[Git][java-team/jalview][master] 4 commits: Adding a memory limitation for autopkgtest

Pierre Gruet gitlab at salsa.debian.org
Sun Feb 7 22:06:35 GMT 2021 


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 <pgtdebian at 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 <pgtdebian at 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
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