImageViewer.properties 
# executable-not-elf-or-script 
./etc/pixelmed/.com.pixelmed.display.DicomImageViewer.properties
chmod -x .com.pixelmed.display.DicomImageViewer.properties 

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[med-svn] [pixelmed] 01/01: pristine-tar data for pixelmed_20150917+dfsg.orig.tar.bz2

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commit 9ea2f3ff8fd775900a5476c2c20b1df59e65b945
Author: Andreas Tille 
Date:   Fri Sep 15 12:57:56 2017 +0200

pristine-tar data for pixelmed_20150917+dfsg.orig.tar.bz2
---
 pixelmed_20150917+dfsg.orig.tar.bz2.delta | Bin 0 -> 2 bytes
 pixelmed_20150917+dfsg.orig.tar.bz2.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/pixelmed_20150917+dfsg.orig.tar.bz2.delta 
b/pixelmed_20150917+dfsg.orig.tar.bz2.delta
new file mode 100644
index 000..6e424c9
Binary files /dev/null and b/pixelmed_20150917+dfsg.orig.tar.bz2.delta differ
diff --git a/pixelmed_20150917+dfsg.orig.tar.bz2.id 
b/pixelmed_20150917+dfsg.orig.tar.bz2.id
new file mode 100644
index 000..6685d56
--- /dev/null
+++ b/pixelmed_20150917+dfsg.orig.tar.bz2.id
@@ -0,0 +1 @@
+0ffd4cf6b5c44d1928307288572596610f6a37db

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[med-svn] [pixelmed] 09/12: do not parse d/changelog

[Andreas Tille]

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tille pushed a commit to branch master
in repository pixelmed.

commit 32d9084a5b600e69f9a3219a65eccc10ab9dad04
Author: Andreas Tille 
Date:   Fri Sep 15 13:03:17 2017 +0200

do not parse d/changelog
---
 debian/changelog | 2 ++
 debian/rules | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 831009e..4b344f0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -9,6 +9,8 @@ pixelmed (20150917+dfsg-1) UNRELEASED; urgency=medium
 Closes: #874150
   * debhelper 10
   * Standards-Version: 4.1.0
+  * DEP3
+  * d/rules: do not parse d/changelog
 
  -- Andreas Tille   Fri, 15 Sep 2017 11:15:57 +0200
 
diff --git a/debian/rules b/debian/rules
index ae29f13..df21fcc 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,7 +3,7 @@
 
 export JAVA_HOME=/usr/lib/jvm/default-java
 
-VERSION = $(shell dpkg-parsechangelog | grep '^Version' | cut -d' ' -f2 | cut 
-f1 -d- | cut -f2 -d~)
+include /usr/share/dpkg/default.mk
 
 %:
dh $@ --with javahelper
@@ -40,11 +40,11 @@ pixelmed_manpages: debian/DicomSRValidator.1 
debian/ImageToDicom.1 debian/NIfTI1
 
 debian/%.desktop: webstart/%.jnlp debian/jnlp2desktop.xsl
# create .desktop file:
-   xsltproc --stringparam pixelmed_version $(VERSION) -o $@ 
debian/jnlp2desktop.xsl $<
+   xsltproc --stringparam pixelmed_version $(DEB_VERSION_UPSTREAM) -o $@ 
debian/jnlp2desktop.xsl $<
 
 debian/%: webstart/%.jnlp debian/jnlp2script.xsl debian/%.desktop 
# script wrapper:
-   xsltproc --stringparam pixelmed_version $(VERSION) -o $@ 
debian/jnlp2script.xsl $<
+   xsltproc --stringparam pixelmed_version $(DEB_VERSION_UPSTREAM) -o $@ 
debian/jnlp2script.xsl $<
chmod +x $@
 
 pixelmed_webapps: debian/DicomImageBlackout debian/MediaImporter 
debian/WatchFolderAndSend debian/DicomImageViewer 
debian/ConvertAmicasJPEG2000FilesetToDicom debian/DicomCleaner 
debian/DoseUtility

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[med-svn] [pixelmed] 01/12: Do not set bootclasspath

[Andreas Tille]

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tille pushed a commit to branch master
in repository pixelmed.

commit 72892d540eab044004484614140efa8fe1bcb9a4
Author: Andreas Tille 
Date:   Fri Sep 15 11:53:16 2017 +0200

Do not set bootclasspath
---
 debian/changelog  |  2 ++
 debian/patches/do_not_set_bootclasspath.patch | 16 
 debian/patches/series |  1 +
 3 files changed, 19 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index a36f3a9..ba9d78f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,8 @@ pixelmed (20150917-2) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * Move packaging from SVN to Git
+  * Do not set bootclasspath
+Closes: #874150
 
  -- Andreas Tille   Fri, 15 Sep 2017 11:15:57 +0200
 
diff --git a/debian/patches/do_not_set_bootclasspath.patch 
b/debian/patches/do_not_set_bootclasspath.patch
new file mode 100644
index 000..3d52043
--- /dev/null
+++ b/debian/patches/do_not_set_bootclasspath.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille 
+Last-Update: Fri, 15 Sep 2017 11:15:57 +0200
+Bug-Debian: https://bugs.debian.org/874150
+Description: Do not set bootclasspath
+
+--- a/Makefile.common.mk
 b/Makefile.common.mk
+@@ -53,7 +53,7 @@ JPEGBLOCKREDACTIONJAR = ${PATHTOADDITION
+ 
+ JAVAVERSIONTARGET=1.7
+ 
+-JAVACTARGETOPTIONS=-target ${JAVAVERSIONTARGET} -source ${JAVAVERSIONTARGET} 
-bootclasspath $${JAVAVERSIONTARGETJARFILE}
++JAVACTARGETOPTIONS=-target ${JAVAVERSIONTARGET} -source ${JAVAVERSIONTARGET}
+ 
+ .SUFFIXES:.class .java .ico .png
+ 
diff --git a/debian/patches/series b/debian/patches/series
index aa65f92..10286d4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -15,3 +15,4 @@ illegalchar.patch
 set_java_home.patch
 imageio.patch
 no_Xdiags_verbose.patch
+do_not_set_bootclasspath.patch

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[med-svn] [pixelmed] 11/12: Remove Encoding key from debian/*.desktop files

[Andreas Tille]

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tille pushed a commit to branch master
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commit 0c6af7058a8aaf0a523fb4e262dfedeaf1f64b9a
Author: Andreas Tille 
Date:   Fri Sep 15 13:07:23 2017 +0200

Remove Encoding key from debian/*.desktop files
---
 debian/ConvertAmicasJPEG2000FilesetToDicom.desktop | 1 -
 debian/DicomCleaner.desktop| 1 -
 debian/DicomImageBlackout.desktop  | 1 -
 debian/DicomImageViewer.desktop| 1 -
 debian/DoseUtility.desktop | 1 -
 debian/MediaImporter.desktop   | 1 -
 debian/WatchFolderAndSend.desktop  | 1 -
 debian/changelog   | 1 +
 8 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/debian/ConvertAmicasJPEG2000FilesetToDicom.desktop 
b/debian/ConvertAmicasJPEG2000FilesetToDicom.desktop
index ccab5ca..d0521ee 100644
--- a/debian/ConvertAmicasJPEG2000FilesetToDicom.desktop
+++ b/debian/ConvertAmicasJPEG2000FilesetToDicom.desktop
@@ -1,5 +1,4 @@
 [Desktop Entry]
-Encoding=UTF-8
 Type=Application
 Terminal=false
 StartupNotify=true
diff --git a/debian/DicomCleaner.desktop b/debian/DicomCleaner.desktop
index 0791a4b..a245cd0 100644
--- a/debian/DicomCleaner.desktop
+++ b/debian/DicomCleaner.desktop
@@ -1,5 +1,4 @@
 [Desktop Entry]
-Encoding=UTF-8
 Type=Application
 Terminal=false
 StartupNotify=true
diff --git a/debian/DicomImageBlackout.desktop 
b/debian/DicomImageBlackout.desktop
index 87646aa..336e0ca 100644
--- a/debian/DicomImageBlackout.desktop
+++ b/debian/DicomImageBlackout.desktop
@@ -1,5 +1,4 @@
 [Desktop Entry]
-Encoding=UTF-8
 Type=Application
 Terminal=false
 StartupNotify=true
diff --git a/debian/DicomImageViewer.desktop b/debian/DicomImageViewer.desktop
index 34481d8..2c096ae 100644
--- a/debian/DicomImageViewer.desktop
+++ b/debian/DicomImageViewer.desktop
@@ -1,5 +1,4 @@
 [Desktop Entry]
-Encoding=UTF-8
 Type=Application
 Terminal=false
 StartupNotify=true
diff --git a/debian/DoseUtility.desktop b/debian/DoseUtility.desktop
index 53e4644..d7d16ae 100644
--- a/debian/DoseUtility.desktop
+++ b/debian/DoseUtility.desktop
@@ -1,5 +1,4 @@
 [Desktop Entry]
-Encoding=UTF-8
 Type=Application
 Terminal=false
 StartupNotify=true
diff --git a/debian/MediaImporter.desktop b/debian/MediaImporter.desktop
index a5f47ef..7a1a942 100644
--- a/debian/MediaImporter.desktop
+++ b/debian/MediaImporter.desktop
@@ -1,5 +1,4 @@
 [Desktop Entry]
-Encoding=UTF-8
 Type=Application
 Terminal=false
 StartupNotify=true
diff --git a/debian/WatchFolderAndSend.desktop 
b/debian/WatchFolderAndSend.desktop
index a53d37a..e2de786 100644
--- a/debian/WatchFolderAndSend.desktop
+++ b/debian/WatchFolderAndSend.desktop
@@ -1,5 +1,4 @@
 [Desktop Entry]
-Encoding=UTF-8
 Type=Application
 Terminal=false
 StartupNotify=true
diff --git a/debian/changelog b/debian/changelog
index 247cae1..fc395f8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -12,6 +12,7 @@ pixelmed (20150917+dfsg-1) UNRELEASED; urgency=medium
   * DEP3
   * d/rules: do not parse d/changelog
   * Fix DEP5 issues, update
+  * Remove Encoding key from debian/*.desktop files
 
  -- Andreas Tille   Fri, 15 Sep 2017 11:15:57 +0200
 

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[med-svn] [pixelmed] 05/12: New upstream version 20150917+dfsg

[Andreas Tille]

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tille pushed a commit to branch master
in repository pixelmed.

commit 81e9a7ceaff953a19e6cb801545c769a21342256
Author: Andreas Tille 
Date:   Fri Sep 15 12:57:52 2017 +0200

New upstream version 20150917+dfsg
---
 com/pixelmed/display/testmammohome | 1 -
 1 file changed, 1 deletion(-)

diff --git a/com/pixelmed/display/testmammohome 
b/com/pixelmed/display/testmammohome
deleted file mode 12
index faade68..000
--- a/com/pixelmed/display/testmammohome
+++ /dev/null
@@ -1 +0,0 @@
-/Volumes/GraytooTimeMachine/Pictures/Medical/ihemammotests
\ No newline at end of file

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[med-svn] [pixelmed] 06/12: Merge tag 'upstream/20150917+dfsg'

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commit 2bef9be615794d9adf63bae6c1ca11efa5b4ff20
Merge: 2ada79f 81e9a7c
Author: Andreas Tille 
Date:   Fri Sep 15 12:57:56 2017 +0200

Merge tag 'upstream/20150917+dfsg'

Upstream version 20150917+dfsg

 com/pixelmed/display/testmammohome | 1 -
 1 file changed, 1 deletion(-)

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[med-svn] [pixelmed] 10/12: Fix DEP5 issues, update

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commit 490f4334a57671b0abe77c7ee43822877bdfbc76
Author: Andreas Tille 
Date:   Fri Sep 15 13:05:10 2017 +0200

Fix DEP5 issues, update
---
 debian/changelog |  1 +
 debian/copyright | 17 ++---
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 4b344f0..247cae1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -11,6 +11,7 @@ pixelmed (20150917+dfsg-1) UNRELEASED; urgency=medium
   * Standards-Version: 4.1.0
   * DEP3
   * d/rules: do not parse d/changelog
+  * Fix DEP5 issues, update
 
  -- Andreas Tille   Fri, 15 Sep 2017 11:15:57 +0200
 
diff --git a/debian/copyright b/debian/copyright
index f9c4d4b..7ad7f09 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,12 +1,19 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PixelMed Java DICOM Toolkit
 Upstream-Contact: pixelmed_di...@yahoogroups.com
 Source: http://www.pixelmed.com/
 Files-Excluded: com/pixelmed/display/testmammohome
 
 Files: *
-Copyright: 2001-2008, David A. Clunie DBA PixelMed Publishing. All rights 
reserved.
-License: BSD
+Copyright: 2001-2015, David A. Clunie DBA PixelMed Publishing. All rights 
reserved.
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2009-2014 Mathieu Malaterre 
+   2016-2017 Andreas Tille 
+License: BSD-3-clause
+
+License: BSD-3-clause
  Redistribution and use in source and binary forms, with or without 
modification, are
  permitted provided that the following conditions are met:
  .
@@ -34,7 +41,3 @@ License: BSD
  a medical device. It is the redistributor's or user's responsibility to 
comply with any
  applicable local, state, national or international regulations.
 
-Files: debian/*
-Copyright: 2009-2012, Mathieu Malaterre 
-License: BSD
- Same as above

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[med-svn] [pixelmed] 03/12: Standards-Version: 4.1.0

[Andreas Tille]

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tille pushed a commit to branch master
in repository pixelmed.

commit 88966c87d9b579987d635f8a131abc50ff2b2afe
Author: Andreas Tille 
Date:   Fri Sep 15 11:54:18 2017 +0200

Standards-Version: 4.1.0
---
 debian/changelog | 1 +
 debian/control   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 090bc18..a8d9ee0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,7 @@ pixelmed (20150917-2) UNRELEASED; urgency=medium
   * Do not set bootclasspath
 Closes: #874150
   * debhelper 10
+  * Standards-Version: 4.1.0
 
  -- Andreas Tille   Fri, 15 Sep 2017 11:15:57 +0200
 
diff --git a/debian/control b/debian/control
index 9c0b3cc..108d096 100644
--- a/debian/control
+++ b/debian/control
@@ -15,7 +15,7 @@ Build-Depends-Indep: default-jdk,
  libvecmath-java,
  libpixelmed-codec-java,
  libjsonp-java
-Standards-Version: 3.9.8
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pixelmed.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/pixelmed.git
 Homepage: http://www.pixelmed.com

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[med-svn] [pixelmed] annotated tag upstream/20150917+dfsg created (now ec2c0ad)

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at  ec2c0ad   (tag)
   tagging  81e9a7ceaff953a19e6cb801545c769a21342256 (commit)
  replaces  upstream/20150917
 tagged by  Andreas Tille
on  Fri Sep 15 12:57:56 2017 +0200

- Log -
Upstream version 20150917+dfsg

Andreas Tille (1):
  New upstream version 20150917+dfsg

---

This annotated tag includes the following new commits:

   new  81e9a7c   New upstream version 20150917+dfsg

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listed as "adds" were already present in the repository and have only
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[med-svn] [gmap] tag debian/2017-09-11-1 created (now 97539d2)

[Alex Mestiashvili]

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malex-guest pushed a change to tag debian/2017-09-11-1
in repository gmap.

at  97539d2   (commit)
No new revisions were added by this update.

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[med-svn] [pixelmed] 12/12: Upload to unstable

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository pixelmed.

commit 7d1b74612b664ff77e0c1f7e56bc8c42a4bddf89
Author: Andreas Tille 
Date:   Fri Sep 15 13:18:51 2017 +0200

Upload to unstable
---
 debian/changelog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index fc395f8..f2bb7a6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-pixelmed (20150917+dfsg-1) UNRELEASED; urgency=medium
+pixelmed (20150917+dfsg-1) unstable; urgency=medium
 
   [ Mathieu Malaterre ]
   * Remove self from Uploaders
@@ -14,7 +14,7 @@ pixelmed (20150917+dfsg-1) UNRELEASED; urgency=medium
   * Fix DEP5 issues, update
   * Remove Encoding key from debian/*.desktop files
 
- -- Andreas Tille   Fri, 15 Sep 2017 11:15:57 +0200
+ -- Andreas Tille   Fri, 15 Sep 2017 13:07:31 +0200
 
 pixelmed (20150917-1) unstable; urgency=medium
 

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[med-svn] [pixelmed] 04/12: Remove unsafe symlink by repackaging tarball

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository pixelmed.

commit 2ada79f5bdb91da729e7c770421ca79ac5726243
Author: Andreas Tille 
Date:   Fri Sep 15 12:57:14 2017 +0200

Remove unsafe symlink by repackaging tarball
---
 debian/changelog | 2 +-
 debian/copyright | 1 +
 debian/watch | 6 --
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a8d9ee0..831009e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-pixelmed (20150917-2) UNRELEASED; urgency=medium
+pixelmed (20150917+dfsg-1) UNRELEASED; urgency=medium
 
   [ Mathieu Malaterre ]
   * Remove self from Uploaders
diff --git a/debian/copyright b/debian/copyright
index 8c04bbd..f9c4d4b 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,6 +2,7 @@ Format: 
http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PixelMed Java DICOM Toolkit
 Upstream-Contact: pixelmed_di...@yahoogroups.com
 Source: http://www.pixelmed.com/
+Files-Excluded: com/pixelmed/display/testmammohome
 
 Files: *
 Copyright: 2001-2008, David A. Clunie DBA PixelMed Publishing. All rights 
reserved.
diff --git a/debian/watch b/debian/watch
index 035b758..17d1f8e 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,4 @@
-version=3
-http://www.dclunie.com/pixelmed/software/([b\d]+)_current/pixelmedjavadicom_sourcerelease.([\d]+).tar.bz2
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+   
http://www.dclunie.com/pixelmed/software/([b\d]+)_current/pixelmedjavadicom_sourcerelease.([\d]+).tar.bz2

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[med-svn] [pixelmed] branch master updated (b8d224f -> 7d1b746)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository pixelmed.

  from  b8d224f   Move packaging from SVN to Git
   new  72892d5   Do not set bootclasspath
   new  9cb3e3f   debhelper 10
   new  88966c8   Standards-Version: 4.1.0
   new  2ada79f   Remove unsafe symlink by repackaging tarball
   new  81e9a7c   New upstream version 20150917+dfsg
   new  2bef9be   Merge tag 'upstream/20150917+dfsg'
   new  9a24b09   Drop fixme
   new  2dd224b   DEP3
   new  32d9084   do not parse d/changelog
   new  490f433   Fix DEP5 issues, update
   new  0c6af70   Remove Encoding key from debian/*.desktop files
   new  7d1b746   Upload to unstable

The 12 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:
 com/pixelmed/display/testmammohome |  1 -
 debian/ConvertAmicasJPEG2000FilesetToDicom.desktop |  1 -
 debian/DicomCleaner.desktop|  1 -
 debian/DicomImageBlackout.desktop  |  1 -
 debian/DicomImageViewer.desktop|  1 -
 debian/DoseUtility.desktop |  1 -
 debian/MediaImporter.desktop   |  1 -
 debian/WatchFolderAndSend.desktop  |  1 -
 debian/changelog   | 14 +++---
 debian/compat  |  2 +-
 debian/control |  4 ++--
 debian/copyright   | 18 +++---
 debian/patches/do_not_set_bootclasspath.patch  | 16 
 debian/patches/imageio.patch   |  4 
 debian/patches/series  |  1 +
 debian/patches/set_java_home.patch |  4 
 debian/rules   |  7 +++
 debian/watch   |  6 --
 18 files changed, 57 insertions(+), 27 deletions(-)
 delete mode 12 com/pixelmed/display/testmammohome
 create mode 100644 debian/patches/do_not_set_bootclasspath.patch

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[med-svn] [pixelmed] branch pristine-tar updated (3af01e7 -> 9ea2f3f)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch pristine-tar
in repository pixelmed.

  from  3af01e7   pristine-tar data for pixelmed_20150917.orig.tar.bz2
   new  9ea2f3f   pristine-tar data for pixelmed_20150917+dfsg.orig.tar.bz2

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:
 pixelmed_20150917+dfsg.orig.tar.bz2.delta | Bin 0 -> 2 bytes
 pixelmed_20150917+dfsg.orig.tar.bz2.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 pixelmed_20150917+dfsg.orig.tar.bz2.delta
 create mode 100644 pixelmed_20150917+dfsg.orig.tar.bz2.id

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[med-svn] r24046 - trunk/packages/pixelmed/trunk

[Andreas Tille]

Author: tille
Date: 2017-09-15 10:01:30 + (Fri, 15 Sep 2017)
New Revision: 24046

Added:
   trunk/packages/pixelmed/trunk/README.status
Removed:
   trunk/packages/pixelmed/trunk/debian/
Log:
Document move to Git


Added: trunk/packages/pixelmed/trunk/README.status
===
--- trunk/packages/pixelmed/trunk/README.status (rev 0)
+++ trunk/packages/pixelmed/trunk/README.status 2017-09-15 10:01:30 UTC (rev 
24046)
@@ -0,0 +1,7 @@
+---
+Format: 1
+Status: git
+SVNDeleteRevision: 24045
+URL: https://git.debian.org/git/debian-med/pixelmed.git
+Comment: >
+  This package is now managed in a Git repository.


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[med-svn] [pixelmed] branch pristine-tar created (now 3af01e7)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch pristine-tar
in repository pixelmed.

at  3af01e7   pristine-tar data for pixelmed_20150917.orig.tar.bz2

This branch includes the following new commits:

   new  3af01e7   pristine-tar data for pixelmed_20150917.orig.tar.bz2

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.


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[med-svn] [pixelmed] branch master created (now b8d224f)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository pixelmed.

at  b8d224f   Move packaging from SVN to Git

This branch includes the following new commits:

   new  74fa6d8   fix layout
   new  78a62d9   first package
   new  fe33645   s/Debian-Med/Debian Med/
   new  9481d18   add crypto stuff from bouncycastle
   new  e6f96e9   Bump up version + start using libjmdns now that it is in 
unstable
   new  95b2ea9   vecmath1.2 has been removed from testing... switch to 
vecmath1.5
   new  14638a1   fix copyright, fix lintian
   new  78ea9c2   add the DicomImageViewer and ECGViewer
   new  a809bac   install properties files in /etc/pixelmed now
   new  8710ebb   lintian fixes
   new  57efb4b   Do not use HOME dir
   new  f415221   Use newer libvecmath
   new  55ac7e5   Adding the jnlp example
   new  34dd511   Install icons + fix date
   new  21e9dc3   macos-resource-fork-file-in-package lintian
   new  07d580d   Do not install the jnlp for now
   new  ca125b0   add man pages
   new  33ae01a   Build-Depends-Indep; enhanced description
   new  2c19436   Get rid of binary data and broken link from the source 
tarball
   new  9c40082   remove more data files
   new  0a235f9   Hopefully fix compilation issue
   new  e611940   Update to 20100217
   new  9261b36   preparation for new upload
   new  c70693f   working toward next release
   new  ba3eb9b   add DoseUtility
   new  24d8302   need java-wrappers now
   new  cf1ac28   Update lintian
   new  4d81a5f   Prepare for new upstream. Use quilt to refresh patches.
   new  b717b47   Missing changes
   new  e25801e   Missing Build-Dep.
   new  4394fe0   Update Std Version.
   new  ac81367   Make sure GZIP has option --best and --no-name
   new  123800e   Prepare new release
   new  a7edd71   Fix comp error
   new  2a257de   fix parent class
   new  3a5db51   Fix some more issues
   new  13a3d7e   New patch
   new  968afa7   remove for now
   new  ae4f614   Use new libcommons
   new  05fe73a   Fix lintian error. Fix compilation with newer jmdns API
   new  5ee8c92   Document force to JmDNS 3.4
   new  7a794df   Remove svn prop for viewvc
   new  9ddcd0e   switch to dh 8
   new  9c56349   missing etc file
   new  b189eb1   final touch
   new  0e4a8f0   add tests
   new  478089e   Remove some tests
   new  8196aec   refresh patch
   new  f80197a   prepare for next upload
   new  9349de0   prepare next upload
   new  562f784   remove testnetwork
   new  74d6de8   prepare next upload
   new  d48f8f0   Some cleanup
   new  cc4c675   refresh patches
   new  9fb20f5   Prepare next upstream
   new  3b42111   Some cleanups
   new  44aef4f   Fix fonts issues
   new  23aa2b1   Add info
   new  f381fd0   Prepare next upload
   new  2161b17   upload 20120405
   new  b223ace   Update patch
   new  e01e7d3   uploaded 20120508
   new  0b4979a   Update README
   new  aa14d77   Prepare next upload
   new  c8e1bed   Target java 1.7
   new  4922484   Prepare next upload
   new  269c500   Forgot patch
   new  4fceb05   Fix doc generation
   new  69d0b9d   Remove issue with XSLT
   new  800d579   Simply d/rules
   new  e7207de   Upload JNLP apps
   new  a9ccd51   Missing install rules
   new  187740b   Generates .desktop from JNLP input
   new  5f2e03d   Add script generation
   new  d3f6624   Add version number
   new  502b8bd   Rework pixelmed package
   new  87a73e0   Prepare new upload of pixelmed
   new  6162acc   Fix javadoc execution + add xz compression
   new  5ba7db7   Add StructuredReport dumper
   new  9ec9c0a   Prepare new upload
   new  2c5913d   Rework patches
   new  7a81d33   Add man pages
   new  03e1b34   import diff
   new  8e2044b   prepare next upload
   new  201d0c8   really depends on it
   new  aeb5142   remove test
   new  9c9a277   remove test
   new  50a1cb7   new upstream
   new  5626b7b   fix build
   new  1ece71a   new upload
   new  0946111   New upstream version, added myself to uploaders
   new  8b628a8   cme fix dpkg-control
   new  3071f8c   Refresh some patches
   new  30cab7c   Refresh more patches
   new  84e7253   Refresh more patches
   new  b8c4a46   Add Build-Depends: libcommons-compress-java
   new  2339183   Try to build latest version but failed
   new  60603df   Build-Depends: libpixelmed-codec-java
   new  7379f78   Get the code build but 4 tests are failing
   new  83d7e7d   Ignore failing build time tests to finally get this 
package updated - I wonder whether somebody else might care better for this 
orphaned package
   new  b74b669   Remove self from Uploaders
  

[med-svn] [pixelmed] 01/01: pristine-tar data for pixelmed_20150917.orig.tar.bz2

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch pristine-tar
in repository pixelmed.

commit 3af01e7c36f5cef04d1f875fe7339a79af1d26f1
Author: Andreas Tille 
Date:   Fri Sep 15 11:12:47 2017 +0200

pristine-tar data for pixelmed_20150917.orig.tar.bz2
---
 pixelmed_20150917.orig.tar.bz2.delta | Bin 0 -> 27883 bytes
 pixelmed_20150917.orig.tar.bz2.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/pixelmed_20150917.orig.tar.bz2.delta 
b/pixelmed_20150917.orig.tar.bz2.delta
new file mode 100644
index 000..32855ec
Binary files /dev/null and b/pixelmed_20150917.orig.tar.bz2.delta differ
diff --git a/pixelmed_20150917.orig.tar.bz2.id 
b/pixelmed_20150917.orig.tar.bz2.id
new file mode 100644
index 000..5b05312
--- /dev/null
+++ b/pixelmed_20150917.orig.tar.bz2.id
@@ -0,0 +1 @@
+be1762046ae98cfa7127bf77a2fd9e37b87952cb

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[med-svn] [pixelmed] branch upstream created (now 28d19b1)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository pixelmed.

at  28d19b1   New upstream version 20150917

No new revisions were added by this update.

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[med-svn] [fast5] branch master updated (0fb2b16 -> c66dbbd)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch master
in repository fast5.

  from  0fb2b16   Prepare new revision
   new  c66dbbd   Added references to registries.

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 | 3 +++
 debian/upstream/metadata | 7 +++
 2 files changed, 10 insertions(+)
 create mode 100644 debian/upstream/metadata

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[med-svn] [fast5] 01/01: Added references to registries.

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository fast5.

commit c66dbbdaa6b31a42d993da705bf9b10b0768e6e0
Author: Steffen Moeller 
Date:   Fri Sep 15 13:44:24 2017 +0200

Added references to registries.
---
 debian/changelog | 3 +++
 debian/upstream/metadata | 7 +++
 2 files changed, 10 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index c4f872e..b35768f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,9 @@ fast5 (0.5.9-1) UNRELEASED; urgency=medium
   * Imported Upstream version 0.5.9
   * Update patches
 
+  * d/debian/upstream/metadata: References to registries
+(Steffen Moeller)
+
  -- Afif Elghraoui   Thu, 29 Dec 2016 00:43:11 -0800
 
 fast5 (0.5.8-1) unstable; urgency=medium
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 000..9100d71
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Registry:
+ - Name: bio.tools
+   Entry: NA
+ - Name: OMICtools
+   Entry: NA
+ - Name: RRID
+   Entry: NA

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[med-svn] [fast5] 03/03: Getting 0.6.2 to build binaries.

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository fast5.

commit c435e524abee308b93415681c215c74a586af289
Author: Steffen Moeller 
Date:   Fri Sep 15 14:17:53 2017 +0200

Getting 0.6.2 to build binaries.
---
 debian/changelog | 14 ++
 debian/patches/functional.patch  | 12 
 debian/patches/hdf5include.patch | 13 +
 debian/patches/rpath.patch   | 22 +++---
 debian/patches/series|  6 --
 debian/rules |  2 ++
 6 files changed, 56 insertions(+), 13 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index b35768f..4a34d20 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,17 @@
+fast5 (0.6.2-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version.
+  * Updated policy to 4.1.0 (no changes reguired)
+  * Patches
+- Uncommented two older patches that do not seem to fit current
+  build structure
+- Added patch for gcc-7 compatibility
+- Added patch to adjusted include path for hdf5.h
+  * ./debian/rules binary works, still trouble with generated files
+
+ -- Steffen Moeller   Fri, 15 Sep 2017 13:46:49 +0200
+
 fast5 (0.5.9-1) UNRELEASED; urgency=medium
 
   * Imported Upstream version 0.5.9
diff --git a/debian/patches/functional.patch b/debian/patches/functional.patch
new file mode 100644
index 000..bca2b63
--- /dev/null
+++ b/debian/patches/functional.patch
@@ -0,0 +1,12 @@
+Index: fast5/src/logger.hpp
+===
+--- fast5.orig/src/logger.hpp
 fast5/src/logger.hpp
+@@ -72,6 +72,7 @@
+ #include 
+ #include 
+ #include 
++#include 
+ 
+ namespace logger
+ {
diff --git a/debian/patches/hdf5include.patch b/debian/patches/hdf5include.patch
new file mode 100644
index 000..6dd31ea
--- /dev/null
+++ b/debian/patches/hdf5include.patch
@@ -0,0 +1,13 @@
+Index: fast5/src/hdf5_tools.hpp
+===
+--- fast5.orig/src/hdf5_tools.hpp
 fast5/src/hdf5_tools.hpp
+@@ -27,7 +27,7 @@
+ 
+ namespace hdf5
+ {
+-#include 
++#include 
+ }
+ 
+ namespace hdf5_tools
diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch
index 94fe9e7..0bd2438 100644
--- a/debian/patches/rpath.patch
+++ b/debian/patches/rpath.patch
@@ -2,16 +2,16 @@ Description: Don't set RPATH for compiled Python extensions
 Author: Afif Elghraoui 
 Forwarded: not-needed
 Last-Update: 2016-10-20
+Index: fast5/python/setup.py
+===
 --- fast5.orig/python/setup.py
 +++ fast5/python/setup.py
-@@ -69,10 +69,6 @@
- hdf5_lib_dir,
- boost_lib_dir,
- ],
--runtime_library_dirs=[
--hdf5_lib_dir,
--boost_lib_dir,
--],
- libraries=[
- hdf5_lib,
- boost_python_lib,
+@@ -53,7 +53,7 @@ extensions = [
+ sources=['fast5/fast5.' + ['cpp', 'pyx'][use_cython]],
+ include_dirs=[fast5_src_dir],
+ library_dirs=[hdf5_lib_dir],
+-runtime_library_dirs=[hdf5_lib_dir],
++#runtime_library_dirs=[hdf5_lib_dir],
+ libraries=[hdf5_lib],
+ extra_compile_args=extra_compile_args,
+ extra_link_args=extra_link_args,
diff --git a/debian/patches/series b/debian/patches/series
index 7dc224e..2f38c1c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,5 @@
-relative-paths.patch
-examples.patch
+#relative-paths.patch
+#examples.patch
 rpath.patch
+functional.patch
+hdf5include.patch
diff --git a/debian/rules b/debian/rules
index f8f630d..e517f10 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,6 +10,8 @@ export HDF5_INCLUDE_DIR=/usr/include/hdf5/serial
 export HDF5_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
 export BOOST_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH)
 
+export CXXFLAGS += -std=c++11
+
 %:
dh $@ --with python2,python3 --buildsystem=pybuild \
--sourcedirectory=python

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[med-svn] [fast5] branch master updated (c66dbbd -> c435e52)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch master
in repository fast5.

  from  c66dbbd   Added references to registries.
   new  1a33a45   New upstream version 0.6.2
   new  0276783   Updated version 0.6.2 from 'upstream/0.6.2'
   new  c435e52   Getting 0.6.2 to build binaries.

The 3 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:
 .travis.Dockerfile.in |   17 +-
 .travis.yml   |2 +-
 .version_files|2 +-
 README.org|   91 +-
 VERSION   |2 +-
 debian/changelog  |   14 +
 debian/patches/functional.patch   |   12 +
 debian/patches/hdf5include.patch  |   13 +
 debian/patches/rpath.patch|   22 +-
 debian/patches/series |6 +-
 debian/rules  |2 +
 python/.gitignore |1 +
 python/Makefile   |   20 +-
 python/bin/f5ls   |  249 
 python/bin/f5pack |  240 
 python/fast5/.version.py.in   |1 -
 python/fast5/__init__.py  |   10 -
 python/fast5/fast5.pyx|  523 +++
 python/fast5/source/fast5.cpp |  182 ---
 python/fast5/version.py   |1 -
 python/setup.py   |   86 +-
 src/.fast5_version.hpp.in |   16 +
 src/.gitignore|1 +
 src/Bit_Packer.hpp|  152 ++
 src/File_Packer.hpp   |  982 +
 src/Huffman_Packer.hpp|  357 +
 src/Makefile  |   42 +-
 src/cwmap.fast5_ed_len_1.inl  |  103 ++
 src/cwmap.fast5_ed_skip_1.inl |4 +
 src/cwmap.fast5_ev_move_1.inl |6 +
 src/cwmap.fast5_ev_rel_skip_1.inl |4 +
 src/cwmap.fast5_fq_bp_1.inl   |7 +
 src/cwmap.fast5_fq_qv_1.inl   |   35 +
 src/cwmap.fast5_rw_1.inl  |  204 +++
 src/f5-mod.cpp|   14 +-
 src/f5dump.cpp|   96 +-
 src/f5ls-full.cpp |   35 +-
 src/f5ls.cpp  |   17 +-
 src/f5pack.cpp|  185 +++
 src/fast5.hpp | 2788 -
 src/fast5_version.hpp |   16 +
 src/hdf5-mod.cpp  |   12 +
 src/hdf5_tools.hpp|  316 -
 src/huffman-decode.cpp|   55 +
 src/huffman-encode.cpp|   44 +
 src/hufftk|  171 +++
 src/logger.hpp|  378 +
 src/tmp.cpp   |7 +
 48 files changed, 6396 insertions(+), 1147 deletions(-)
 create mode 100644 debian/patches/functional.patch
 create mode 100644 debian/patches/hdf5include.patch
 create mode 100755 python/bin/f5ls
 create mode 100755 python/bin/f5pack
 delete mode 100644 python/fast5/.version.py.in
 delete mode 100755 python/fast5/__init__.py
 create mode 100644 python/fast5/fast5.pyx
 delete mode 100644 python/fast5/source/fast5.cpp
 delete mode 100644 python/fast5/version.py
 mode change 100644 => 100755 python/setup.py
 create mode 100644 src/.fast5_version.hpp.in
 create mode 100644 src/Bit_Packer.hpp
 create mode 100644 src/File_Packer.hpp
 create mode 100644 src/Huffman_Packer.hpp
 create mode 100644 src/cwmap.fast5_ed_len_1.inl
 create mode 100644 src/cwmap.fast5_ed_skip_1.inl
 create mode 100644 src/cwmap.fast5_ev_move_1.inl
 create mode 100644 src/cwmap.fast5_ev_rel_skip_1.inl
 create mode 100644 src/cwmap.fast5_fq_bp_1.inl
 create mode 100644 src/cwmap.fast5_fq_qv_1.inl
 create mode 100644 src/cwmap.fast5_rw_1.inl
 create mode 100644 src/f5pack.cpp
 create mode 100644 src/fast5_version.hpp
 create mode 100644 src/huffman-decode.cpp
 create mode 100644 src/huffman-encode.cpp
 create mode 100755 src/hufftk
 create mode 100644 src/logger.hpp

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[med-svn] [fast5] 02/03: Updated version 0.6.2 from 'upstream/0.6.2'

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository fast5.

commit 0276783d87d3604f16d4da5f6634e6f4133311e7
Merge: c66dbbd 1a33a45
Author: Steffen Moeller 
Date:   Fri Sep 15 13:45:51 2017 +0200

Updated version 0.6.2 from 'upstream/0.6.2'

with Debian dir 62dcca775a6723e6136d38caace9e6ecd5f64209

 .travis.Dockerfile.in |   17 +-
 .travis.yml   |2 +-
 .version_files|2 +-
 README.org|   91 +-
 VERSION   |2 +-
 python/.gitignore |1 +
 python/Makefile   |   20 +-
 python/bin/f5ls   |  249 
 python/bin/f5pack |  240 
 python/fast5/.version.py.in   |1 -
 python/fast5/__init__.py  |   10 -
 python/fast5/fast5.pyx|  523 +++
 python/fast5/source/fast5.cpp |  182 ---
 python/fast5/version.py   |1 -
 python/setup.py   |   86 +-
 src/.fast5_version.hpp.in |   16 +
 src/.gitignore|1 +
 src/Bit_Packer.hpp|  152 ++
 src/File_Packer.hpp   |  982 +
 src/Huffman_Packer.hpp|  357 +
 src/Makefile  |   42 +-
 src/cwmap.fast5_ed_len_1.inl  |  103 ++
 src/cwmap.fast5_ed_skip_1.inl |4 +
 src/cwmap.fast5_ev_move_1.inl |6 +
 src/cwmap.fast5_ev_rel_skip_1.inl |4 +
 src/cwmap.fast5_fq_bp_1.inl   |7 +
 src/cwmap.fast5_fq_qv_1.inl   |   35 +
 src/cwmap.fast5_rw_1.inl  |  204 +++
 src/f5-mod.cpp|   14 +-
 src/f5dump.cpp|   96 +-
 src/f5ls-full.cpp |   35 +-
 src/f5ls.cpp  |   17 +-
 src/f5pack.cpp|  185 +++
 src/fast5.hpp | 2788 -
 src/fast5_version.hpp |   16 +
 src/hdf5-mod.cpp  |   12 +
 src/hdf5_tools.hpp|  316 -
 src/huffman-decode.cpp|   55 +
 src/huffman-encode.cpp|   44 +
 src/hufftk|  171 +++
 src/logger.hpp|  378 +
 src/tmp.cpp   |7 +
 42 files changed, 6340 insertions(+), 1134 deletions(-)

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[med-svn] [invesalius] 01/01: d/p/20: Fix import of dicom serie with one unique slice, Closes: #779655

[Thiago Franco Moraes]

This is an automated email from the git hooks/post-receive script.

tfmoraes-guest pushed a commit to branch master
in repository invesalius.

commit 3903e7f8c298943bb0cf3dc62f5417ce4f1c4933
Author: Thiago Franco de Moraes 
Date:   Fri Sep 15 10:47:34 2017 -0300

d/p/20: Fix import of dicom serie with one unique slice, Closes: #779655
---
 debian/patches/20_fix_one_slice_import.patch | 84 
 debian/patches/series|  2 +-
 2 files changed, 85 insertions(+), 1 deletion(-)

diff --git a/debian/patches/20_fix_one_slice_import.patch 
b/debian/patches/20_fix_one_slice_import.patch
new file mode 100644
index 000..08b231e
--- /dev/null
+++ b/debian/patches/20_fix_one_slice_import.patch
@@ -0,0 +1,84 @@
+Description: Fix import of dicom serie with one unique slice.
+Author: Thiago Franco de Moraes 
+Debian-Bug: https://bugs.debian.org/779655
+
+--- a/invesalius/control.py
 b/invesalius/control.py
+@@ -408,6 +408,10 @@ class Controller():
+ 
+ def OnLoadImportPanel(self, evt):
+ patient_series = evt.data
++if self.progress_dialog:
++self.progress_dialog.Close()
++self.progress_dialog = None
++
+ ok = self.LoadImportPanel(patient_series)
+ if ok:
+ Publisher.sendMessage('Show import panel')
+--- a/invesalius/data/imagedata_utils.py
 b/invesalius/data/imagedata_utils.py
+@@ -523,7 +523,8 @@ def dcm2memmap(files, slice_size, orientation, 
resolution_percentage):
+ returns it and its related filename.
+ """
+ message = _("Generating multiplanar visualization...")
+-update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = 
"ProgressDialog")
++if len(files) > 1:
++update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = 
"ProgressDialog")
+ 
+ temp_file = tempfile.mktemp()
+ 
+@@ -584,7 +585,8 @@ def dcm2memmap(files, slice_size, orientation, 
resolution_percentage):
+ else:
+ array.shape = matrix.shape[1], matrix.shape[2]
+ matrix[n] = array
+-update_progress(cont,message)
++if len(files) > 1:
++update_progress(cont,message)
+ cont += 1
+ 
+ matrix.flush()
+--- a/invesalius/data/slice_.py
 b/invesalius/data/slice_.py
+@@ -633,7 +633,7 @@ class Slice(object):
+ if np.any(self.q_orientation[1::]):
+ transforms.apply_view_matrix_transform(self.matrix, 
self.spacing, M, slice_number, orientation, self.interp_method, 
self.matrix.min(), tmp_array)
+ if self._type_projection == const.PROJECTION_NORMAL:
+-n_image = tmp_array.squeeze()
++n_image = tmp_array[0]
+ else:
+ if inverted:
+ tmp_array = tmp_array[::-1]
+@@ -681,7 +681,7 @@ class Slice(object):
+ transforms.apply_view_matrix_transform(self.matrix, 
self.spacing, M, slice_number, orientation, self.interp_method, 
self.matrix.min(), tmp_array)
+ 
+ if self._type_projection == const.PROJECTION_NORMAL:
+-n_image = tmp_array.squeeze()
++n_image = tmp_array[:, 0, :]
+ else:
+ #if slice_number == 0:
+ #slice_number = 1
+@@ -731,7 +731,7 @@ class Slice(object):
+ transforms.apply_view_matrix_transform(self.matrix, 
self.spacing, M, slice_number, orientation, self.interp_method, 
self.matrix.min(), tmp_array)
+ 
+ if self._type_projection == const.PROJECTION_NORMAL:
+-n_image = tmp_array.squeeze()
++n_image = tmp_array[:, :, 0]
+ else:
+ if inverted:
+ tmp_array = tmp_array[:, :, ::-1]
+--- a/invesalius/gui/import_panel.py
 b/invesalius/gui/import_panel.py
+@@ -186,11 +186,8 @@ class InnerPanel(wx.Panel):
+ slice_amont = group.nslices
+ 
+ nslices_result = slice_amont / (interval + 1)
+-if (nslices_result > 1):
+-Publisher.sendMessage('Open DICOM group', (group, interval, 
+-[self.first_image_selection, 
self.last_image_selection]))
+-else:
+-dlg.MissingFilesForReconstruction()
++Publisher.sendMessage('Open DICOM group', (group, interval, 
++[self.first_image_selection, 
self.last_image_selection]))
+ 
+ class TextPanel(wx.Panel):
+ def __init__(self, parent):
diff --git a/debian/patches/series b/debian/patches/series
index 9ea65a7..d36421d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
 10_sample_path.patch
 10_import_cython_modules.patch
-20_fix_division_by_zero.patch
+20_fix_one_slice_import.patch

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[med-svn] [invesalius] branch master updated (acc76ac -> 3903e7f)

[Thiago Franco Moraes]

This is an automated email from the git hooks/post-receive script.

tfmoraes-guest pushed a change to branch master
in repository invesalius.

  from  acc76ac   Standards-Version: 4.1.0, upload to unstable
   new  3903e7f   d/p/20: Fix import of dicom serie with one unique slice, 
Closes: #779655

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/patches/20_fix_one_slice_import.patch | 84 
 debian/patches/series|  2 +-
 2 files changed, 85 insertions(+), 1 deletion(-)
 create mode 100644 debian/patches/20_fix_one_slice_import.patch

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[med-svn] [fast5] branch upstream updated (d798d48 -> 1a33a45)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch upstream
in repository fast5.

  from  d798d48   Imported Upstream version 0.5.9
  adds  1a33a45   New upstream version 0.6.2

No new revisions were added by this update.

Summary of changes:
 .travis.Dockerfile.in |   17 +-
 .travis.yml   |2 +-
 .version_files|2 +-
 README.org|   91 +-
 VERSION   |2 +-
 python/.gitignore |1 +
 python/Makefile   |   20 +-
 python/bin/f5ls   |  249 
 python/bin/f5pack |  240 
 python/fast5/.version.py.in   |1 -
 python/fast5/__init__.py  |   10 -
 python/fast5/fast5.pyx|  523 +++
 python/fast5/source/fast5.cpp |  182 ---
 python/fast5/version.py   |1 -
 python/setup.py   |   86 +-
 src/.fast5_version.hpp.in |   16 +
 src/.gitignore|1 +
 src/Bit_Packer.hpp|  152 ++
 src/File_Packer.hpp   |  982 +
 src/Huffman_Packer.hpp|  357 +
 src/Makefile  |   42 +-
 src/cwmap.fast5_ed_len_1.inl  |  103 ++
 src/cwmap.fast5_ed_skip_1.inl |4 +
 src/cwmap.fast5_ev_move_1.inl |6 +
 src/cwmap.fast5_ev_rel_skip_1.inl |4 +
 src/cwmap.fast5_fq_bp_1.inl   |7 +
 src/cwmap.fast5_fq_qv_1.inl   |   35 +
 src/cwmap.fast5_rw_1.inl  |  204 +++
 src/f5-mod.cpp|   14 +-
 src/f5dump.cpp|   96 +-
 src/f5ls-full.cpp |   35 +-
 src/f5ls.cpp  |   17 +-
 src/f5pack.cpp|  185 +++
 src/fast5.hpp | 2788 -
 src/fast5_version.hpp |   16 +
 src/hdf5-mod.cpp  |   12 +
 src/hdf5_tools.hpp|  316 -
 src/huffman-decode.cpp|   55 +
 src/huffman-encode.cpp|   44 +
 src/hufftk|  171 +++
 src/logger.hpp|  378 +
 src/tmp.cpp   |7 +
 42 files changed, 6340 insertions(+), 1134 deletions(-)
 create mode 100755 python/bin/f5ls
 create mode 100755 python/bin/f5pack
 delete mode 100644 python/fast5/.version.py.in
 delete mode 100755 python/fast5/__init__.py
 create mode 100644 python/fast5/fast5.pyx
 delete mode 100644 python/fast5/source/fast5.cpp
 delete mode 100644 python/fast5/version.py
 mode change 100644 => 100755 python/setup.py
 create mode 100644 src/.fast5_version.hpp.in
 create mode 100644 src/Bit_Packer.hpp
 create mode 100644 src/File_Packer.hpp
 create mode 100644 src/Huffman_Packer.hpp
 create mode 100644 src/cwmap.fast5_ed_len_1.inl
 create mode 100644 src/cwmap.fast5_ed_skip_1.inl
 create mode 100644 src/cwmap.fast5_ev_move_1.inl
 create mode 100644 src/cwmap.fast5_ev_rel_skip_1.inl
 create mode 100644 src/cwmap.fast5_fq_bp_1.inl
 create mode 100644 src/cwmap.fast5_fq_qv_1.inl
 create mode 100644 src/cwmap.fast5_rw_1.inl
 create mode 100644 src/f5pack.cpp
 create mode 100644 src/fast5_version.hpp
 create mode 100644 src/huffman-decode.cpp
 create mode 100644 src/huffman-encode.cpp
 create mode 100755 src/hufftk
 create mode 100644 src/logger.hpp

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[med-svn] [rdp-classifier] branch upstream created (now e64f251)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository rdp-classifier.

at  e64f251   New upstream version 2.10.2

No new revisions were added by this update.

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[med-svn] [rdp-classifier] branch pristine-tar created (now c15ac82)

[Andreas Tille]

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tille pushed a change to branch pristine-tar
in repository rdp-classifier.

at  c15ac82   pristine-tar data for rdp-classifier_2.10.2.orig.tar.gz

This branch includes the following new commits:

   new  c15ac82   pristine-tar data for rdp-classifier_2.10.2.orig.tar.gz

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[med-svn] [rdp-classifier] branch master created (now c425480)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository rdp-classifier.

at  c425480   Move packaging from SVN to Git

This branch includes the following new commits:

   new  562f85a   Package looks good, needs some more love. It is one of 
those packages that may help qiime in some way.
   new  652952f   Fix Vcs fields globally in all remaining packages because 
I'm bored by warnings in logfiles when investigating machine readable files of 
not yet uploaded packages
   new  7389381   This package is not (just now) fully OSS, but I'm working 
on it in the hope that it will be.  Bringing build up-to-date for 2.5.
   new  7ce8d80   I think this is everything I need to get it working 
properly.
   new  0540a72   Please use "dfsg" (rather than "repack" or something 
else) to normalise repackaged version strings; moreover use -0ubuntuX for 
something which is a "pre-Debian" release;  Watch file now regards dfsg version 
string
   new  5810b6c   Wrote get-orig-source target to make sure we are basing 
our work on the same source tarball.  If you do not like xz compression for 
whatever reason just set COMPRESSION=gz in debian/get-orig-source
   new  c84acf3   Forgot to add ~dfsg to version string
   new  45a0566   debian/files should not be kept in SVN
   new  a70bb65   Use explicit path ... just to be sure
   new  bb01aec   Fixed DEP5 issue; Fixed links; tested xz compression for 
binary with no amazing change, so leaved this as comment; debhelper 8 ... would 
prefer 9 but no idea whether this spoils any other plan
   new  b384af8   help2html-ed + polished manpage
   new  154cdc0   Enable +dfsg suffix
   new  9779e11   Add Files-Excluded to document what was removed from 
original source
   new  9c571d2   Do not end dirs to remove with '/' according to 
discussion on debian-devel
   new  ca2887d   This is a work in progress.  I'm committing now to save 
Andreas from repeating my work.  In particular I have working packages for the 
dependencies - librdp-readseq-java (>= 0.1.20140425),
librdp-alignment-java ( >= 0.1.20140606),
librdp-taxonomy-tree-java ( >= 0.1.20140606) But this all needs updating.  
Also, I'm not sure my fetcher script is really a good idea.
   new  303b849   Trivial update for new version Note that get-orig-source 
is totally hosed and I had to reconstruct the tarball manually.
   new  6751d5c   Make sure we will not forget that get-orig-source does 
not work currently
   new  719201c   I think debian/get-orig-source file can simply be removed 
since Files-Excluded should work
   new  873449b   Adapt d/control to Debian Med policy
   new  5dab5f2   Rework description according to homepage
   new  e07dae4   Adapted d/watch to point to github
   new  ec665a0   Update copyright
   new  4febd84   The current download of 2.10 is not extraordinarily large 
any more so there is no need to strip data from it.
   new  f680d6d   Seems the information given in README.source is not valid 
any more
   new  0f3176e   Clean up d/changelog from irrelevant entries of never 
released Debian versions, new upstream version, update d/copyright
   new  52becbf   Move script targeting to /usr/bin to debian/bin
   new  cfe67f0   There is no data dir to install in the source tarball any 
more
   new  87ea970   Remove duplicated entries from manpage
   new  7aef063   Citation data
   new  3a3d9ac   Additional hint in README.Debian
   new  aba9fc0   Upload to unstable (=new)
   new  aaab75c   Added missing license paragraph
   new  5bb9463   fix java 9 compilation
   new  e64f251   New upstream version 2.10.2
   new  0834ac3   Updated version 2.10.2 from 'upstream/2.10.2'
   new  c425480   Move packaging from SVN to Git

The 36 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
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[med-svn] [fast5] branch pristine-tar updated (113fb82 -> eafb888)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch pristine-tar
in repository fast5.

  from  113fb82   pristine-tar data for fast5_0.5.9.orig.tar.gz
   new  eafb888   pristine-tar data for fast5_0.6.2.orig.tar.gz

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:
 fast5_0.6.2.orig.tar.gz.delta | Bin 0 -> 2145 bytes
 fast5_0.6.2.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 fast5_0.6.2.orig.tar.gz.delta
 create mode 100644 fast5_0.6.2.orig.tar.gz.id

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[med-svn] [fast5] branch master updated (c435e52 -> 377c1fa)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch master
in repository fast5.

  from  c435e52   Getting 0.6.2 to build binaries.
   new  377c1fa   Fairly lintian-clean 0.6.2, just uploaded.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 debian/changelog  |  4 +++-
 debian/clean  |  2 ++
 debian/control| 29 -
 debian/python-fast5-bin.dirs  |  1 +
 debian/python3-fast5-bin.dirs |  1 +
 debian/rules  |  6 ++
 debian/source/options |  1 +
 7 files changed, 42 insertions(+), 2 deletions(-)
 create mode 100644 debian/clean
 create mode 100644 debian/python-fast5-bin.dirs
 create mode 100644 debian/python3-fast5-bin.dirs
 create mode 100644 debian/source/options

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[med-svn] [fast5] 01/01: Fairly lintian-clean 0.6.2, just uploaded.

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository fast5.

commit 377c1fa07f49b97e1fc54db1d96b081811eb95ba
Author: Steffen Moeller 
Date:   Fri Sep 15 17:27:35 2017 +0200

Fairly lintian-clean 0.6.2, just uploaded.
---
 debian/changelog  |  4 +++-
 debian/clean  |  2 ++
 debian/control| 29 -
 debian/python-fast5-bin.dirs  |  1 +
 debian/python3-fast5-bin.dirs |  1 +
 debian/rules  |  6 ++
 debian/source/options |  1 +
 7 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 4a34d20..ad6b400 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-fast5 (0.6.2-1) UNRELEASED; urgency=medium
+fast5 (0.6.2-1) unstable; urgency=medium
 
   * Team upload.
   * New upstream version.
@@ -9,6 +9,8 @@ fast5 (0.6.2-1) UNRELEASED; urgency=medium
 - Added patch for gcc-7 compatibility
 - Added patch to adjusted include path for hdf5.h
   * ./debian/rules binary works, still trouble with generated files
+  * Added separate packages for the binaries to avoid conflicts between
+the Python2 and Python3 versions of the same binaries.
 
  -- Steffen Moeller   Fri, 15 Sep 2017 13:46:49 +0200
 
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 000..d61d3a4
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,2 @@
+python/*.egg-info/*
+fast5/python/fast5/fast5.cpp
diff --git a/debian/control b/debian/control
index 1bbc454..eeac9d8 100644
--- a/debian/control
+++ b/debian/control
@@ -12,7 +12,7 @@ Build-Depends:
python-setuptools,
python3-all-dev,
python3-setuptools,
-Standards-Version: 3.9.8
+Standards-Version: 4.1.0
 Homepage: https://github.com/mateidavid/fast5
 Vcs-Git: https://anonscm.debian.org/git/debian-med/fast5.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fast5.git
@@ -42,8 +42,35 @@ Description: library for reading Oxford Nanopore Fast5 files 
-- Python 2
  .
  This package provides the Python 2 library
 
+Package: python-fast5-bin
+Conflicts: python3-fast5-bin
+Section: science
+Architecture: all
+Depends: python,
+   ${misc:Depends},
+   ${python:Depends},
+   python-fast5
+Description: executables of the Oxford Nanopore Fast5 library
+ The library ships two executables: f5ls and f5packk
+ .
+ This package only depends on Python 2.
+
+Package: python3-fast5-bin
+Conflicts: python-fast5-bin
+Section: science
+Architecture: all
+Depends: python3,
+   ${misc:Depends},
+   ${python:Depends},
+   python3-fast5
+Description: executables of the Oxford Nanopore Fast5 library
+ The library ships two executables: f5ls and f5packk
+ .
+ This package only depends on Python 3.
+
 Package: python3-fast5
 Section: python
+Conflicts: python-fast5
 Architecture: any
 Depends:
${shlibs:Depends},
diff --git a/debian/python-fast5-bin.dirs b/debian/python-fast5-bin.dirs
new file mode 100644
index 000..e772481
--- /dev/null
+++ b/debian/python-fast5-bin.dirs
@@ -0,0 +1 @@
+usr/bin
diff --git a/debian/python3-fast5-bin.dirs b/debian/python3-fast5-bin.dirs
new file mode 100644
index 000..e772481
--- /dev/null
+++ b/debian/python3-fast5-bin.dirs
@@ -0,0 +1 @@
+usr/bin
diff --git a/debian/rules b/debian/rules
index e517f10..7782b8d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -31,3 +31,9 @@ override_dh_auto_clean:
 
 override_dh_compress:
dh_compress -X .cpp
+
+override_dh_install:
+   dh_install
+   mv debian/python-fast5/usr/bin/* debian/python-fast5-bin/usr/bin/
+   mv debian/python3-fast5/usr/bin/* debian/python3-fast5-bin/usr/bin/
+   rm -rf debian/python-fast5/usr/bin/ debian/python3-fast5/usr/bin/
diff --git a/debian/source/options b/debian/source/options
new file mode 100644
index 000..aac7459
--- /dev/null
+++ b/debian/source/options
@@ -0,0 +1 @@
+extend-diff-ignore="^[^/]+\.egg-info/|python/fast5/fast5.cpp"

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[med-svn] [fast5] annotated tag upstream/0.6.2 created (now 0b9488d)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to annotated tag upstream/0.6.2
in repository fast5.

at  0b9488d   (tag)
   tagging  1a33a450a6cf3f504cc66a0a1fc6c8956df3cfa1 (commit)
  replaces  upstream/0.5.9
 tagged by  Steffen Moeller
on  Fri Sep 15 13:45:51 2017 +0200

- Log -
Upstream version 0.6.2

Steffen Moeller (1):
  New upstream version 0.6.2

---

No new revisions were added by this update.

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[med-svn] r24047 - in trunk/packages/rdp-classifier/trunk/debian: . bin patches

[Olivier Sallou]

Author: osallou
Date: 2017-09-15 15:28:08 + (Fri, 15 Sep 2017)
New Revision: 24047

Added:
   trunk/packages/rdp-classifier/trunk/debian/patches/
   
trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch
   trunk/packages/rdp-classifier/trunk/debian/patches/series
Modified:
   trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier
   trunk/packages/rdp-classifier/trunk/debian/changelog
   trunk/packages/rdp-classifier/trunk/debian/control
   trunk/packages/rdp-classifier/trunk/debian/junit.xml
   trunk/packages/rdp-classifier/trunk/debian/rules
Log:
fix java 9 compilation

Modified: trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier
===
--- trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier   
2017-09-15 10:01:30 UTC (rev 24046)
+++ trunk/packages/rdp-classifier/trunk/debian/bin/rdp_classifier   
2017-09-15 15:28:08 UTC (rev 24047)
@@ -14,4 +14,4 @@
 
 JAR=/usr/share/rdp-classifier/rdp_classifier.jar
 
-exec java -Xms512M -Xmx512M -jar "$JAR" "$@"
+exec java $JAVA_OPTS -Xms512M -Xmx512M -jar "$JAR" "$@"

Modified: trunk/packages/rdp-classifier/trunk/debian/changelog
===
--- trunk/packages/rdp-classifier/trunk/debian/changelog2017-09-15 
10:01:30 UTC (rev 24046)
+++ trunk/packages/rdp-classifier/trunk/debian/changelog2017-09-15 
15:28:08 UTC (rev 24047)
@@ -1,3 +1,11 @@
+rdp-classifier (2.10.2-2) UNRELEASED; urgency=medium
+
+  * d/control,d/junit.xml: fixes for Java 9 compilation (Closes #875789).
+  * debian/bin/rdp_classifier: add optional env variable JAVA_OPTS
+to java command line
+
+ -- Olivier Sallou   Fri, 15 Sep 2017 13:25:30 +
+
 rdp-classifier (2.10.2-1) unstable; urgency=medium
 
   * Initial upload to Debian (Closes: #790926)

Modified: trunk/packages/rdp-classifier/trunk/debian/control
===
--- trunk/packages/rdp-classifier/trunk/debian/control  2017-09-15 10:01:30 UTC 
(rev 24046)
+++ trunk/packages/rdp-classifier/trunk/debian/control  2017-09-15 15:28:08 UTC 
(rev 24047)
@@ -15,7 +15,8 @@
librdp-taxonomy-tree-java (>= 1.2.0),
libjfreechart-java,
ant,
-   ant-optional
+   ant-optional,
+   ant-contrib
 Standards-Version: 3.9.6
 Vcs-Browser: 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rdp-classifier/trunk/
 Vcs-Svn: 
svn://anonscm.debian.org/debian-med/trunk/packages/rdp-classifier/trunk/

Modified: trunk/packages/rdp-classifier/trunk/debian/junit.xml
===
--- trunk/packages/rdp-classifier/trunk/debian/junit.xml2017-09-15 
10:01:30 UTC (rev 24046)
+++ trunk/packages/rdp-classifier/trunk/debian/junit.xml2017-09-15 
15:28:08 UTC (rev 24047)
@@ -1,21 +1,44 @@
 
 
 
+
+
+
+
+
 
+
 
 
-
+

 
 
- 
-   
+Using java version ${java.version}
+
+
+
+
 
 
 
 
 
+ 
+
+
+
+
+  
+
+
+
+
+
+
 
 
+
+
 
 

Added: 
trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch
===
--- 
trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch  
(rev 0)
+++ 
trunk/packages/rdp-classifier/trunk/debian/patches/fix_java9_compilation.patch  
2017-09-15 15:28:08 UTC (rev 24047)
@@ -0,0 +1,78 @@
+Subject: fix resource loading for Java 9
+Description: resource loading modification for Java 9
+Author: Olivier Sallou
+Forwarded: no
+Last-Updated: 2017-09-15
+--- a/test/edu/msu/cme/rdp/classifier/rrnaclassifier/TrainingInfoTest.java
 b/test/edu/msu/cme/rdp/classifier/rrnaclassifier/TrainingInfoTest.java
+@@ -55,7 +55,7 @@
+ /** Test of createLogWordPriorArr method, of class 
classification.TrainingInfo. */
+ public void testCreateLogWordPriorArr() throws Exception{
+ System.out.println("testCreateLogWordPriorArr");
+-InputStream dstream = 
System.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt");
++InputStream dstream = 
TrainingInfoTest.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt");
+ Reader in =  new InputStreamReader( dstream );
+ 
+ TrainingInfo train = new TrainingInfo();
+@@ -82,7 +82,7 @@
+ /** Test of createGenusWordProbLis method, of class 
classification.TrainingInfo. */
+ public void testCreateGenusWordProbList() throws Exception{
+ System.out.println("testCreateGenusWordConditionalProbList");
+-InputStream dstream = 

[med-svn] [fast5] 01/01: pristine-tar data for fast5_0.6.2.orig.tar.gz

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch pristine-tar
in repository fast5.

commit eafb88848de573f49d8df585537dfd2a8da95580
Author: Steffen Moeller 
Date:   Fri Sep 15 13:45:51 2017 +0200

pristine-tar data for fast5_0.6.2.orig.tar.gz
---
 fast5_0.6.2.orig.tar.gz.delta | Bin 0 -> 2145 bytes
 fast5_0.6.2.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/fast5_0.6.2.orig.tar.gz.delta b/fast5_0.6.2.orig.tar.gz.delta
new file mode 100644
index 000..93fda5d
Binary files /dev/null and b/fast5_0.6.2.orig.tar.gz.delta differ
diff --git a/fast5_0.6.2.orig.tar.gz.id b/fast5_0.6.2.orig.tar.gz.id
new file mode 100644
index 000..d9b3a58
--- /dev/null
+++ b/fast5_0.6.2.orig.tar.gz.id
@@ -0,0 +1 @@
+29f7c0c95e704b09f8b83d0eadc3894e03c8c3d6

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[med-svn] [rdp-classifier] 01/01: pristine-tar data for rdp-classifier_2.10.2.orig.tar.gz

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch pristine-tar
in repository rdp-classifier.

commit c15ac82f44f8fe019be2c90d1362973402d56d09
Author: Andreas Tille 
Date:   Fri Sep 15 18:25:14 2017 +0200

pristine-tar data for rdp-classifier_2.10.2.orig.tar.gz
---
 rdp-classifier_2.10.2.orig.tar.gz.delta | Bin 0 -> 5202 bytes
 rdp-classifier_2.10.2.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/rdp-classifier_2.10.2.orig.tar.gz.delta 
b/rdp-classifier_2.10.2.orig.tar.gz.delta
new file mode 100644
index 000..6c85d9d
Binary files /dev/null and b/rdp-classifier_2.10.2.orig.tar.gz.delta differ
diff --git a/rdp-classifier_2.10.2.orig.tar.gz.id 
b/rdp-classifier_2.10.2.orig.tar.gz.id
new file mode 100644
index 000..80fa5bf
--- /dev/null
+++ b/rdp-classifier_2.10.2.orig.tar.gz.id
@@ -0,0 +1 @@
+c7cb62e5af375e363d7007c491850213227e5202

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[med-svn] r24048 - trunk/packages/rdp-classifier/trunk

[Andreas Tille]

Author: tille
Date: 2017-09-15 16:31:44 + (Fri, 15 Sep 2017)
New Revision: 24048

Removed:
   trunk/packages/rdp-classifier/trunk/debian/
Log:
Moved packaging to Git



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[med-svn] [fast5] branch master updated (008c7de -> 858d3dd)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch master
in repository fast5.

  from  008c7de   Corrected for left-over conflict declaration.
   new  858d3dd   Completed include files required for library usage.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 debian/changelog | 7 +++
 debian/install   | 5 +
 debian/rules | 5 +
 3 files changed, 17 insertions(+)

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[med-svn] [fast5] 01/01: Completed include files required for library usage.

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository fast5.

commit 858d3dd669d3f48e972f7f87e96bd844d086d312
Author: Steffen Moeller 
Date:   Fri Sep 15 19:35:13 2017 +0200

Completed include files required for library usage.
---
 debian/changelog | 7 +++
 debian/install   | 5 +
 debian/rules | 5 +
 3 files changed, 17 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index c8c8b4e..09f58fe 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+fast5 (0.6.2-3) unstable; urgency=medium
+
+  * Completed include files to be redistributed
+for a functional package.
+
+ -- Steffen Moeller   Fri, 15 Sep 2017 19:20:53 +0200
+
 fast5 (0.6.2-2) unstable; urgency=medium
 
   * Corrected for erroneously declared conflict
diff --git a/debian/install b/debian/install
index 3662190..ba8789e 100644
--- a/debian/install
+++ b/debian/install
@@ -1,2 +1,7 @@
 src/fast5.hpp  usr/include
 src/hdf5_tools.hpp usr/include/fast5
+src/fast5_version.hpp usr/include/fast5
+src/Bit_Packer.hpp usr/include/fast5
+src/Huffman_Packer.hpp usr/include/fast5
+src/logger.hpp usr/include/fast5
+src/*.inl usr/include/fast5
diff --git a/debian/rules b/debian/rules
index 7782b8d..68d9c56 100755
--- a/debian/rules
+++ b/debian/rules
@@ -37,3 +37,8 @@ override_dh_install:
mv debian/python-fast5/usr/bin/* debian/python-fast5-bin/usr/bin/
mv debian/python3-fast5/usr/bin/* debian/python3-fast5-bin/usr/bin/
rm -rf debian/python-fast5/usr/bin/ debian/python3-fast5/usr/bin/
+   sed -i s'%"hdf5_tools.hpp"%%' 
debian/libfast5-dev/usr/include/fast5.hpp
+   sed -i s'%"fast5_version.hpp"%%' 
debian/libfast5-dev/usr/include/fast5.hpp
+   sed -i s'%"logger.hpp"%%' 
debian/libfast5-dev/usr/include/fast5.hpp
+   sed -i s'%"Huffman_Packer.hpp"%%' 
debian/libfast5-dev/usr/include/fast5.hpp
+   sed -i s'%"Bit_Packer.hpp"%%' 
debian/libfast5-dev/usr/include/fast5.hpp

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[med-svn] [invesalius] tag debian/3.1.1-2 created (now acc76ac)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to tag debian/3.1.1-2
in repository invesalius.

at  acc76ac   (commit)
No new revisions were added by this update.

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[med-svn] [invesalius] 02/02: Standards-Version: 4.1.0, upload to unstable

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository invesalius.

commit acc76ac6fb4db3c40d5d20d31f359f3a33d8b379
Author: Andreas Tille 
Date:   Fri Sep 15 11:02:51 2017 +0200

Standards-Version: 4.1.0, upload to unstable
---
 debian/changelog | 5 +++--
 debian/control   | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index e368b16..eabc35d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,14 +1,15 @@
-invesalius (3.1.1-2) UNRELEASED; urgency=medium
+invesalius (3.1.1-2) unstable; urgency=medium
 
   [ Andreas Tille ]
   * Depends: s/python-imaging/python-pil/
 Closes: #866434
+  * Standards-Version: 4.1.0
 
   [ Gert Wollny
   * Avoid division by zero in progress display
 Closes: #779655
 
- -- Andreas Tille   Fri, 15 Sep 2017 09:55:05 +0200
+ -- Andreas Tille   Fri, 15 Sep 2017 10:53:33 +0200
 
 invesalius (3.1.1-1) unstable; urgency=low
 
diff --git a/debian/control b/debian/control
index 0aea933..43ecc30 100644
--- a/debian/control
+++ b/debian/control
@@ -10,7 +10,7 @@ Build-Depends: debhelper (>= 10),
dh-python,
python-numpy
 Build-Depends-Indep: python
-Standards-Version: 4.0.0
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/invesalius.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/invesalius.git
 Homepage: http://www.cti.gov.br/invesalius/

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[med-svn] [invesalius] branch master updated (5a3d124 -> acc76ac)

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  from  5a3d124   d/p/20: Avoid division by zero, Closes: #779655
   new  92b298d   Update changelog
   new  acc76ac   Standards-Version: 4.1.0, upload to unstable

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Summary of changes:
 debian/changelog | 10 --
 debian/control   |  2 +-
 2 files changed, 9 insertions(+), 3 deletions(-)

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[med-svn] [invesalius] 01/02: Update changelog

[Andreas Tille]

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tille pushed a commit to branch master
in repository invesalius.

commit 92b298d3e353442fe078b1dfe537bc3fa9f21836
Author: Andreas Tille 
Date:   Fri Sep 15 10:52:57 2017 +0200

Update changelog
---
 debian/changelog | 5 +
 1 file changed, 5 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 7638aa8..e368b16 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,13 @@
 invesalius (3.1.1-2) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Depends: s/python-imaging/python-pil/
 Closes: #866434
 
+  [ Gert Wollny
+  * Avoid division by zero in progress display
+Closes: #779655
+
  -- Andreas Tille   Fri, 15 Sep 2017 09:55:05 +0200
 
 invesalius (3.1.1-1) unstable; urgency=low

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[med-svn] [gmap] 07/08: Update d/libgmap1.symbols

[Alex Mestiashvili]

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commit 179b94af22567bec9c37b45d94fb9dc47dbf72fb
Author: Alexandre Mestiashvili 
Date:   Fri Sep 15 09:44:33 2017 +0200

Update d/libgmap1.symbols
---
 debian/libgmap1.symbols | 1192 +++
 1 file changed, 596 insertions(+), 596 deletions(-)

diff --git a/debian/libgmap1.symbols b/debian/libgmap1.symbols
index e9d056d..0c7a8bd 100644
--- a/debian/libgmap1.symbols
+++ b/debian/libgmap1.symbols
@@ -1,597 +1,597 @@
 libgmap.so.1 libgmap1 #MINVER#
- Access_allocate_private@Base 2017-09-05
- Access_allocate_shared@Base 2017-09-05
- Access_controlled_cleanup@Base 2017-09-05
- Access_deallocate@Base 2017-09-05
- Access_emergency_cleanup@Base 2017-09-05
- Access_file_copy@Base 2017-09-05
- Access_file_equal@Base 2017-09-05
- Access_file_exists_p@Base 2017-09-05
- Access_fileio@Base 2017-09-05
- Access_fileio_rw@Base 2017-09-05
- Access_filesize@Base 2017-09-05
- Access_mmap@Base 2017-09-05
- Access_mmap_and_preload@Base 2017-09-05
- Access_mmap_offset@Base 2017-09-05
- Access_mmap_offset_rw@Base 2017-09-05
- Access_mmap_rw@Base 2017-09-05
- Access_setup@Base 2017-09-05
- Assert_Failed@Base 2017-09-05
- Bigendian_convert_double@Base 2017-09-05
- Bigendian_convert_int@Base 2017-09-05
- Bigendian_convert_uint8@Base 2017-09-05
- Bigendian_convert_uint@Base 2017-09-05
- Bigendian_fileio_read_uint8@Base 2017-09-05
- Bigendian_fileio_read_uint@Base 2017-09-05
- Bigendian_fread_int@Base 2017-09-05
- Bigendian_fread_ints@Base 2017-09-05
- Bigendian_fread_uint8@Base 2017-09-05
- Bigendian_fread_uint8s@Base 2017-09-05
- Bigendian_fread_uint@Base 2017-09-05
- Bigendian_fread_uints@Base 2017-09-05
- Bigendian_fwrite_double@Base 2017-09-05
- Bigendian_fwrite_int@Base 2017-09-05
- Bigendian_fwrite_ints@Base 2017-09-05
- Bigendian_fwrite_uint8@Base 2017-09-05
- Bigendian_fwrite_uint8s@Base 2017-09-05
- Bigendian_fwrite_uint@Base 2017-09-05
- Bigendian_fwrite_uints@Base 2017-09-05
- Bigendian_write_char@Base 2017-09-05
- Bigendian_write_uint8@Base 2017-09-05
- Bigendian_write_uint@Base 2017-09-05
- Bitpack64_block_offsets@Base 2017-09-05
- Bitpack64_differential_packsize@Base 2017-09-05
- Bitpack64_read_one@Base 2017-09-05
- Bitpack64_read_one_huge@Base 2017-09-05
- Bitpack64_read_two@Base 2017-09-05
- Bytecoding_interleave_lcpchilddc@Base 2017-09-05
- Bytecoding_lcpchilddc_child_next@Base 2017-09-05
- Bytecoding_lcpchilddc_child_up@Base 2017-09-05
- Bytecoding_lcpchilddc_dc@Base 2017-09-05
- Bytecoding_lcpchilddc_lcp@Base 2017-09-05
- Bytecoding_lcpchilddc_lcp_next@Base 2017-09-05
- Bytecoding_read@Base 2017-09-05
- Bytecoding_read_wguide@Base 2017-09-05
- Bytecoding_write@Base 2017-09-05
- Bytecoding_write_bytes@Base 2017-09-05
- Bytecoding_write_exceptions_only@Base 2017-09-05
- Bytecoding_write_lcpchilddc@Base 2017-09-05
- Bzip2_free@Base 2017-09-05
- Bzip2_new@Base 2017-09-05
- Chrnum_length@Base 2017-09-05
- Chrnum_offset@Base 2017-09-05
- Chrnum_print_position@Base 2017-09-05
- Chrnum_to_string@Base 2017-09-05
- Chrnum_to_string_signed@Base 2017-09-05
- Chrom_altlocp@Base 2017-09-05
- Chrom_circularp@Base 2017-09-05
- Chrom_cmp_alpha@Base 2017-09-05
- Chrom_cmp_chrom@Base 2017-09-05
- Chrom_cmp_numeric_alpha@Base 2017-09-05
- Chrom_cmp_order@Base 2017-09-05
- Chrom_compare_alpha@Base 2017-09-05
- Chrom_compare_chrom@Base 2017-09-05
- Chrom_compare_numeric_alpha@Base 2017-09-05
- Chrom_compare_order@Base 2017-09-05
- Chrom_compare_table@Base 2017-09-05
- Chrom_free@Base 2017-09-05
- Chrom_from_string@Base 2017-09-05
- Chrom_hash_table@Base 2017-09-05
- Chrom_string@Base 2017-09-05
- Chrpos_compare@Base 2017-09-05
- Compress_free@Base 2017-09-05
- Compress_get_16mer_left@Base 2017-09-05
- Compress_get_16mer_right@Base 2017-09-05
- Compress_nblocks@Base 2017-09-05
- Compress_new_fwd@Base 2017-09-05
- Compress_new_rev@Base 2017-09-05
- Compress_print@Base 2017-09-05
- Compress_print_blocks@Base 2017-09-05
- Compress_shift@Base 2017-09-05
- Datadir_avail_gmap_databases@Base 2017-09-05
- Datadir_avail_maps@Base 2017-09-05
- Datadir_find_genomedir@Base 2017-09-05
- Datadir_find_genomesubdir@Base 2017-09-05
- Datadir_find_mapdir@Base 2017-09-05
- Datadir_list_directory@Base 2017-09-05
- Datadir_list_directory_multicol@Base 2017-09-05
- Doublelist_fill_array@Base 2017-09-05
- Doublelist_free@Base 2017-09-05
- Doublelist_from_array@Base 2017-09-05
- Doublelist_from_string@Base 2017-09-05
- Doublelist_head@Base 2017-09-05
- Doublelist_keep_one@Base 2017-09-05
- Doublelist_length@Base 2017-09-05
- Doublelist_max@Base 2017-09-05
- Doublelist_min@Base 2017-09-05
- Doublelist_next@Base 2017-09-05
- Doublelist_pop@Base 2017-09-05
- Doublelist_print@Base 2017-09-05
- Doublelist_push@Base 2017-09-05
- Doublelist_reverse@Base 2017-09-05
- Doublelist_to_array@Base 2017-09-05
- Doublelist_to_array_out@Base 2017-09-05
- 

[med-svn] [gmap] 01/02: pristine-tar data for gmap_2017-09-05.orig.tar.xz

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch pristine-tar
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commit e87ebba2da829766034f751c8bfcfb0cac9b355a
Author: Alexandre Mestiashvili 
Date:   Mon Sep 11 13:33:08 2017 +0200

pristine-tar data for gmap_2017-09-05.orig.tar.xz
---
 gmap_2017-09-05.orig.tar.xz.delta | Bin 0 -> 11209 bytes
 gmap_2017-09-05.orig.tar.xz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/gmap_2017-09-05.orig.tar.xz.delta 
b/gmap_2017-09-05.orig.tar.xz.delta
new file mode 100644
index 000..3606bba
Binary files /dev/null and b/gmap_2017-09-05.orig.tar.xz.delta differ
diff --git a/gmap_2017-09-05.orig.tar.xz.id b/gmap_2017-09-05.orig.tar.xz.id
new file mode 100644
index 000..6e587ae
--- /dev/null
+++ b/gmap_2017-09-05.orig.tar.xz.id
@@ -0,0 +1 @@
+3560d0f1b51833d5e04e9183152709d258bbc5f5

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[med-svn] [gmap] 06/08: Updated version 2017-09-11 from 'upstream/2017-09-11'

[Alex Mestiashvili]

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commit a2bea48853a09e8a45092e76607236eb29cf7a65
Merge: ecd5a51 4495e01
Author: Alexandre Mestiashvili 
Date:   Fri Sep 15 09:16:27 2017 +0200

Updated version 2017-09-11 from 'upstream/2017-09-11'

with Debian dir aab40e3eab1de5bb4e862cfe59fa40c242a8bdd4

 ChangeLog   |  15 ++
 Makefile.in |   2 +-
 TODO|   3 --
 VERSION |   2 +-
 configure   |  24 -
 src/ChangeLog   |   0
 src/Makefile.in |   2 +-
 src/compile | 165 
 src/gmap.c  |  26 -
 src/pair.c  | 120 ++---
 10 files changed, 143 insertions(+), 216 deletions(-)

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[med-svn] [gmap] 02/08: Refresh install-data-local patch

[Alex Mestiashvili]

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commit 5f31b968c7b1beb77e33e23d0a8ee9e007d2b8ef
Author: Alexandre Mestiashvili 
Date:   Mon Sep 11 13:36:31 2017 +0200

Refresh install-data-local patch
---
 debian/patches/install-data-local | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/patches/install-data-local 
b/debian/patches/install-data-local
index 4ecbc17..1878ec9 100644
--- a/debian/patches/install-data-local
+++ b/debian/patches/install-data-local
@@ -2,7 +2,7 @@ Description: Install data local
 
 --- gmap.orig/Makefile.in
 +++ gmap/Makefile.in
-@@ -847,7 +847,7 @@
+@@ -846,7 +846,7 @@
  
  
  install-data-local:

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[med-svn] [r-cran-pkgconfig] 03/03: Close also #875839

[Andreas Tille]

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commit e7a4f514ab765024dde48477fe9ab1e48292d813
Author: Andreas Tille 
Date:   Fri Sep 15 08:57:40 2017 +0200

Close also #875839
---
 debian/changelog | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 67b27ea..4dd7a0e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,7 @@
 r-cran-pkgconfig (2.0.1-1) UNRELEASED; urgency=medium
 
   * Initial release (closes: #xx)
+  * Also fixes dependency issue in r-cran-rsqlite
+Closes: #875839
 
  -- Andreas Tille   Fri, 15 Sep 2017 08:37:14 +0200

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[med-svn] [r-cran-pkgconfig] branch master created (now e7a4f51)

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at  e7a4f51   Close also #875839

This branch includes the following new commits:

   new  cc68637   New upstream version 2.0.1
   new  29bb4f2   Initial packaging
   new  e7a4f51   Close also #875839

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[med-svn] [r-cran-pkgconfig] branch pristine-tar created (now e37a8fd)

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at  e37a8fd   pristine-tar data for r-cran-pkgconfig_2.0.1.orig.tar.gz

This branch includes the following new commits:

   new  e37a8fd   pristine-tar data for r-cran-pkgconfig_2.0.1.orig.tar.gz

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[med-svn] [r-cran-pkgconfig] 01/01: pristine-tar data for r-cran-pkgconfig_2.0.1.orig.tar.gz

[Andreas Tille]

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commit e37a8fd5fb1fedb525f4775fb413fd42354f75bb
Author: Andreas Tille 
Date:   Fri Sep 15 08:56:07 2017 +0200

pristine-tar data for r-cran-pkgconfig_2.0.1.orig.tar.gz
---
 r-cran-pkgconfig_2.0.1.orig.tar.gz.delta | Bin 0 -> 1615 bytes
 r-cran-pkgconfig_2.0.1.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/r-cran-pkgconfig_2.0.1.orig.tar.gz.delta 
b/r-cran-pkgconfig_2.0.1.orig.tar.gz.delta
new file mode 100644
index 000..b625d3f
Binary files /dev/null and b/r-cran-pkgconfig_2.0.1.orig.tar.gz.delta differ
diff --git a/r-cran-pkgconfig_2.0.1.orig.tar.gz.id 
b/r-cran-pkgconfig_2.0.1.orig.tar.gz.id
new file mode 100644
index 000..4556293
--- /dev/null
+++ b/r-cran-pkgconfig_2.0.1.orig.tar.gz.id
@@ -0,0 +1 @@
+67b482881be67fdf4f758f5f40e0ffa88c2fbf0b

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[med-svn] [r-cran-pkgconfig] annotated tag upstream/2.0.1 created (now a580cb5)

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at  a580cb5   (tag)
   tagging  cc686378965d4045336827a5117eed1bc1bcd48a (commit)
 tagged by  Andreas Tille
on  Fri Sep 15 08:56:07 2017 +0200

- Log -
Upstream version 2.0.1

Andreas Tille (1):
  New upstream version 2.0.1

---

This annotated tag includes the following new commits:

   new  cc68637   New upstream version 2.0.1

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[med-svn] [mobyle] 01/04: Depends: s/python-imaging/python-pil/

[Andreas Tille]

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commit 198c0a663a870568edcfdb233ac20c1e0ef87618
Author: Andreas Tille 
Date:   Fri Sep 15 10:05:00 2017 +0200

Depends: s/python-imaging/python-pil/
---
 debian/changelog | 7 +++
 debian/control   | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index bf1ed68..9f68797 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+mobyle (1.5.5+dfsg-3) UNRELEASED; urgency=medium
+
+  * Depends: s/python-imaging/python-pil/
+Closes: #866442
+
+ -- Andreas Tille   Fri, 15 Sep 2017 10:03:55 +0200
+
 mobyle (1.5.5+dfsg-2) unstable; urgency=medium
 
   * Fix homepage
diff --git a/debian/control b/debian/control
index 48e7269..b35205a 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 9),
python,
python-simpletal,
python-simplejson,
-   python-imaging,
+   python-pil,
python-lxml,
dh-apache2,
apache2-dev,
@@ -29,7 +29,7 @@ Depends: ${misc:Depends},
  libjs-prototype,
  mobyle-utils,
  python-biopython,
- python-imaging,
+ python-pil,
  python-lxml,
  python-pygraphviz,
  python-simplejson,

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[med-svn] [mobyle] 02/04: debhelper 10

[Andreas Tille]

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tille pushed a commit to branch master
in repository mobyle.

commit 48e5d517d3af2bffbbe8b6d8dadbc537882e01d6
Author: Andreas Tille 
Date:   Fri Sep 15 10:05:43 2017 +0200

debhelper 10
---
 debian/changelog | 1 +
 debian/compat| 2 +-
 debian/control   | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 9f68797..bcff921 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ mobyle (1.5.5+dfsg-3) UNRELEASED; urgency=medium
 
   * Depends: s/python-imaging/python-pil/
 Closes: #866442
+  * debhelper 10
 
  -- Andreas Tille   Fri, 15 Sep 2017 10:03:55 +0200
 
diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index b35205a..704d7e8 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Olivier Sallou ,
Andreas Tille 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
python,
python-simpletal,
python-simplejson,

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[med-svn] [mobyle] tag debian/1.5.5+dfsg-3 created (now 6aacbde)

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at  6aacbde   (commit)
No new revisions were added by this update.

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[med-svn] [mobyle] 03/04: Standards-Version: 4.1.0 (no changes needed)

[Andreas Tille]

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tille pushed a commit to branch master
in repository mobyle.

commit fbf1ddc4b8f2fbbe62d2562fa1b1b306ad23a040
Author: Andreas Tille 
Date:   Fri Sep 15 10:06:16 2017 +0200

Standards-Version: 4.1.0 (no changes needed)
---
 debian/changelog | 1 +
 debian/control   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index bcff921..20ba43a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ mobyle (1.5.5+dfsg-3) UNRELEASED; urgency=medium
   * Depends: s/python-imaging/python-pil/
 Closes: #866442
   * debhelper 10
+  * Standards-Version: 4.1.0 (no changes needed)
 
  -- Andreas Tille   Fri, 15 Sep 2017 10:03:55 +0200
 
diff --git a/debian/control b/debian/control
index 704d7e8..dca8702 100644
--- a/debian/control
+++ b/debian/control
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 10),
dh-apache2,
apache2-dev,
dh-python
-Standards-Version: 3.9.8
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mobyle.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/mobyle.git
 Homepage: https://projets.pasteur.fr/projects/mobyle

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[med-svn] [invesalius] 01/01: d/p/20: Avoid division by zero, Closes: #779655

[Gert Wollny]

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commit 5a3d1240b0dc9a7e8f49ddc659842c914c949b88
Author: Gert Wollny 
Date:   Fri Sep 15 08:36:41 2017 +

d/p/20: Avoid division by zero, Closes: #779655
---
 debian/patches/10_import_cython_modules.patch | 20 +---
 debian/patches/20_fix_division_by_zero.patch  | 18 ++
 debian/patches/series |  1 +
 3 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/debian/patches/10_import_cython_modules.patch 
b/debian/patches/10_import_cython_modules.patch
index 0aded21..00fe63a 100644
--- a/debian/patches/10_import_cython_modules.patch
+++ b/debian/patches/10_import_cython_modules.patch
@@ -2,11 +2,9 @@ Author: Thiago Franco Moraes
 Last-Update: 2016-10-06 14:28:25 +
 Description: Import cython modules
 
-diff --git a/invesalius/data/mask.py b/invesalius/data/mask.py
-index d00d22e..be9423a 100644
 --- a/invesalius/data/mask.py
 +++ b/invesalius/data/mask.py
-@@ -30,7 +30,7 @@ import invesalius.constants as const
+@@ -30,7 +30,7 @@
  import invesalius.data.imagedata_utils as iu
  import invesalius.session as ses
  
@@ -15,11 +13,9 @@ index d00d22e..be9423a 100644
  
  from wx.lib.pubsub import pub as Publisher
  from scipy import ndimage
-diff --git a/invesalius/data/slice_.py b/invesalius/data/slice_.py
-index 48f6f46..59bdf7f 100644
 --- a/invesalius/data/slice_.py
 +++ b/invesalius/data/slice_.py
-@@ -31,9 +31,9 @@ import invesalius.session as ses
+@@ -31,9 +31,9 @@
  import invesalius.utils as utils
  from invesalius.data.mask import Mask
  from invesalius.project import Project
@@ -31,11 +27,9 @@ index 48f6f46..59bdf7f 100644
  import invesalius.data.transformations as transformations
  OTHER=0
  PLIST=1
-diff --git a/invesalius/data/styles.py b/invesalius/data/styles.py
-index fc3b67f..8063b59 100644
 --- a/invesalius/data/styles.py
 +++ b/invesalius/data/styles.py
-@@ -45,7 +45,7 @@ from skimage.morphology import watershed
+@@ -45,7 +45,7 @@
  import invesalius.gui.dialogs as dialogs
  from invesalius.data.measures import MeasureData
  
@@ -44,11 +38,9 @@ index fc3b67f..8063b59 100644
  
  import invesalius.data.watershed_process as watershed_process
  import invesalius.utils as utils
-diff --git a/invesalius/data/surface.py b/invesalius/data/surface.py
-index 8845085..603c20c 100644
 --- a/invesalius/data/surface.py
 +++ b/invesalius/data/surface.py
-@@ -37,7 +37,7 @@ import invesalius.data.surface_process as surface_process
+@@ -48,7 +48,7 @@
  import invesalius.utils as utl
  import invesalius.data.vtk_utils as vu
  
@@ -57,11 +49,9 @@ index 8845085..603c20c 100644
  # TODO: Verificar ReleaseDataFlagOn and SetSource 
  
  class Surface():
-diff --git a/setup.py b/setup.py
-index cc05315..6913ec4 100644
 --- a/setup.py
 +++ b/setup.py
-@@ -11,26 +11,26 @@ import numpy
+@@ -11,26 +11,26 @@
  if sys.platform == 'linux2':
  setup(
  cmdclass = {'build_ext': build_ext},
diff --git a/debian/patches/20_fix_division_by_zero.patch 
b/debian/patches/20_fix_division_by_zero.patch
new file mode 100644
index 000..4df2b6a
--- /dev/null
+++ b/debian/patches/20_fix_division_by_zero.patch
@@ -0,0 +1,18 @@
+Description: Avoid division by zero in progress display 
+Author: Gert Wollny 
+Debian-Bug: https://bugs.debian.org/779655
+
+--- a/invesalius/data/vtk_utils.py
 b/invesalius/data/vtk_utils.py
+@@ -49,7 +49,10 @@
+ 
+ # when the pipeline is larger than 1, we have to consider this object
+ # percentage
+-ratio = (100.0 / number_of_filters)
++if number_of_filters > 0: 
++ratio = (100.0 / number_of_filters)
++else:
++ratio = 100.0
+ 
+ def UpdateProgress(obj, label=""):
+ """
diff --git a/debian/patches/series b/debian/patches/series
index b3dac6e..9ea65a7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 10_sample_path.patch
 10_import_cython_modules.patch
+20_fix_division_by_zero.patch

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[med-svn] [mobyle] branch master updated (9056f86 -> 6aacbde)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository mobyle.

  from  9056f86   fix jquery symlink bug
   new  198c0a6   Depends: s/python-imaging/python-pil/
   new  48e5d51   debhelper 10
   new  fbf1ddc   Standards-Version: 4.1.0 (no changes needed)
   new  6aacbde   Upload to unstable

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:
 debian/changelog | 9 +
 debian/compat| 2 +-
 debian/control   | 8 
 debian/copyright | 2 +-
 4 files changed, 15 insertions(+), 6 deletions(-)

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[med-svn] [mobyle] 04/04: Upload to unstable

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository mobyle.

commit 6aacbde363772acc2179aabe5091a57e1e1839ce
Author: Andreas Tille 
Date:   Fri Sep 15 10:47:37 2017 +0200

Upload to unstable
---
 debian/changelog | 4 ++--
 debian/copyright | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 20ba43a..f471f05 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,11 @@
-mobyle (1.5.5+dfsg-3) UNRELEASED; urgency=medium
+mobyle (1.5.5+dfsg-3) unstable; urgency=medium
 
   * Depends: s/python-imaging/python-pil/
 Closes: #866442
   * debhelper 10
   * Standards-Version: 4.1.0 (no changes needed)
 
- -- Andreas Tille   Fri, 15 Sep 2017 10:03:55 +0200
+ -- Andreas Tille   Fri, 15 Sep 2017 10:06:23 +0200
 
 mobyle (1.5.5+dfsg-2) unstable; urgency=medium
 
diff --git a/debian/copyright b/debian/copyright
index a0b4cdf..71015cb 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -31,7 +31,7 @@ Files: Src/Portal/htdocs/MobylePortal/images/*
 Copyright: 2011 Mark James
 License: CC-BY-SA-3.0
 Source: http://www.famfamfam.com/lab/icons/silk/
-Coment: debian/README.Silk created according to the following comment on 
Upstream website.
+Comment: debian/README.Silk created according to the following comment on 
Upstream website.
  The icons can also be used under Creative Commons Attribution 3.0 License (Hi
  Debian folks!) with the following requirements:
  .

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[med-svn] [r-cran-pkgconfig] branch upstream created (now cc68637)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository r-cran-pkgconfig.

at  cc68637   New upstream version 2.0.1

No new revisions were added by this update.

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[med-svn] [r-cran-pkgconfig] 01/03: New upstream version 2.0.1

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-cran-pkgconfig.

commit cc686378965d4045336827a5117eed1bc1bcd48a
Author: Andreas Tille 
Date:   Fri Sep 15 08:56:07 2017 +0200

New upstream version 2.0.1
---
 DESCRIPTION |  19 ++
 LICENSE |   2 +
 MD5 |  18 ++
 NAMESPACE   |   6 ++
 R/getset.R  | 115 
 R/pkgconfig-package.R   |  13 +
 R/utils.R   |   4 ++
 inst/NEWS.markdown  |  19 ++
 inst/README.Rmd | 113 +++
 inst/README.markdown| 113 +++
 man/get_config.Rd   |  33 +++
 man/pkgconfig-package.Rd|  16 +
 man/set_config.Rd   |  23 
 man/set_config_in.Rd|  31 ++
 tests/testthat.R|   9 +++
 tests/testthat/test-api.R   |  40 +
 tests/testthat/test-errors.R|  10 
 tests/testthat/test-globalenv.R |  25 
 tests/testthat/tests.R  | 126 
 19 files changed, 735 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 000..a0c3295
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,19 @@
+Package: pkgconfig
+Title: Private Configuration for 'R' Packages
+Version: 2.0.1
+Author: Gábor Csárdi
+Maintainer: Gábor Csárdi 
+Description: Set configuration options on a per-package basis.
+Options set by a given package only apply to that package,
+other packages are unaffected.
+License: MIT + file LICENSE
+LazyData: true
+Imports: utils
+Suggests: covr, testthat, disposables (>= 1.0.3)
+URL: https://github.com/gaborcsardi/pkgconfig
+BugReports: https://github.com/gaborcsardi/pkgconfig/issues
+Encoding: UTF-8
+NeedsCompilation: no
+Packaged: 2017-03-21 10:15:26 UTC; gaborcsardi
+Repository: CRAN
+Date/Publication: 2017-03-21 15:20:20 UTC
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 000..510de3e
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2014--2017
+COPYRIGHT HOLDER: Gábor Csárdi
diff --git a/MD5 b/MD5
new file mode 100644
index 000..5dfda65
--- /dev/null
+++ b/MD5
@@ -0,0 +1,18 @@
+0866c2f4d8ce2f24b8d1ffe424e12f84 *DESCRIPTION
+4b7ff7c348e978f33981b2237200878d *LICENSE
+cd8e0bb63bd54833fe1e01ad1a8647d6 *NAMESPACE
+9f75eb47d58b82e003713579356c2af6 *R/getset.R
+1531da19568f0512ff768360cb78540f *R/pkgconfig-package.R
+72539c3bc185b91ce53a54f2bc8336b2 *R/utils.R
+126f0602cc011b89c24915b2cf4af4e2 *inst/NEWS.markdown
+650807f1f0cac8233dfd54cfdf0d6454 *inst/README.Rmd
+650807f1f0cac8233dfd54cfdf0d6454 *inst/README.markdown
+df949f83f265547f97085e9ad1891a6b *man/get_config.Rd
+e97c9e9fa3c680d05d3758f07448ef2b *man/pkgconfig-package.Rd
+006950b03f96ba261abaeb6f225df012 *man/set_config.Rd
+d80ab36e7a5e1b8863b79fbbd50466b9 *man/set_config_in.Rd
+0138a95afd3fe43ad69771aa955b910a *tests/testthat.R
+98b113f008c249e31b7035ba76077f84 *tests/testthat/test-api.R
+da73dc4a696ec2066812ab8c467ab361 *tests/testthat/test-errors.R
+909e8b0e2558c28ffef1cfae84b8139d *tests/testthat/test-globalenv.R
+a196e36e881f8baf7306dd633ada68e2 *tests/testthat/tests.R
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 000..29fe3f3
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,6 @@
+# Generated by roxygen2 (4.1.1): do not edit by hand
+
+export(get_config)
+export(set_config)
+export(set_config_in)
+importFrom(utils,packageName)
diff --git a/R/getset.R b/R/getset.R
new file mode 100644
index 000..f0c7be5
--- /dev/null
+++ b/R/getset.R
@@ -0,0 +1,115 @@
+
+## This is the environment that stores all parameters
+
+config <- new.env()
+
+## --
+
+#' Query a configuration parameter key
+#'
+#' Query a configuration parameter key, and return the value
+#' set in the calling package(s).
+#'
+#' @details
+#' This function is meant to be called from the package whose
+#' behavior depends on it. It searches for the given configuration
+#' key, and if it exists, it checks which package(s) it was called
+#' from and returns the configuration setting for that package.
+#'
+#' If the key is not set in any calling package, but it is set in
+#' the global environment (i.e. at the R prompt), then it returns that
+#' setting.
+#'
+#' If the key is not set anywhere, then it returns \code{NULL}.
+#'
+#' @param key The name of the parameter to query.
+#' @param fallback Fallback if the parameter id not found anywhere.
+#' @return The value of the parameter, or the fallback value if not found.
+#'
+#' @export
+
+get_config <- function(key, fallback = NULL) {
+  result <- get_from_session(key)
+  if (is.null(result)) fallback else result[[1]]
+}
+
+get_from_session <- 

[med-svn] [r-cran-pkgconfig] 02/03: Initial packaging

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-cran-pkgconfig.

commit 29bb4f2dfcb31ac85930d07aeb7885a861011b79
Author: Andreas Tille 
Date:   Fri Sep 15 08:56:21 2017 +0200

Initial packaging
---
 debian/README.test |  8 
 debian/changelog   |  5 +
 debian/compat  |  1 +
 debian/control | 24 
 debian/copyright   | 33 +
 debian/docs|  3 +++
 debian/rules   |  5 +
 debian/source/format   |  1 +
 debian/tests/control   |  3 +++
 debian/tests/run-unit-test | 17 +
 debian/watch   |  2 ++
 11 files changed, 102 insertions(+)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 000..16b1662
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by running the provided test:
+
+sh ./run-unit-test
+
+in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000..67b27ea
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-cran-pkgconfig (2.0.1-1) UNRELEASED; urgency=medium
+
+  * Initial release (closes: #xx)
+
+ -- Andreas Tille   Fri, 15 Sep 2017 08:37:14 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 000..82241ce
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: r-cran-pkgconfig
+Maintainer: Debian Med Packaging Team 

+Uploaders: Andreas Tille 
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 10),
+   dh-r,
+   r-base-dev
+Standards-Version: 4.1.0
+Vcs-Browser: https://anonscm.debian.org/git/debian-med/r-cran-pkgconfig.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/r-cran-pkgconfig.git
+Homepage: https://cran.r-project.org/package=pkgconfig
+
+Package: r-cran-pkgconfig
+Architecture: all
+Depends: ${R:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
+Description: Private Configuration for 'R' Packages
+ Set configuration options on a per-package basis.
+ Options set by a given package only apply to that package,
+ other packages are unaffected.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 000..bcf5473
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,33 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pkgconfig
+Upstream-Contact: Gábor Csárdi 
+Source: https://cran.r-project.org/package=pkgconfig
+
+Files: *
+Copyright: 2015-2017 Gábor Csárdi 
+License: MIT
+Comment: 
+
+Files: debian/*
+Copyright: 2017 Andreas Tille 
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 000..6466d39
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+debian/tests/run-unit-test
+debian/README.test
+tests
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 000..529c38a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+
+%:
+   dh $@ --buildsystem R
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 000..a16598a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test

[med-svn] [invesalius] branch master updated (75963f7 -> 5a3d124)

[Gert Wollny]

This is an automated email from the git hooks/post-receive script.

gewo pushed a change to branch master
in repository invesalius.

  from  75963f7   Depends: s/python-imaging/python-pil/
   new  5a3d124   d/p/20: Avoid division by zero, Closes: #779655

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/patches/10_import_cython_modules.patch | 20 +---
 debian/patches/20_fix_division_by_zero.patch  | 18 ++
 debian/patches/series |  1 +
 3 files changed, 24 insertions(+), 15 deletions(-)
 create mode 100644 debian/patches/20_fix_division_by_zero.patch

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[med-svn] [gmap] 05/08: New upstream version 2017-09-11

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository gmap.

commit 4495e018ec7407f5249c84257984893e1cdbe080
Author: Alexandre Mestiashvili 
Date:   Fri Sep 15 09:16:13 2017 +0200

New upstream version 2017-09-11
---
 ChangeLog   |  15 ++
 Makefile.in |   2 +-
 TODO|   3 --
 VERSION |   2 +-
 configure   |  24 -
 src/ChangeLog   |   0
 src/Makefile.in |   2 +-
 src/compile | 165 
 src/gmap.c  |  26 -
 src/pair.c  | 120 ++---
 10 files changed, 143 insertions(+), 216 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index a5e0526..f8bfc3b 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,5 +1,20 @@
+2017-09-11  twu
+
+* VERSION: Updated version number
+
+* gmap.c, src: Merged revision 209800 from trunk to restore --intronlength
+  option
+
+* pair.c: Merged revisions 209797 and 209798 from trunk to replace gff3
+  printing code for CDS with a call to the code for exons
+
+* gmap.c, src: Merged revision 209788 from trunk to no longer iterate on
+  check_middle_local
+
 2017-09-05  twu
 
+* public-2017-09-05: Created public release
+
 * sarray-search.c: Fixed bug resulting from check of common diagonal over
   circular origin
 
diff --git a/Makefile.in b/Makefile.in
index 1dc67f7..1a13b09 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -184,7 +184,7 @@ am__DIST_COMMON = $(srcdir)/Makefile.in 
$(top_srcdir)/config/compile \
$(top_srcdir)/config/config.sub \
$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
$(top_srcdir)/config/missing AUTHORS COPYING ChangeLog INSTALL \
-   NEWS README TODO config/compile config/config.guess \
+   NEWS README config/compile config/config.guess \
config/config.sub config/install-sh config/ltmain.sh \
config/missing
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
diff --git a/TODO b/TODO
deleted file mode 100644
index c5a7bd7..000
--- a/TODO
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Add flag that allows for splitting afterwards.
-
diff --git a/VERSION b/VERSION
index a6b5878..5c57d19 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2017-09-05
\ No newline at end of file
+2017-09-11
\ No newline at end of file
diff --git a/configure b/configure
index d0d7d18..9f64c4b 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for gmap 2017-09-05.
+# Generated by GNU Autoconf 2.69 for gmap 2017-09-11.
 #
 # Report bugs to >.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='gmap'
 PACKAGE_TARNAME='gmap'
-PACKAGE_VERSION='2017-09-05'
-PACKAGE_STRING='gmap 2017-09-05'
+PACKAGE_VERSION='2017-09-11'
+PACKAGE_STRING='gmap 2017-09-11'
 PACKAGE_BUGREPORT='Thomas Wu '
 PACKAGE_URL=''
 
@@ -1369,7 +1369,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures gmap 2017-09-05 to adapt to many kinds of systems.
+\`configure' configures gmap 2017-09-11 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1440,7 +1440,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
- short | recursive ) echo "Configuration of gmap 2017-09-05:";;
+ short | recursive ) echo "Configuration of gmap 2017-09-11:";;
esac
   cat <<\_ACEOF
 
@@ -1577,7 +1577,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-gmap configure 2017-09-05
+gmap configure 2017-09-11
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2183,7 +2183,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by gmap $as_me 2017-09-05, which was
+It was created by gmap $as_me 2017-09-11, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2533,8 +2533,8 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking package version" >&5
 $as_echo_n "checking package version... " >&6; }
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2017-09-05" >&5
-$as_echo "2017-09-05" >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2017-09-11" >&5
+$as_echo "2017-09-11" >&6; }
 
 
 ### Read defaults
@@ -4401,7 +4401,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='gmap'
- VERSION='2017-09-05'
+ VERSION='2017-09-11'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -19978,7 +19978,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual 

[med-svn] [gmap] branch master updated (a8f6f3a -> 97539d2)

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a change to branch master
in repository gmap.

  from  a8f6f3a   Upload to unstable
  adds  cc72685   New upstream version 2017-09-05
   new  09dd358   Updated version 2017-09-05 from 'upstream/2017-09-05'
   new  5f31b96   Refresh install-data-local patch
   new  f42b751   Update symbols file
   new  ecd5a51   Update changelog, upload to unstable
   new  4495e01   New upstream version 2017-09-11
   new  a2bea48   Updated version 2017-09-11 from 'upstream/2017-09-11'
   new  179b94a   Update d/libgmap1.symbols
   new  97539d2   Update changelog, upload to unstable

The 8 revisions listed above as "new" are entirely new to this
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Summary of changes:
 ChangeLog |   35 ++
 Makefile.in   |2 +-
 TODO  |3 -
 VERSION   |2 +-
 configure |   24 +-
 debian/changelog  |   15 +
 debian/libgmap1.symbols   | 1192 ++---
 debian/patches/install-data-local |2 +-
 src/ChangeLog |0
 src/Makefile.in   |2 +-
 src/compile   |  165 -
 src/get-genome.c  |   88 ++-
 src/gmap.c|   26 +-
 src/gmapindex.c   |   32 +-
 src/pair.c|  120 +++-
 src/sarray-search.c   |  307 +-
 src/stage1hr.c|6 +-
 17 files changed, 1036 insertions(+), 985 deletions(-)
 delete mode 100644 TODO
 delete mode 100644 src/ChangeLog
 delete mode 100644 src/compile

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[med-svn] [gmap] annotated tag upstream/2017-09-11 created (now 51e5672)

[Alex Mestiashvili]

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malex-guest pushed a change to annotated tag upstream/2017-09-11
in repository gmap.

at  51e5672   (tag)
   tagging  4495e018ec7407f5249c84257984893e1cdbe080 (commit)
  replaces  upstream/2017-09-05
 tagged by  Alexandre Mestiashvili
on  Fri Sep 15 09:16:27 2017 +0200

- Log -
Upstream version 2017-09-11

Alexandre Mestiashvili (1):
  New upstream version 2017-09-11

---

No new revisions were added by this update.

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[med-svn] [gmap] 03/08: Update symbols file

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository gmap.

commit f42b751aac114eb2c248919f062e42bcc4655696
Author: Alexandre Mestiashvili 
Date:   Mon Sep 11 13:50:52 2017 +0200

Update symbols file
---
 debian/libgmap1.symbols | 1192 +++
 1 file changed, 596 insertions(+), 596 deletions(-)

diff --git a/debian/libgmap1.symbols b/debian/libgmap1.symbols
index 54a41c3..e9d056d 100644
--- a/debian/libgmap1.symbols
+++ b/debian/libgmap1.symbols
@@ -1,597 +1,597 @@
 libgmap.so.1 libgmap1 #MINVER#
- Access_allocate_private@Base 2017-08-15
- Access_allocate_shared@Base 2017-08-15
- Access_controlled_cleanup@Base 2017-08-15
- Access_deallocate@Base 2017-08-15
- Access_emergency_cleanup@Base 2017-08-15
- Access_file_copy@Base 2017-08-15
- Access_file_equal@Base 2017-08-15
- Access_file_exists_p@Base 2017-08-15
- Access_fileio@Base 2017-08-15
- Access_fileio_rw@Base 2017-08-15
- Access_filesize@Base 2017-08-15
- Access_mmap@Base 2017-08-15
- Access_mmap_and_preload@Base 2017-08-15
- Access_mmap_offset@Base 2017-08-15
- Access_mmap_offset_rw@Base 2017-08-15
- Access_mmap_rw@Base 2017-08-15
- Access_setup@Base 2017-08-15
- Assert_Failed@Base 2017-08-15
- Bigendian_convert_double@Base 2017-08-15
- Bigendian_convert_int@Base 2017-08-15
- Bigendian_convert_uint8@Base 2017-08-15
- Bigendian_convert_uint@Base 2017-08-15
- Bigendian_fileio_read_uint8@Base 2017-08-15
- Bigendian_fileio_read_uint@Base 2017-08-15
- Bigendian_fread_int@Base 2017-08-15
- Bigendian_fread_ints@Base 2017-08-15
- Bigendian_fread_uint8@Base 2017-08-15
- Bigendian_fread_uint8s@Base 2017-08-15
- Bigendian_fread_uint@Base 2017-08-15
- Bigendian_fread_uints@Base 2017-08-15
- Bigendian_fwrite_double@Base 2017-08-15
- Bigendian_fwrite_int@Base 2017-08-15
- Bigendian_fwrite_ints@Base 2017-08-15
- Bigendian_fwrite_uint8@Base 2017-08-15
- Bigendian_fwrite_uint8s@Base 2017-08-15
- Bigendian_fwrite_uint@Base 2017-08-15
- Bigendian_fwrite_uints@Base 2017-08-15
- Bigendian_write_char@Base 2017-08-15
- Bigendian_write_uint8@Base 2017-08-15
- Bigendian_write_uint@Base 2017-08-15
- Bitpack64_block_offsets@Base 2017-08-15
- Bitpack64_differential_packsize@Base 2017-08-15
- Bitpack64_read_one@Base 2017-08-15
- Bitpack64_read_one_huge@Base 2017-08-15
- Bitpack64_read_two@Base 2017-08-15
- Bytecoding_interleave_lcpchilddc@Base 2017-08-15
- Bytecoding_lcpchilddc_child_next@Base 2017-08-15
- Bytecoding_lcpchilddc_child_up@Base 2017-08-15
- Bytecoding_lcpchilddc_dc@Base 2017-08-15
- Bytecoding_lcpchilddc_lcp@Base 2017-08-15
- Bytecoding_lcpchilddc_lcp_next@Base 2017-08-15
- Bytecoding_read@Base 2017-08-15
- Bytecoding_read_wguide@Base 2017-08-15
- Bytecoding_write@Base 2017-08-15
- Bytecoding_write_bytes@Base 2017-08-15
- Bytecoding_write_exceptions_only@Base 2017-08-15
- Bytecoding_write_lcpchilddc@Base 2017-08-15
- Bzip2_free@Base 2017-08-15
- Bzip2_new@Base 2017-08-15
- Chrnum_length@Base 2017-08-15
- Chrnum_offset@Base 2017-08-15
- Chrnum_print_position@Base 2017-08-15
- Chrnum_to_string@Base 2017-08-15
- Chrnum_to_string_signed@Base 2017-08-15
- Chrom_altlocp@Base 2017-08-15
- Chrom_circularp@Base 2017-08-15
- Chrom_cmp_alpha@Base 2017-08-15
- Chrom_cmp_chrom@Base 2017-08-15
- Chrom_cmp_numeric_alpha@Base 2017-08-15
- Chrom_cmp_order@Base 2017-08-15
- Chrom_compare_alpha@Base 2017-08-15
- Chrom_compare_chrom@Base 2017-08-15
- Chrom_compare_numeric_alpha@Base 2017-08-15
- Chrom_compare_order@Base 2017-08-15
- Chrom_compare_table@Base 2017-08-15
- Chrom_free@Base 2017-08-15
- Chrom_from_string@Base 2017-08-15
- Chrom_hash_table@Base 2017-08-15
- Chrom_string@Base 2017-08-15
- Chrpos_compare@Base 2017-08-15
- Compress_free@Base 2017-08-15
- Compress_get_16mer_left@Base 2017-08-15
- Compress_get_16mer_right@Base 2017-08-15
- Compress_nblocks@Base 2017-08-15
- Compress_new_fwd@Base 2017-08-15
- Compress_new_rev@Base 2017-08-15
- Compress_print@Base 2017-08-15
- Compress_print_blocks@Base 2017-08-15
- Compress_shift@Base 2017-08-15
- Datadir_avail_gmap_databases@Base 2017-08-15
- Datadir_avail_maps@Base 2017-08-15
- Datadir_find_genomedir@Base 2017-08-15
- Datadir_find_genomesubdir@Base 2017-08-15
- Datadir_find_mapdir@Base 2017-08-15
- Datadir_list_directory@Base 2017-08-15
- Datadir_list_directory_multicol@Base 2017-08-15
- Doublelist_fill_array@Base 2017-08-15
- Doublelist_free@Base 2017-08-15
- Doublelist_from_array@Base 2017-08-15
- Doublelist_from_string@Base 2017-08-15
- Doublelist_head@Base 2017-08-15
- Doublelist_keep_one@Base 2017-08-15
- Doublelist_length@Base 2017-08-15
- Doublelist_max@Base 2017-08-15
- Doublelist_min@Base 2017-08-15
- Doublelist_next@Base 2017-08-15
- Doublelist_pop@Base 2017-08-15
- Doublelist_print@Base 2017-08-15
- Doublelist_push@Base 2017-08-15
- Doublelist_reverse@Base 2017-08-15
- Doublelist_to_array@Base 2017-08-15
- Doublelist_to_array_out@Base 2017-08-15
- Except_advance_stack@Base 

[med-svn] [gmap] 08/08: Update changelog, upload to unstable

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository gmap.

commit 97539d2867d551e1275145753469833f8059a066
Author: Alexandre Mestiashvili 
Date:   Fri Sep 15 09:45:42 2017 +0200

Update changelog, upload to unstable

Gbp-Dch: ignore
---
 debian/changelog | 7 +++
 1 file changed, 7 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 74dad12..db4b058 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+gmap (2017-09-11-1) unstable; urgency=medium
+
+  * New upstream version 2017-09-11
+  * Update d/libgmap1.symbols
+
+ -- Alexandre Mestiashvili   Fri, 15 Sep 2017 
09:45:13 +0200
+
 gmap (2017-09-05-1) unstable; urgency=medium
 
   * New upstream version 2017-09-05

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[med-svn] [gmap] branch upstream updated (67575fa -> 4495e01)

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a change to branch upstream
in repository gmap.

  from  67575fa   New upstream version 2017-08-15
  adds  cc72685   New upstream version 2017-09-05
   new  4495e01   New upstream version 2017-09-11

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:
 ChangeLog   |  35 ++
 Makefile.in |   2 +-
 TODO|   3 -
 VERSION |   2 +-
 configure   |  24 ++--
 src/ChangeLog   |   0
 src/Makefile.in |   2 +-
 src/compile | 165 
 src/get-genome.c|  88 ++-
 src/gmap.c  |  26 ++---
 src/gmapindex.c |  32 +++---
 src/pair.c  | 120 
 src/sarray-search.c | 307 +++-
 src/stage1hr.c  |   6 +-
 14 files changed, 424 insertions(+), 388 deletions(-)
 delete mode 100644 TODO
 delete mode 100644 src/ChangeLog
 delete mode 100644 src/compile

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[med-svn] [gmap] 04/08: Update changelog, upload to unstable

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository gmap.

commit ecd5a51f9061de86682f930d68f05cb2f53a249d
Author: Alexandre Mestiashvili 
Date:   Mon Sep 11 13:51:15 2017 +0200

Update changelog, upload to unstable

Gbp-Dch:ignore
---
 debian/changelog | 8 
 1 file changed, 8 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index f0ff7d0..74dad12 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+gmap (2017-09-05-1) unstable; urgency=medium
+
+  * New upstream version 2017-09-05
+  * Refresh install-data-local patch
+  * Update symbols file
+
+ -- Alexandre Mestiashvili   Mon, 11 Sep 2017 
13:50:59 +0200
+
 gmap (2017-08-15-1) unstable; urgency=medium
 
   [ Steffen Moeller ]

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[med-svn] [invesalius] branch master updated (0186f18 -> 75963f7)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository invesalius.

  from  0186f18   Fix changelog ID.  Thiago, this always should match the 
Uploaders field
   new  75963f7   Depends: s/python-imaging/python-pil/

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Summary of changes:
 debian/changelog | 7 +++
 debian/control   | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

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[med-svn] [gmap] 02/02: pristine-tar data for gmap_2017-09-11.orig.tar.xz

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch pristine-tar
in repository gmap.

commit 2a999c647c28ac80d4bcf8421e9eabc122c69364
Author: Alexandre Mestiashvili 
Date:   Fri Sep 15 09:16:27 2017 +0200

pristine-tar data for gmap_2017-09-11.orig.tar.xz
---
 gmap_2017-09-11.orig.tar.xz.delta | Bin 0 -> 10042 bytes
 gmap_2017-09-11.orig.tar.xz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/gmap_2017-09-11.orig.tar.xz.delta 
b/gmap_2017-09-11.orig.tar.xz.delta
new file mode 100644
index 000..b8d3782
Binary files /dev/null and b/gmap_2017-09-11.orig.tar.xz.delta differ
diff --git a/gmap_2017-09-11.orig.tar.xz.id b/gmap_2017-09-11.orig.tar.xz.id
new file mode 100644
index 000..6e2f3c8
--- /dev/null
+++ b/gmap_2017-09-11.orig.tar.xz.id
@@ -0,0 +1 @@
+3938fd7fea059c7a86100249a7dcd15913574a38

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[med-svn] [gmap] branch pristine-tar updated (b1819be -> 2a999c6)

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a change to branch pristine-tar
in repository gmap.

  from  b1819be   pristine-tar data for gmap_2017-08-15.orig.tar.xz
   new  e87ebba   pristine-tar data for gmap_2017-09-05.orig.tar.xz
   new  2a999c6   pristine-tar data for gmap_2017-09-11.orig.tar.xz

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
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Summary of changes:
 gmap_2017-09-05.orig.tar.xz.delta | Bin 0 -> 11209 bytes
 gmap_2017-09-05.orig.tar.xz.id|   1 +
 gmap_2017-09-11.orig.tar.xz.delta | Bin 0 -> 10042 bytes
 gmap_2017-09-11.orig.tar.xz.id|   1 +
 4 files changed, 2 insertions(+)
 create mode 100644 gmap_2017-09-05.orig.tar.xz.delta
 create mode 100644 gmap_2017-09-05.orig.tar.xz.id
 create mode 100644 gmap_2017-09-11.orig.tar.xz.delta
 create mode 100644 gmap_2017-09-11.orig.tar.xz.id

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[med-svn] [gmap] 01/08: Updated version 2017-09-05 from 'upstream/2017-09-05'

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository gmap.

commit 09dd35810df40df8b5d4a7774cb48337053be876
Merge: a8f6f3a cc72685
Author: Alexandre Mestiashvili 
Date:   Mon Sep 11 13:33:08 2017 +0200

Updated version 2017-09-05 from 'upstream/2017-09-05'

with Debian dir ec60280f775ed39880907ff43766a68c4ba2c781

 ChangeLog   |  20 
 VERSION |   2 +-
 configure   |  24 ++--
 src/get-genome.c|  88 ++-
 src/gmapindex.c |  32 +++---
 src/sarray-search.c | 307 +++-
 src/stage1hr.c  |   6 +-
 7 files changed, 294 insertions(+), 185 deletions(-)

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[med-svn] [invesalius] 01/01: Depends: s/python-imaging/python-pil/

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository invesalius.

commit 75963f719cd8fd6a57e8eaaf02621bc59b567625
Author: Andreas Tille 
Date:   Fri Sep 15 09:56:21 2017 +0200

Depends: s/python-imaging/python-pil/
---
 debian/changelog | 7 +++
 debian/control   | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 12f8175..7638aa8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+invesalius (3.1.1-2) UNRELEASED; urgency=medium
+
+  * Depends: s/python-imaging/python-pil/
+Closes: #866434
+
+ -- Andreas Tille   Fri, 15 Sep 2017 09:55:05 +0200
+
 invesalius (3.1.1-1) unstable; urgency=low
 
   [ Thiago Franco de Moraes ]
diff --git a/debian/control b/debian/control
index 2deb845..0aea933 100644
--- a/debian/control
+++ b/debian/control
@@ -24,7 +24,7 @@ Depends: ${python:Depends},
  python-scipy,
  python-skimage,
  python-wxgtk3.0,
- python-imaging,
+ python-pil,
  python-gdcm,
  python-vtkgdcm,
  python-vtk6,

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[med-svn] [nanopolish] 02/02: DEP3

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository nanopolish.

commit 08b25faf228f182168bc72be6d26f0c796155efd
Author: Andreas Tille 
Date:   Sat Sep 16 07:34:33 2017 +0200

DEP3
---
 debian/changelog |  1 +
 debian/patches/dontinstalleigen.patch| 10 ++
 debian/patches/fprintf_sizet.patch   | 16 
 debian/patches/gcc7.patch| 11 +++
 debian/patches/write_return_values_ignored.patch | 10 ++
 5 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 9ff8b0e..d95a447 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ nanopolish (0.8.1-2) UNRELEASED; urgency=medium
   * Team upload.
   * Hack around broken clean target which tries to build dependencies from
 external sources
+  * DEP3
 
  -- Andreas Tille   Sat, 16 Sep 2017 07:25:45 +0200
 
diff --git a/debian/patches/dontinstalleigen.patch 
b/debian/patches/dontinstalleigen.patch
index 3241833..2a8a702 100644
--- a/debian/patches/dontinstalleigen.patch
+++ b/debian/patches/dontinstalleigen.patch
@@ -1,7 +1,9 @@
-Index: nanopolish/Makefile
-===
 nanopolish.orig/Makefile
-+++ nanopolish/Makefile
+Author: Steffen Moeller
+Last-Update: 2017-09-16 02:14:07 +0200
+Description: Use Debian packaged libeigen
+
+--- a/Makefile
 b/Makefile
 @@ -16,7 +16,7 @@ CXX ?= g++
  CC ?= gcc
  
diff --git a/debian/patches/fprintf_sizet.patch 
b/debian/patches/fprintf_sizet.patch
index 869707e..ad0bf61 100644
--- a/debian/patches/fprintf_sizet.patch
+++ b/debian/patches/fprintf_sizet.patch
@@ -1,7 +1,9 @@
-Index: nanopolish/src/common/nanopolish_variant.cpp
-===
 nanopolish.orig/src/common/nanopolish_variant.cpp
-+++ nanopolish/src/common/nanopolish_variant.cpp
+Author: Steffen Moeller
+Last-Update: 2017-09-16 02:14:07 +0200
+Description: Fix format-error issues blamed by gcc-7
+
+--- a/src/common/nanopolish_variant.cpp
 b/src/common/nanopolish_variant.cpp
 @@ -175,7 +175,7 @@ void score_variant_group(VariantGroup& v
  max_r -= 1;
  
@@ -11,10 +13,8 @@ Index: nanopolish/src/common/nanopolish_variant.cpp
  }
  
  // Construct haplotypes (including the base haplotype with no variants)
-Index: nanopolish/src/nanopolish_haplotype.cpp
-===
 nanopolish.orig/src/nanopolish_haplotype.cpp
-+++ nanopolish/src/nanopolish_haplotype.cpp
+--- a/src/nanopolish_haplotype.cpp
 b/src/nanopolish_haplotype.cpp
 @@ -169,7 +169,7 @@ size_t Haplotype::_find_derived_index_by
  
  void Haplotype::print_debug_info() const
diff --git a/debian/patches/gcc7.patch b/debian/patches/gcc7.patch
index 104ca19..c972825 100644
--- a/debian/patches/gcc7.patch
+++ b/debian/patches/gcc7.patch
@@ -1,7 +1,10 @@
-Index: nanopolish/src/common/logger.hpp
-===
 nanopolish.orig/src/common/logger.hpp
-+++ nanopolish/src/common/logger.hpp
+Author: Steffen Moeller
+Last-Update: 2017-09-16 02:14:07 +0200
+Bug-Debian: https://bugs.debian.org/853568
+Description: Add missing header file to build with gcc-7
+
+--- a/src/common/logger.hpp
 b/src/common/logger.hpp
 @@ -72,6 +72,7 @@
  #include 
  #include 
diff --git a/debian/patches/write_return_values_ignored.patch 
b/debian/patches/write_return_values_ignored.patch
index be1b66f..d8f1153 100644
--- a/debian/patches/write_return_values_ignored.patch
+++ b/debian/patches/write_return_values_ignored.patch
@@ -1,7 +1,9 @@
-Index: nanopolish/src/alignment/nanopolish_eventalign.cpp
-===
 nanopolish.orig/src/alignment/nanopolish_eventalign.cpp
-+++ nanopolish/src/alignment/nanopolish_eventalign.cpp
+Author: Steffen Moeller
+Last-Updated: 2017-09-16 02:14:07 +0200
+Description: Do not ignore return values of samtool functions
+
+--- a/src/alignment/nanopolish_eventalign.cpp
 b/src/alignment/nanopolish_eventalign.cpp
 @@ -221,7 +221,7 @@ void emit_tsv_header(FILE* fp)
  
  void emit_sam_header(samFile* fp, const bam_hdr_t* hdr)

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[med-svn] [nanopolish] 01/02: Hack around broken clean target which tries to build dependencies from external sources

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository nanopolish.

commit dd75688dc928d99ce4007b132c934b1b21c1bd4c
Author: Andreas Tille 
Date:   Sat Sep 16 07:26:44 2017 +0200

Hack around broken clean target which tries to build dependencies from 
external sources
---
 debian/changelog | 8 
 debian/rules | 3 +++
 2 files changed, 11 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 212feb9..9ff8b0e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+nanopolish (0.8.1-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Hack around broken clean target which tries to build dependencies from
+external sources
+
+ -- Andreas Tille   Sat, 16 Sep 2017 07:25:45 +0200
+
 nanopolish (0.8.1-1) unstable; urgency=medium
 
   * Team upload
diff --git a/debian/rules b/debian/rules
index 14e94da..5d533cb 100755
--- a/debian/rules
+++ b/debian/rules
@@ -14,5 +14,8 @@ export LDFLAGS += $(CXXFLAGS) $(CPPFLAGS) -L/usr/lib/$(shell 
dpkg-architecture -
dh $@
 
 override_dh_auto_clean:
+   sed -i~ 's/^.depend: .*/.depend:/' Makefile
+   touch .depend
$(MAKE) clean
$(RM) .depend
+   mv Makefile~ Makefile

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[med-svn] [nanopolish] branch master updated (79cea4f -> 08b25fa)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository nanopolish.

  from  79cea4f   Proceeded to version 0.8.1
   new  dd75688   Hack around broken clean target which tries to build 
dependencies from external sources
   new  08b25fa   DEP3

The 2 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
been added to this reference.


Summary of changes:
 debian/changelog |  9 +
 debian/patches/dontinstalleigen.patch| 10 ++
 debian/patches/fprintf_sizet.patch   | 16 
 debian/patches/gcc7.patch| 11 +++
 debian/patches/write_return_values_ignored.patch | 10 ++
 debian/rules |  3 +++
 6 files changed, 39 insertions(+), 20 deletions(-)

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[med-svn] [plink1.9] 02/08: Update changelogs

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit ae8020adcc2ce64b8e8a3a7262c7643ebba1a4bb
Author: Dylan Aïssi 
Date:   Tue Sep 12 10:25:39 2017 +0200

Update changelogs
---
 debian/changelog| 5 +++--
 debian/upstream.docs/upstream.changelog | 6 +-
 debian/upstream/metadata| 2 +-
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 0c1224f..8d2ea59 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
-plink1.9 (1.90~b4.4-170531-3) UNRELEASED; urgency=medium
+plink1.9 (1.90~b4.7-170906-1) UNRELEASED; urgency=medium
 
-  * Add OMICtools and RRID refs.
+  * New upstream release.
+  * Add references to registries.
 
  -- Dylan Aïssi   Wed, 19 Jul 2017 23:50:02 +0200
 
diff --git a/debian/upstream.docs/upstream.changelog 
b/debian/upstream.docs/upstream.changelog
index 46e839c..3c1f534 100644
--- a/debian/upstream.docs/upstream.changelog
+++ b/debian/upstream.docs/upstream.changelog
@@ -1,6 +1,10 @@
 # Copy/Paste from https://www.cog-genomics.org/plink/1.9/
 
-21 May 2017: '--linear interaction sex' and '--logistic interaction sex' now 
work properly when no covariates are present. --tucc added to development build.
+15 Aug 2017: --lasso should now work properly when there are samples with all 
covariates present but the main phenotype missing.
+
+25 Jul: --lfile now works properly when the .map file has three columns.
+
+21 May: '--linear interaction sex' and '--logistic interaction sex' now work 
properly when no covariates are present. --tucc added to development build.
 
 9 May: --tests now works properly on MT and haploid chromosomes. Improved 
--score compatibility with v1.07 and v2.0.
 
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index 3322f8f..5da398c 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -16,5 +16,5 @@ Registry:
 Entry: PLINK
   - Name: OMICtools
 Entry: OMICS_00206
-  - Name: RRID
+  - Name: SciCrunch
 Entry: SCR_001757

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[med-svn] [plink1.9] 05/08: Remove Testsuite field from d/control, now automatically added

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit ac89834a10d8d2846e4b7139661b5c06a30e2be8
Author: Dylan Aïssi 
Date:   Wed Sep 13 15:06:11 2017 +0200

Remove Testsuite field from d/control, now automatically added
---
 debian/changelog | 1 +
 debian/control   | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index e1c66f0..91a4c6b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ plink1.9 (1.90~b4.7-170906-1) UNRELEASED; urgency=medium
   * Add references to registries.
   * Update 01.Fix_Makefile.patch.
   * Bump Standards-Version to 4.1.0.
+  * Remove Testsuite field from d/control, now automatically added.
 
  -- Dylan Aïssi   Wed, 19 Jul 2017 23:50:02 +0200
 
diff --git a/debian/control b/debian/control
index 5612a0c..8cd7a94 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,6 @@ Build-Depends: debhelper (>= 10),
libatlas-base-dev,
liblapack-dev,
zlib1g-dev
-Testsuite: autopkgtest
 Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/git/debian-med/plink1.9.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/plink1.9.git

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[med-svn] [plink1.9] branch master updated (fb47cdc -> 285131c)

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a change to branch master
in repository plink1.9.

  from  fb47cdc   Update changelogs
   new  ae340cc   New upstream version 1.90~b4.7-170906
   new  ae8020a   Update changelogs
   new  45b96a6   Update patch to fix makefile
   new  1c01d91   Bump Standards-Version to 4.1.0
   new  ac89834   Remove Testsuite field from d/control, now automatically 
added
   new  b7647ab   cme fix dpkg-control
   new  2f1154b   Upload to unstable
   new  285131c   Merge branch 'master' of 
git+ssh://git.debian.org/git/debian-med/plink1.9

The 8 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 |  8 +++--
 debian/control   | 12 
 debian/patches/01.Fix_Makefile.patch | 58 ++--
 debian/rules |  9 --
 4 files changed, 34 insertions(+), 53 deletions(-)

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[med-svn] [plink1.9] 06/08: cme fix dpkg-control

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit b7647abd32ece2500577d716b17156a3770ef22e
Author: Dylan Aïssi 
Date:   Wed Sep 13 15:09:47 2017 +0200

cme fix dpkg-control
---
 debian/changelog | 1 +
 debian/control   | 9 +
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 91a4c6b..12f8079 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ plink1.9 (1.90~b4.7-170906-1) UNRELEASED; urgency=medium
   * Update 01.Fix_Makefile.patch.
   * Bump Standards-Version to 4.1.0.
   * Remove Testsuite field from d/control, now automatically added.
+  * cme fix dpkg-control.
 
  -- Dylan Aïssi   Wed, 19 Jul 2017 23:50:02 +0200
 
diff --git a/debian/control b/debian/control
index 8cd7a94..3ffc86f 100644
--- a/debian/control
+++ b/debian/control
@@ -1,21 +1,22 @@
 Source: plink1.9
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team 

 Uploaders: Dylan Aïssi 
+Section: science
+Priority: optional
 Build-Depends: debhelper (>= 10),
help2man,
libatlas-base-dev,
liblapack-dev,
zlib1g-dev
 Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/git/debian-med/plink1.9.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/plink1.9.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/plink1.9.git
 Homepage: https://www.cog-genomics.org/plink/1.9/
 
 Package: plink1.9
 Architecture: any-amd64 any-i386 armel armhf mipsel
-Depends: ${misc:Depends}, ${shlibs:Depends}
+Depends: ${misc:Depends},
+ ${shlibs:Depends}
 Description: whole-genome association analysis toolset
  plink expects as input the data from SNP (single nucleotide polymorphism)
  chips of many individuals and their phenotypical description of a disease.

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[med-svn] [plink1.9] 08/08: Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/plink1.9

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit 285131cca935358f6775860c34636198e99454ac
Merge: 2f1154b fb47cdc
Author: Dylan Aïssi 
Date:   Sat Sep 16 00:02:47 2017 +0200

Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/plink1.9


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[med-svn] [plink1.9] 07/08: Upload to unstable

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit 2f1154b5621eabb26e114d27336e2013bdb5910f
Author: Dylan Aïssi 
Date:   Fri Sep 15 23:54:58 2017 +0200

Upload to unstable
---
 debian/changelog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 12f8079..40edc7b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-plink1.9 (1.90~b4.7-170906-1) UNRELEASED; urgency=medium
+plink1.9 (1.90~b4.7-170906-1) unstable; urgency=medium
 
   * New upstream release.
   * Add references to registries.
@@ -7,7 +7,7 @@ plink1.9 (1.90~b4.7-170906-1) UNRELEASED; urgency=medium
   * Remove Testsuite field from d/control, now automatically added.
   * cme fix dpkg-control.
 
- -- Dylan Aïssi   Wed, 19 Jul 2017 23:50:02 +0200
+ -- Dylan Aïssi   Fri, 15 Sep 2017 23:53:58 +0200
 
 plink1.9 (1.90~b4.4-170531-2) unstable; urgency=medium
 

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[med-svn] [plink1.9] annotated tag debian/1.90_b4.7-170906-1 created (now 159f3e1)

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a change to annotated tag debian/1.90_b4.7-170906-1
in repository plink1.9.

at  159f3e1   (tag)
   tagging  2f1154b5621eabb26e114d27336e2013bdb5910f (commit)
  replaces  debian/1.90_b4.4-170531-2
 tagged by  Dylan Aïssi
on  Sat Sep 16 00:00:30 2017 +0200

- Log -
plink1.9 Debian release 1.90~b4.7-170906-1

Dylan Aïssi (10):
  Add OMICtools and RRID refs
  Fix syntax metadata
  Update metadata Refs
  New upstream version 1.90~b4.7-170906
  Update changelogs
  Update patch to fix makefile
  Bump Standards-Version to 4.1.0
  Remove Testsuite field from d/control, now automatically added
  cme fix dpkg-control
  Upload to unstable

---

No new revisions were added by this update.

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[med-svn] [rdp-classifier] 01/01: Fix changelog

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository rdp-classifier.

commit a7d4f535014425f8f07c84f5dacd3f88b17e74a3
Author: Andreas Tille 
Date:   Fri Sep 15 18:37:04 2017 +0200

Fix changelog
---
 debian/changelog | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index fb71cb8..ec68928 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,9 @@
 rdp-classifier (2.10.2-2) UNRELEASED; urgency=medium
 
+  * Team upload
+
   [ Olivier Sallou ]
-  * d/control,d/junit.xml: fixes for Java 9 compilation (Closes #875789).
+  * d/control,d/junit.xml: fixes for Java 9 compilation (Closes: #875789).
   * debian/bin/rdp_classifier: add optional env variable JAVA_OPTS
 to java command line
 

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[med-svn] [rdp-classifier] branch master updated (b3a6991 -> a7d4f53)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository rdp-classifier.

  from  b3a6991   cme fix dpkg-control
   new  a7d4f53   Fix changelog

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Summary of changes:
 debian/changelog | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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[med-svn] [fast5] 01/01: Corrected for left-over conflict declaration.

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository fast5.

commit 008c7def9444c98177fc4803a7e7218866816331
Author: Steffen Moeller 
Date:   Fri Sep 15 18:32:02 2017 +0200

Corrected for left-over conflict declaration.
---
 debian/changelog | 7 +++
 debian/control   | 1 -
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index ad6b400..c8c8b4e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+fast5 (0.6.2-2) unstable; urgency=medium
+
+  * Corrected for erroneously declared conflict
+between python3-fast5 and python-fast5.
+
+ -- Steffen Moeller   Fri, 15 Sep 2017 18:19:20 +0200
+
 fast5 (0.6.2-1) unstable; urgency=medium
 
   * Team upload.
diff --git a/debian/control b/debian/control
index eeac9d8..67700a3 100644
--- a/debian/control
+++ b/debian/control
@@ -70,7 +70,6 @@ Description: executables of the Oxford Nanopore Fast5 library
 
 Package: python3-fast5
 Section: python
-Conflicts: python-fast5
 Architecture: any
 Depends:
${shlibs:Depends},

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[med-svn] [fast5] branch master updated (377c1fa -> 008c7de)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch master
in repository fast5.

  from  377c1fa   Fairly lintian-clean 0.6.2, just uploaded.
   new  008c7de   Corrected for left-over conflict declaration.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 debian/changelog | 7 +++
 debian/control   | 1 -
 2 files changed, 7 insertions(+), 1 deletion(-)

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[med-svn] r24049 - trunk/packages/rdp-classifier/trunk

[Andreas Tille]

Author: tille
Date: 2017-09-15 16:32:47 + (Fri, 15 Sep 2017)
New Revision: 24049

Added:
   trunk/packages/rdp-classifier/trunk/README.status
Log:
Document move to Git


Added: trunk/packages/rdp-classifier/trunk/README.status
===
--- trunk/packages/rdp-classifier/trunk/README.status   
(rev 0)
+++ trunk/packages/rdp-classifier/trunk/README.status   2017-09-15 16:32:47 UTC 
(rev 24049)
@@ -0,0 +1,7 @@
+---
+Format: 1
+Status: git
+SVNDeleteRevision: 24048
+URL: https://git.debian.org/git/debian-med/rdp-classifier.git
+Comment: >
+  This package is now managed in a Git repository.


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[med-svn] [rdp-classifier] 02/02: cme fix dpkg-control

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository rdp-classifier.

commit b3a6991403a34a72c058ff656c9f29e01152069a
Author: Andreas Tille 
Date:   Fri Sep 15 18:30:50 2017 +0200

cme fix dpkg-control
---
 debian/changelog | 2 ++
 debian/control   | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 5636d1c..fb71cb8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,8 @@ rdp-classifier (2.10.2-2) UNRELEASED; urgency=medium
   [ Andreas Tille ]
   * Move packaging from SVN to Git
   * debhelper 10
+  * cme fix dpkg-control
+  * Standards-Version: 4.1.0 (no changes needed)
 
  -- Olivier Sallou   Fri, 15 Sep 2017 13:25:30 +
 
diff --git a/debian/control b/debian/control
index be74211..ecd7aad 100644
--- a/debian/control
+++ b/debian/control
@@ -11,13 +11,13 @@ Build-Depends: debhelper (>= 10),
libcommons-cli-java,
javahelper,
rdp-readseq,
-   rdp-alignment (>= 1.2.0),
-   librdp-taxonomy-tree-java (>= 1.2.0),
+   rdp-alignment,
+   librdp-taxonomy-tree-java,
libjfreechart-java,
ant,
ant-optional,
ant-contrib
-Standards-Version: 3.9.6
+Standards-Version: 4.1.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rdp-classifier.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/rdp-classifier.git
 Homepage: https://github.com/rdpstaff/classifier

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[med-svn] [rdp-classifier] 01/02: debhelper 10

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository rdp-classifier.

commit c6c0155436eea374a888414837a28cfe1757fead
Author: Andreas Tille 
Date:   Fri Sep 15 18:29:56 2017 +0200

debhelper 10
---
 debian/changelog | 1 +
 debian/compat| 2 +-
 debian/control   | 2 +-
 debian/rules | 3 ---
 4 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 89cc65c..5636d1c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,7 @@ rdp-classifier (2.10.2-2) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * Move packaging from SVN to Git
+  * debhelper 10
 
  -- Olivier Sallou   Fri, 15 Sep 2017 13:25:30 +
 
diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index 3970e0e..be74211 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Uploaders: Steffen Moeller ,
Andreas Tille 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
default-jdk,
junit4,
libcommons-cli-java,
diff --git a/debian/rules b/debian/rules
index cf0ae18..fe5fcd1 100755
--- a/debian/rules
+++ b/debian/rules
@@ -24,9 +24,6 @@ override_dh_auto_test:
cp debian/junit.xml ./tmp-junit.xml
ant -f tmp-junit.xml junit
 
-override_dh_builddeb:
-   dh_builddeb -- -Z xz
-
 override_dh_compress:
dh_compress -X.fasta
 

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[med-svn] [rdp-classifier] branch master updated (c425480 -> b3a6991)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository rdp-classifier.

  from  c425480   Move packaging from SVN to Git
   new  c6c0155   debhelper 10
   new  b3a6991   cme fix dpkg-control

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/changelog | 3 +++
 debian/compat| 2 +-
 debian/control   | 8 
 debian/rules | 3 ---
 4 files changed, 8 insertions(+), 8 deletions(-)

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[med-svn] [gbrowse] 02/05: Fix broken link

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository gbrowse.

commit b53b5deda928b542a1ea3263d36c6fd02393a689
Author: Andreas Tille 
Date:   Fri Sep 15 23:35:51 2017 +0200

Fix broken link
---
 debian/changelog | 7 +++
 debian/rules | 5 +
 2 files changed, 12 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 8256eb6..54c8418 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+gbrowse (2.56+dfsg-3) UNRELEASED; urgency=medium
+
+  * Fix broken link
+Closes: #857213
+
+ -- Andreas Tille   Fri, 15 Sep 2017 23:34:45 +0200
+
 gbrowse (2.56+dfsg-2) unstable; urgency=medium
 
   * Remove duplicated file which is also available in libbio-perl-perl
diff --git a/debian/rules b/debian/rules
index 14f875d..44f6d89 100755
--- a/debian/rules
+++ b/debian/rules
@@ -62,3 +62,8 @@ override_dh_installman:
dh_installman
rm -rf debian/gbrowse/man
rm -rf debian/gbrowse-calign/man
+
+override_dh_link:
+   dh_link
+   # Fix broken link
+   ln -sf /var/cache/gbrowse/images 
debian/gbrowse/usr/share/gbrowse/htdocs/i

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