This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository artemis.
commit 5636cf8f3d0dbec23e280aefaecc7649a94f5e63 Author: Andreas Tille <[email protected]> Date: Thu Dec 8 09:21:45 2016 +0100 Cleanup patches and add DEP3 headers --- debian/changelog | 4 ++ debian/patches/CRAMReferenceSequenceFile.patch | 21 ---------- debian/patches/htsjdk-api-change.patch | 3 ++ debian/patches/java-8-sort.patch | 57 -------------------------- debian/patches/samreader.patch | 6 +++ debian/patches/use-lang3.patch | 4 ++ 6 files changed, 17 insertions(+), 78 deletions(-) diff --git a/debian/changelog b/debian/changelog index 7d37907..f259818 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,10 +1,14 @@ artemis (16.0.17+dfsg-1) UNRELEASED; urgency=medium + [ Sascha Steinbiss ] * Team upload. * New upstream release. * Refresh patches. * Avoid use of deprecated SAM access method to fix FTBFS. + [ Andreas Tille ] + * Cleanup patches and add DEP3 headers + -- Sascha Steinbiss <[email protected]> Wed, 07 Dec 2016 22:19:05 +0000 artemis (16.0.0+dfsg-5) unstable; urgency=medium diff --git a/debian/patches/CRAMReferenceSequenceFile.patch b/debian/patches/CRAMReferenceSequenceFile.patch deleted file mode 100644 index 1ccb12e..0000000 --- a/debian/patches/CRAMReferenceSequenceFile.patch +++ /dev/null @@ -1,21 +0,0 @@ -Description: Override abstract method - Compilation otherwise fails (at least using dependencies from Debian packages) - because an abstract class is not overridden. This patch provides a simple - override of the offending method -Author: Afif Elghraoui <[email protected]> -Forwarded: https://github.com/sanger-pathogens/Artemis/pull/218 -Last-Update: 2015-10-22 ---- artemis.orig/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java -+++ artemis/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java -@@ -107,5 +107,8 @@ - public void reset() - { - } -- -- } -\ No newline at end of file -+ -+ public void close() -+ { -+ } -+ } diff --git a/debian/patches/htsjdk-api-change.patch b/debian/patches/htsjdk-api-change.patch index f05d5ee..4de961d 100644 --- a/debian/patches/htsjdk-api-change.patch +++ b/debian/patches/htsjdk-api-change.patch @@ -1,5 +1,8 @@ Description: adjust log configuration to new API Author: Sascha Steinbiss <[email protected]> +Bug-Debian: https://bugs.debian.org/808851 +Last-Update: 2016-03-25 11:24:07 +0000 + --- a/uk/ac/sanger/artemis/components/alignment/BamView.java +++ b/uk/ac/sanger/artemis/components/alignment/BamView.java @@ -116,7 +116,7 @@ diff --git a/debian/patches/java-8-sort.patch b/debian/patches/java-8-sort.patch deleted file mode 100644 index dc384d5..0000000 --- a/debian/patches/java-8-sort.patch +++ /dev/null @@ -1,57 +0,0 @@ -Description: fix name clash with Java 8 List.sort() -Author: Sascha Steinbiss <[email protected]> ---- a/uk/ac/sanger/artemis/AlignMatchVector.java -+++ b/uk/ac/sanger/artemis/AlignMatchVector.java -@@ -107,7 +107,7 @@ - * @param cmp The returned vector will be sorted with this Comparator. - **/ - public void sort (final Comparator cmp) { -- vector = vector.sort (cmp); -+ vector = vector.mysort (cmp); - } - - /** ---- a/uk/ac/sanger/artemis/FeatureVector.java -+++ b/uk/ac/sanger/artemis/FeatureVector.java -@@ -154,7 +154,7 @@ - public FeatureVector sort (final Comparator cmp) { - final FeatureVector return_vector = (FeatureVector) clone (); - -- return_vector.vector = return_vector.vector.sort (cmp); -+ return_vector.vector = return_vector.vector.mysort (cmp); - - return return_vector; - } ---- a/uk/ac/sanger/artemis/io/KeyVector.java -+++ b/uk/ac/sanger/artemis/io/KeyVector.java -@@ -65,7 +65,7 @@ - * Sorts the elements of the vector using a simple O(n^2) selection - * sort. - */ -- public void sort() -+ public void mysort() - { - int smallest; - ---- a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java -+++ b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java -@@ -175,7 +175,7 @@ - return null; - } - -- return_vector.sort (); -+ return_vector.mysort (); - return return_vector; - } - ---- a/uk/ac/sanger/artemis/util/FastVector.java -+++ b/uk/ac/sanger/artemis/util/FastVector.java -@@ -91,7 +91,7 @@ - * Return a sorted copy of this vector. - * @param cmp The returned vector will be sorted with this Comparator. - **/ -- public FastVector sort(final Comparator cmp) -+ public FastVector mysort(final Comparator cmp) - { - final FastVector return_vector = (FastVector)clone(); - Collections.sort(return_vector, cmp); diff --git a/debian/patches/samreader.patch b/debian/patches/samreader.patch index d81535c..6353b9b 100644 --- a/debian/patches/samreader.patch +++ b/debian/patches/samreader.patch @@ -1,3 +1,9 @@ +Description: Implement new htsjdk API + See https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910 +Author: Sascha Steinbiss <[email protected]> +Bug-Debian: https://bugs.debian.org/846671 +Last-Update: 2016-12-07 23:37:52 +0000 + --- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java +++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java @@ -31,7 +31,7 @@ diff --git a/debian/patches/use-lang3.patch b/debian/patches/use-lang3.patch index 4441b30..04e7a16 100644 --- a/debian/patches/use-lang3.patch +++ b/debian/patches/use-lang3.patch @@ -1,3 +1,7 @@ +Description: use lang3 +Author: Sascha Steinbiss +Last-Update: 2016-12-07 23:37:09 +0000 + --- a/uk/ac/sanger/artemis/io/GFF3Encoder.java +++ b/uk/ac/sanger/artemis/io/GFF3Encoder.java @@ -22,7 +22,7 @@ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/artemis.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
