Pierre Gruet pushed to branch master at Debian Java Maintainers / jalview
Commits: 6b9b33af by Pierre Gruet at 2021-02-07T21:58:56+01:00 Adding a memory limitation for autopkgtest - - - - - d4860f7d by Pierre Gruet at 2021-02-07T21:59:19+01:00 Fixing a typo in d/tests/run-unit-test - - - - - acf3eeae by Pierre Gruet at 2021-02-07T22:10:02+01:00 Removing now useless d/TODO and d/dirs files - - - - - a9e09313 by Pierre Gruet at 2021-02-07T23:05:15+01:00 Upload to unstable - - - - - 5 changed files: - − debian/TODO - debian/changelog - − debian/dirs - debian/tests/run-unit-test - debian/tests/someCommandLineInvocations Changes: ===================================== debian/TODO deleted ===================================== @@ -1,52 +0,0 @@ -The following dependencies appear not to be in Debian: - - [javac] src/jalview/datamodel/SequenceI.java:26: error: package fr.orsay.lri.varna.models.rna does not exist - [javac] src/jalview/datamodel/Sequence.java:37: error: package fr.orsay.lri.varna.models.rna does not exist - [javac] src/jalview/util/ImageMaker.java:39: error: package org.jfree.graphics2d.svg does not exist - [javac] src/jalview/util/ImageMaker.java:40: error: package org.jfree.graphics2d.svg does not exist - [javac] src/jalview/gui/DasSourceBrowser.java:50: error: package org.biodas.jdas.schema.sources does not exist - [javac] src/jalview/gui/DasSourceBrowser.java:51: error: package org.biodas.jdas.schema.sources does not exist - [javac] src/jalview/gui/DasSourceBrowser.java:52: error: package org.biodas.jdas.schema.sources does not exist - [javac] src/jalview/gui/DasSourceBrowser.java:53: error: package org.biodas.jdas.schema.sources does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:51: error: package org.biodas.jdas.client does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:52: error: package org.biodas.jdas.client.adapters.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:53: error: package org.biodas.jdas.client.adapters.features.DasGFFAdapter does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:54: error: package org.biodas.jdas.client.threads does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:55: error: package org.biodas.jdas.schema.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:56: error: package org.biodas.jdas.schema.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:57: error: package org.biodas.jdas.schema.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:58: error: package org.biodas.jdas.schema.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:59: error: package org.biodas.jdas.schema.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:60: error: package org.biodas.jdas.schema.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:61: error: package org.biodas.jdas.schema.features does not exist - [javac] src/jalview/ws/DasSequenceFeatureFetcher.java:62: error: package org.biodas.jdas.schema.sources does not exist - [javac] src/jalview/ws/dbsources/das/api/jalviewSourceI.java:27: error: package org.biodas.jdas.schema.sources does not exist - [javac] src/jalview/ws/dbsources/das/api/jalviewSourceI.java:28: error: package org.biodas.jdas.schema.sources does not exist - [javac] src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java:25: error: package org.biodas.jdas.client.threads does not exist - [javac] src/jalview/datamodel/SecondaryStructureAnnotation.java:23: error: package fr.orsay.lri.varna.models.rna does not exist - [javac] src/jalview/ext/htsjdk/HtsContigDb.java:23: error: package htsjdk.samtools does not exist - [javac] src/jalview/ext/htsjdk/HtsContigDb.java:24: error: package htsjdk.samtools does not exist - [javac] src/jalview/ext/htsjdk/HtsContigDb.java:25: error: package htsjdk.samtools.reference does not exist - [javac] src/jalview/ext/htsjdk/HtsContigDb.java:26: error: package htsjdk.samtools.reference does not exist - [javac] src/jalview/ext/htsjdk/HtsContigDb.java:27: error: package htsjdk.samtools.reference does not exist - [javac] src/jalview/ext/htsjdk/HtsContigDb.java:28: error: package htsjdk.samtools.util does not exist - [javac] src/jalview/ext/htsjdk/HtsContigDb.java:54: error: package htsjdk.samtools.reference does not exist - [javac] src/jalview/ext/varna/RnaModel.java:26: error: package fr.orsay.lri.varna.models.rna does not exist - [javac] src/jalview/gui/AppVarna.java:52: error: package fr.orsay.lri.varna does not exist - [javac] src/jalview/gui/AppVarna.java:53: error: package fr.orsay.lri.varna.exceptions does not exist - [javac] src/jalview/gui/AppVarna.java:54: error: package fr.orsay.lri.varna.exceptions does not exist - [javac] src/jalview/gui/AppVarna.java:55: error: package fr.orsay.lri.varna.exceptions does not exist - [javac] src/jalview/gui/AppVarna.java:56: error: package fr.orsay.lri.varna.interfaces does not exist - [javac] src/jalview/gui/AppVarna.java:57: error: package fr.orsay.lri.varna.models does not exist - [javac] src/jalview/gui/AppVarna.java:58: error: package fr.orsay.lri.varna.models does not exist - [javac] src/jalview/gui/AppVarna.java:59: error: package fr.orsay.lri.varna.models.annotations does not exist - [javac] src/jalview/gui/AppVarna.java:60: error: package fr.orsay.lri.varna.models.rna does not exist - [javac] src/jalview/gui/AppVarna.java:61: error: package fr.orsay.lri.varna.models.rna does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:58: error: package fr.orsay.lri.varna does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:59: error: package fr.orsay.lri.varna.components does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:60: error: package fr.orsay.lri.varna.exceptions does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:61: error: package fr.orsay.lri.varna.exceptions does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:62: error: package fr.orsay.lri.varna.exceptions does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:63: error: package fr.orsay.lri.varna.models does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:64: error: package fr.orsay.lri.varna.models does not exist - [javac] src/jalview/gui/AppVarnaBinding.java:65: error: package fr.orsay.lri.varna.models.rna does not exist ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +jalview (2.11.1.3+dfsg2-2) unstable; urgency=high + + * Adding a memory limitation in the autopkgtest + * Fixing a typo in d/tests/run-unit-test + * Removing now useless d/TODO and d/dirs files + + -- Pierre Gruet <pgtdeb...@free.fr> Sun, 07 Feb 2021 22:06:13 +0100 + jalview (2.11.1.3+dfsg2-1) unstable; urgency=medium [ Pierre Gruet ] ===================================== debian/dirs deleted ===================================== @@ -1,2 +0,0 @@ -usr/share/java -usr/bin \ No newline at end of file ===================================== debian/tests/run-unit-test ===================================== @@ -21,7 +21,7 @@ jalview -nodisplay -open uniref50.fa -eps uniref50_out.eps if [ $? -eq 0 ]; then echo "Output generated in eps format in $(pwd)/uniref50_out.eps" else - echo "Failes to generate output in eps format" + echo "Failed to generate output in eps format" fi jalview -nodisplay -open uniref50.fa -html uniref50_out.html @@ -29,7 +29,7 @@ jalview -nodisplay -open uniref50.fa -html uniref50_out.html if [ $? -eq 0 ]; then echo "Output generated in html format in $(pwd)/uniref50_out.html" else - echo "Failes to generate output in eps format" + echo "Failed to generate output in eps format" fi jalview -nodisplay -open uniref50.fa -png uniref50_out.png @@ -37,5 +37,5 @@ jalview -nodisplay -open uniref50.fa -png uniref50_out.png if [ $? -eq 0 ]; then echo "Output generated in png format in $(pwd)/uniref50_out.png" else - echo "Failes to generate output in png format" + echo "Failed to generate output in png format" fi ===================================== debian/tests/someCommandLineInvocations ===================================== @@ -1,7 +1,7 @@ #!/bin/sh # autopkgtest check: take an example input file and have outputs in different # formats, to be compared with reference ones.. -# (C) 2020 Pierre Gruet. +# (C) 2020-2021 Pierre Gruet. # Author: Pierre Gruet <pgtdeb...@free.fr> set -e @@ -11,12 +11,12 @@ WORKDIR=$(mktemp -d) trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM cd $WORKDIR -jalview -nodisplay -open $SOURCEDIR/examples/uniref50.fa -blc uniref50_out.blc -jalview -nodisplay -open $SOURCEDIR/examples/uniref50.fa -fasta uniref50_out.mfa -jalview -nodisplay -open $SOURCEDIR/examples/uniref50.fa -pfam uniref50_out.pfam -jalview -nodisplay -open $SOURCEDIR/examples/uniref50.fa -pir uniref50_out.pir -jalview -nodisplay -open $SOURCEDIR/examples/uniref50.fa -clustal uniref50_out1.aln -jalview -nodisplay -open $SOURCEDIR/examples/uniref50.fa -pileup uniref50_out2.aln +jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -blc uniref50_out.blc +jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -fasta uniref50_out.mfa +jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -pfam uniref50_out.pfam +jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -pir uniref50_out.pir +jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -clustal uniref50_out1.aln +jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -pileup uniref50_out2.aln diff uniref50_out.blc $SOURCEDIR/debian/tests/expectedOutputs/test_uniref50_out.blc View it on GitLab: https://salsa.debian.org/java-team/jalview/-/compare/bbfa20ea2bbfe1a4c49bd69710137c1307a35292...a9e093130a3a616b9bb06791a05f4f5f2f0ff3a1 -- View it on GitLab: https://salsa.debian.org/java-team/jalview/-/compare/bbfa20ea2bbfe1a4c49bd69710137c1307a35292...a9e093130a3a616b9bb06791a05f4f5f2f0ff3a1 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ pkg-java-commits mailing list pkg-java-comm...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-java-commits