Run of fresh-releases for igv

Try this locally (using silver-platter):

debian-svp new-upstream igv 
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Processing: igv
Total 11691 (delta 7990), reused 11319 (delta 7625)

Total 126 (delta 31), reused 121 (delta 26)

Total 0 (delta 0), reused 0 (delta 0)
Using upstream branch https://github.com/broadinstitute/IGV (guessed)
(14/39)
Total 77416 (delta 15), reused 39 (delta 13), pack-reused 77360
Using version string 2.6.3.
No upstream upstream-revision format specified, trying tag:2.6.3
No upstream upstream-revision format specified, trying tag:igv-2.6.3
No upstream upstream-revision format specified, trying tag:v2.6.3
Using uscan to look for the upstream tarball.
uscan warn: No files matched excluded pattern as the last matching glob: lib/jfreechart*
uscan warn: No files matched excluded pattern as the last matching glob: lib/jide-oss-*
Total 77416 (delta 15), reused 39 (delta 13), pack-reused 77360
test3 does not point to a valid object
v.2.3.77 does not point to a valid object
v2.2.0-b1-Dec19 does not point to a valid object
v2.2.0-b2 does not point to a valid object
v2.2.1 does not point to a valid object
v2.2.10 does not point to a valid object
v2.2.11 does not point to a valid object
v2.2.12 does not point to a valid object
v2.2.13 does not point to a valid object
v2.2.2 does not point to a valid object
v2.2.3 does not point to a valid object
v2.2.4 does not point to a valid object
v2.2.5 does not point to a valid object
v2.2.6 does not point to a valid object
v2.2.7 does not point to a valid object
v2.2.8 does not point to a valid object
v2.2.9 does not point to a valid object
v2.3.75 does not point to a valid object
v2.3.76 does not point to a valid object
v2.3.78 does not point to a valid object
v2.3.79 does not point to a valid object
v2.3.80 does not point to a valid object
v2.3.81 does not point to a valid object
v2.3.82 does not point to a valid object
v2.3.83 does not point to a valid object
v2.3.84 does not point to a valid object
v2.3.85 does not point to a valid object
v2.3.86 does not point to a valid object
v2.3.87 does not point to a valid object
v2.3.88 does not point to a valid object
v2.3.89 does not point to a valid object
v2.3.90 does not point to a valid object
v2.3.91 does not point to a valid object
v2.3.92 does not point to a valid object
v2.3.93 does not point to a valid object
v2.3.94 does not point to a valid object
v2.3.95 does not point to a valid object
v2.3.96 does not point to a valid object
v2.3.97 does not point to a valid object
v2.3.98 does not point to a valid object
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Committing to: /home/janitor/tmp/tmplpd4ngt0/igv/
modified .gitignore
modified .travis.yml
modified README.md
modified build.gradle
added build_java11.gradle
deleted build_java9.gradle
modified debian/changelog
added genomes/db/1kg_ref
added genomes/db/1kg_ref/1kg_ref_dataServerRegistry.txt
added genomes/db/1kg_v37
added genomes/db/1kg_v37/1kg_v37_dataServerRegistry.txt
modified genomes/db/AGPv3.31/AGPv3.31_dataServerRegistry.txt
added genomes/db/D.discoideum
added genomes/db/D.discoideum/D.discoideum_dataServerRegistry.txt
added genomes/db/GSM552910
added genomes/db/GSM552910/GSM552910_dataServerRegistry.txt
added genomes/db/S_pombe_709
added genomes/db/S_pombe_709/S_pombe_709_dataServerRegistry.txt
added genomes/db/WS241
added genomes/db/WS241/ws241_dataServerRegistry.txt
added genomes/db/b37
added genomes/db/b37/b37_dataServerRegistry.txt
added genomes/db/canFam2
added genomes/db/canFam2/canFam2_dataServerRegistry.txt
added genomes/db/ce4
added genomes/db/ce4/ce4_dataServerRegistry.txt
added genomes/db/ce6
added genomes/db/ce6/ce6_annotations.xml
added genomes/db/ce6/ce6_dataServerRegistry.txt
added genomes/db/danRer11
added genomes/db/danRer11/danRer11_annotations.xml
added genomes/db/danRer11/danRer11_dataServerRegistry.txt
added genomes/db/dm2
added genomes/db/dm2/dm2_dataServerRegistry.txt
added genomes/db/dm3
added genomes/db/dm3/dm3_dataServerRegistry.txt
added genomes/db/dmel_r5.33
added genomes/db/dmel_r5.33/dmel_r5.33_dataServerRegistry.txt
modified genomes/db/galGal5/galGal5_annotations.xml
modified genomes/db/galGal5/galGal5_dataServerRegistry.txt
added genomes/db/hg18
added genomes/db/hg18/hg18_dataServerRegistry.txt
modified genomes/db/hg19/hg19_annotations.xml
modified genomes/db/hg19/hg19_dataServerRegistry.txt
modified genomes/db/hg38/hg38_annotations.xml
modified genomes/db/hg38/hg38_dataServerRegistry.txt
modified genomes/db/mm10/mm10_annotations.xml
modified genomes/db/mm10/mm10_dataServerRegistry.txt
added genomes/db/mm8
added genomes/db/mm8/mm8_dataServerRegistry.txt
added genomes/db/mm9
added genomes/db/mm9/epigenetics_mm9_public.xml
added genomes/db/mm9/mm9_annotations.xml
added genomes/db/mm9/mm9_dataServerRegistry.txt
added genomes/db/rn4
added genomes/db/rn4/rn4_annotations.xml
added genomes/db/rn4/rn4_dataServerRegistry.txt
added genomes/db/tair9
added genomes/db/tair9/tair9_dataServerRegistry.txt
added genomes/db/ws220/WS220_dataServerRegistry.txt
added genomes/db/xenTro2
added genomes/db/xenTro2/xenTro2_dataServerRegistry.txt
modified genomes/genomes.txt
modified genomes/sizes/sacCer3.chrom.sizes
modified gradle/wrapper/gradle-wrapper.jar
modified gradle/wrapper/gradle-wrapper.properties
modified gradle.properties
added lib/jide-common-3.7.3.jar
deleted lib_java9
deleted lib_java9/jide-oss-2018.04.18-master.jar
modified license.txt
added resources/IGV_64.ico
modified scripts/igv.bat
modified scripts/igv.sh
added scripts/igv_32.bat
modified scripts/igvtools_gui
added scripts/java11
added scripts/java11/IGV_mac.app.command
added scripts/java11/Info.plist.template
added scripts/java11/igv.args
added scripts/java11/igv.bat
added scripts/java11/igv.command
added scripts/java11/igv.sh
added scripts/java11/igv_hidpi.sh
added scripts/java11/igvtools
added scripts/java11/igvtools.bat
added scripts/java11/igvtools_gui
added scripts/java11/igvtools_gui.bat
added scripts/java11/igvtools_gui.command
added scripts/java11/igvtools_gui_hidpi
added scripts/java11/igvtools_readme.txt
added scripts/java11/readme.txt
added scripts/java11/test_suite.args
deleted scripts/java9
deleted scripts/java9/Info.plist.template
deleted scripts/java9/igv.args
deleted scripts/java9/igv.bat
deleted scripts/java9/igv.command
deleted scripts/java9/igv.sh
deleted scripts/java9/igv_hidpi.sh
deleted scripts/java9/igvtools
deleted scripts/java9/igvtools_gui
deleted scripts/java9/igvtools_gui.bat
deleted scripts/java9/igvtools_gui.command
deleted scripts/java9/igvtools_gui_hidpi
deleted scripts/java9/igvtools_readme.txt
deleted scripts/java9/readme.txt
deleted scripts/java9/test_suite.args
added scripts/nsis
added scripts/nsis/installer.nsi
added scripts/nsis/license_win.txt
modified src/main/java/org/broad/igv/DirectoryManager.java
modified src/main/java/org/broad/igv/Globals.java
modified src/main/java/org/broad/igv/batch/CommandExecutor.java
modified src/main/java/org/broad/igv/batch/CommandListener.java
added src/main/java/org/broad/igv/bedpe
added src/main/java/org/broad/igv/bedpe/BedPE.java
added src/main/java/org/broad/igv/bedpe/BedPEFeature.java
added src/main/java/org/broad/igv/bedpe/BedPEInterFeature.java
added src/main/java/org/broad/igv/bedpe/BedPEParser.java
added src/main/java/org/broad/igv/bedpe/BedPERenderer.java
added src/main/java/org/broad/igv/bedpe/BedPEShape.java
added src/main/java/org/broad/igv/bedpe/BedPEUtils.java
added src/main/java/org/broad/igv/bedpe/InteractionTrack.java
added src/main/java/org/broad/igv/bedpe/NestedArcRenderer.java
added src/main/java/org/broad/igv/bedpe/PEBlockRenderer.java
added src/main/java/org/broad/igv/bedpe/ProportionalArcRenderer.java
modified src/main/java/org/broad/igv/data/DatasetDataSource.java
modified src/main/java/org/broad/igv/feature/FeatureFileUtils.java
modified src/main/java/org/broad/igv/feature/FeatureUtils.java
modified src/main/java/org/broad/igv/feature/IGVFeature.java
modified src/main/java/org/broad/igv/feature/Mutation.java
modified src/main/java/org/broad/igv/feature/MutationTrackLoader.java
modified src/main/java/org/broad/igv/feature/basepair/BasePairRenderer.java
modified src/main/java/org/broad/igv/feature/basepair/BasePairTrack.java
deleted src/main/java/org/broad/igv/feature/bedpe
deleted src/main/java/org/broad/igv/feature/bedpe/BedPEFeature.java
deleted src/main/java/org/broad/igv/feature/bedpe/BedPEParser.java
deleted src/main/java/org/broad/igv/feature/bedpe/BedPEUtils.java
deleted src/main/java/org/broad/igv/feature/bedpe/InteractionTrack.java
modified src/main/java/org/broad/igv/feature/genome/GenomeListItem.java
modified src/main/java/org/broad/igv/feature/genome/GenomeManager.java
modified src/main/java/org/broad/igv/feature/genome/RemoveGenomesDialog.java
modified src/main/java/org/broad/igv/feature/tribble/CodecFactory.java
modified src/main/java/org/broad/igv/feature/tribble/GFFCodec.java
modified src/main/java/org/broad/igv/feature/tribble/IGVBEDCodec.java
modified src/main/java/org/broad/igv/feature/tribble/MUTCodec.java
modified src/main/java/org/broad/igv/feature/tribble/reader/IGVComponentMethods.java
deleted src/main/java/org/broad/igv/ga4gh
deleted src/main/java/org/broad/igv/ga4gh/Ga4ghAPIHelper.java
deleted src/main/java/org/broad/igv/ga4gh/Ga4ghAlignment.java
deleted src/main/java/org/broad/igv/ga4gh/Ga4ghAlignmentReader.java
deleted src/main/java/org/broad/igv/ga4gh/Ga4ghDataset.java
deleted src/main/java/org/broad/igv/ga4gh/Ga4ghLoadDialog.java
deleted src/main/java/org/broad/igv/ga4gh/Ga4ghProvider.java
deleted src/main/java/org/broad/igv/ga4gh/Ga4ghReadset.java
deleted src/main/java/org/broad/igv/ga4gh/GoogleUtils.java
deleted src/main/java/org/broad/igv/ga4gh/OAuthUtils.java
added src/main/java/org/broad/igv/google
added src/main/java/org/broad/igv/google/Ga4ghAPIHelper.java
added src/main/java/org/broad/igv/google/Ga4ghAlignment.java
added src/main/java/org/broad/igv/google/Ga4ghAlignmentReader.java
added src/main/java/org/broad/igv/google/Ga4ghDataset.java
added src/main/java/org/broad/igv/google/Ga4ghProvider.java
added src/main/java/org/broad/igv/google/Ga4ghReadset.java
added src/main/java/org/broad/igv/google/GoogleUtils.java
added src/main/java/org/broad/igv/google/OAuthUtils.java
modified src/main/java/org/broad/igv/gs/GSOpenSessionMenuAction.java
modified src/main/java/org/broad/igv/maf/MAFParser.java
modified src/main/java/org/broad/igv/prefs/Constants.java
modified src/main/java/org/broad/igv/prefs/IGVPreferences.java
modified src/main/java/org/broad/igv/prefs/PreferenceEditorNew.java
modified src/main/java/org/broad/igv/prefs/PreferencesEditor.java
modified src/main/java/org/broad/igv/renderer/IGVFeatureRenderer.java
modified src/main/java/org/broad/igv/renderer/LineplotRenderer.java
modified src/main/java/org/broad/igv/renderer/SpliceJunctionRenderer.java
modified src/main/java/org/broad/igv/renderer/XYPlotRenderer.java
modified src/main/java/org/broad/igv/sam/AlignmentPacker.java
modified src/main/java/org/broad/igv/sam/AlignmentTrack.java
modified src/main/java/org/broad/igv/sam/Row.java
modified src/main/java/org/broad/igv/sam/SAMAlignment.java
modified src/main/java/org/broad/igv/sam/reader/AlignmentReaderFactory.java
modified src/main/java/org/broad/igv/sam/reader/BAMReader.java
modified src/main/java/org/broad/igv/sashimi/SashimiJunctionRenderer.java
modified src/main/java/org/broad/igv/session/IGVSessionReader.java
modified src/main/java/org/broad/igv/session/SessionWriter.java
modified src/main/java/org/broad/igv/track/AbstractTrack.java
modified src/main/java/org/broad/igv/track/FeatureTrack.java
modified src/main/java/org/broad/igv/track/GFFFeatureSource.java
modified src/main/java/org/broad/igv/track/MergedTracks.java
modified src/main/java/org/broad/igv/track/MutationTrack.java
modified src/main/java/org/broad/igv/track/PackedFeatures.java
modified src/main/java/org/broad/igv/track/PackedFeaturesSpliceJunctions.java
modified src/main/java/org/broad/igv/track/RenderContext.java
modified src/main/java/org/broad/igv/track/TrackLoader.java
modified src/main/java/org/broad/igv/track/TrackMenuUtils.java
modified src/main/java/org/broad/igv/track/TribbleFeatureSource.java
modified src/main/java/org/broad/igv/ui/HeatmapScaleDialog.java
modified src/main/java/org/broad/igv/ui/IGV.java
modified src/main/java/org/broad/igv/ui/IGVMenuBar.java
modified src/main/java/org/broad/igv/ui/Main.java
modified src/main/java/org/broad/igv/ui/UIConstants.java
deleted src/main/java/org/broad/igv/ui/action/BrowseGa4ghAction.java
modified src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java
modified src/main/java/org/broad/igv/ui/action/MenuAction.java
modified src/main/java/org/broad/igv/ui/action/OpenSessionMenuAction.java
added src/main/java/org/broad/igv/ui/action/ReloadSessionMenuAction.java
modified src/main/java/org/broad/igv/ui/color/ColorPanel.java
modified src/main/java/org/broad/igv/ui/commandbar/GenomeComboBox.java
modified src/main/java/org/broad/igv/ui/commandbar/GenomeListManager.java
modified src/main/java/org/broad/igv/ui/commandbar/IGVCommandBar.java
modified src/main/java/org/broad/igv/ui/legend/LegendPanel.java
modified src/main/java/org/broad/igv/ui/panel/AttributeHeaderPanel.java
modified src/main/java/org/broad/igv/ui/panel/CytobandPanel.java
modified src/main/java/org/broad/igv/ui/panel/ReferenceFrame.java
modified src/main/java/org/broad/igv/ui/panel/RegionMenu.java
modified src/main/java/org/broad/igv/ui/panel/RulerPanel.java
modified src/main/java/org/broad/igv/ui/panel/TrackNamePanel.java
modified src/main/java/org/broad/igv/ui/panel/ZoomSliderPanel.java
modified src/main/java/org/broad/igv/ui/util/LoadFromURLDialog.java
added src/main/java/org/broad/igv/util/FeatureCache.java
modified src/main/java/org/broad/igv/util/FileUtils.java
modified src/main/java/org/broad/igv/util/HttpUtils.java
modified src/main/java/org/broad/igv/util/ParsingUtils.java
modified src/main/java/org/broad/igv/util/ResourceLocator.java
modified src/main/java/org/broad/igv/util/TutorialUtils.java
modified src/main/java/org/broad/igv/util/stream/IGVSeekableStreamFactory.java
modified src/main/java/org/broad/igv/util/stream/IGVUrlHelper.java
added src/main/java/org/broad/igv/util/stream/IGVUrlHelperFactory.java
modified src/main/java/org/broad/igv/variant/VariantMenu.java
modified src/main/java/org/broad/igv/variant/VariantTrack.java
added src/main/java11
added src/main/java11/module-info.java
added src/main/java11/org
added src/main/java11/org/broad
added src/main/java11/org/broad/igv
added src/main/java11/org/broad/igv/ui
added src/main/java11/org/broad/igv/ui/DesktopIntegration.java
deleted src/main/java9
deleted src/main/java9/module-info.java
deleted src/main/java9/org
deleted src/main/java9/org/broad
deleted src/main/java9/org/broad/igv
deleted src/main/java9/org/broad/igv/ui
deleted src/main/java9/org/broad/igv/ui/DesktopIntegration.java
deleted src/main/resources/org/broad/igv/ga4gh
deleted src/main/resources/org/broad/igv/ga4gh/Ga4ghLoadDialog.jfd
deleted src/main/resources/org/broad/igv/ga4gh/resources
deleted src/main/resources/org/broad/igv/ga4gh/resources/config.json
added src/main/resources/org/broad/igv/google
added src/main/resources/org/broad/igv/google/Ga4ghLoadDialog.jfd
added src/main/resources/org/broad/igv/google/resources
added src/main/resources/org/broad/igv/google/resources/config.json
modified src/main/resources/org/broad/igv/prefs/preferences.tab
modified src/test/java/org/broad/igv/feature/tribble/MUTCodecTest.java
modified src/test/java/org/broad/igv/maf/MAFParserTest.java
modified src/test/java/org/broad/igv/track/PackedFeaturesTest.java
modified test/data/bam/BAMFileIndexTest/index_test.bam
modified test/data/bam/BAMFileIndexTest/index_test.bam.bai
modified test/data/bam/BAMFileIndexTest/index_test.bam.csi
deleted test/data/maf/LAST_alignment_simulated_SV.maf
deleted test/data/maf/LAST_alignment_simulated_SV.sam
added test/data/maf/tcga_test.maf
added test/data/maf/test.maf
added test/data/maf/test.maflite.tsv
deleted test/data/maf/ucscSample.maf
deleted test/data/maf/ucscSimpleExample.maf
added test/data/maf_ucsc
added test/data/maf_ucsc/LAST_alignment_simulated_SV.maf
added test/data/maf_ucsc/LAST_alignment_simulated_SV.sam
added test/data/maf_ucsc/ucscSample.maf
added test/data/maf_ucsc/ucscSimpleExample.maf
modified test/data/sessions/canFam2_local.xml
added test/data/sessions/ecoloi.bed
added test/data/sessions/fasta_local.xml
added test/data/sessions/fasta_local_absolute.xml
Committed revision 235.
Worker failed: An error (1) occurred refreshing quilt patches: None

Applying patch debian/patches/fix_gradle.patch
can't find file to patch at input line 12
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|Subject: adapt gradle build for debian
|Description: gradle build file needs to add debian based libraries
| Needs some adaptation also to support Java 9 modules.
| All Debian libraries do not provide Module name in their manifest. In this
| case, system tries to get it from Jar name, so module names need also to be
| adapted for those libraries to match Debian jar names.
|Author: Olivier Sallou <osallou@debian.org>
|Last-Updated: 2018-10-17
|Forwarded: no
|--- a/build_java9.gradle
|+++ b/build_java9.gradle
--------------------------
No file to patch.  Skipping patch.
5 out of 5 hunks ignored
can't find file to patch at input line 95
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- a/src/main/java9/module-info.java
|+++ b/src/main/java9/module-info.java
--------------------------
No file to patch.  Skipping patch.
2 out of 2 hunks ignored
patching file src/main/java/org/broad/igv/util/stream/IGVSeekableBufferedStream.java
Patch debian/patches/fix_gradle.patch does not apply (enforce with -f)

Elapsed time: 1:02:28.735245

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