[med-svn] [Git][med-team/libgoby-java][master] 7 commits: Use secure URI in Homepage field.
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sat Nov 19 06:36:58 GMT 2022
Pierre Gruet pushed to branch master at Debian Med / libgoby-java
Commits:
b8e3eb95 by Pierre Gruet at 2022-11-16T22:23:02+01:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
caa5ddae by Pierre Gruet at 2022-11-18T21:40:37+01:00
Adding a --add-opens argument to run the tests with OpenJDK17
- - - - -
26935d77 by Pierre Gruet at 2022-11-18T21:40:55+01:00
Updating changelog
- - - - -
c0bf1e17 by Pierre Gruet at 2022-11-18T23:16:16+01:00
Honouring Build-Depends-Indep
- - - - -
27d21bd3 by Pierre Gruet at 2022-11-18T23:16:33+01:00
Simplifying d/maven.rules
- - - - -
bab0d490 by Pierre Gruet at 2022-11-19T00:23:08+01:00
Reworking autopkgtest to provide it with a temp home dir
- - - - -
8b772a23 by Pierre Gruet at 2022-11-19T00:23:21+01:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/maven.rules
- + debian/patches/adding_opens_arg_for_tests.patch
- debian/patches/series
- debian/tests/test-fasta-to-compact
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libgoby-java (3.3.1+dfsg2-9) unstable; urgency=medium
+
+ * Updating d/watch to follow the change in the Github layout
+ * Use secure URI in Homepage field.
+ * Adding a --add-opens argument to run the tests with OpenJDK17
+ * Reworking autopkgtest to provide it with a temporary home directory
+
+ -- Pierre Gruet <pgt at debian.org> Sat, 19 Nov 2022 00:23:11 +0100
+
libgoby-java (3.3.1+dfsg2-8) unstable; urgency=medium
* Raising Standards version to 4.6.1 (no change)
=====================================
debian/control
=====================================
@@ -7,48 +7,48 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
maven-debian-helper,
javahelper,
- default-jdk,
- ant,
- ant-contrib,
- libjbzip2-java,
- libcommons-collections3-java,
- libcommons-configuration-java,
- libcommons-exec-java,
- libcommons-io-java,
- libcommons-lang-java,
- libcommons-logging-java,
- libcommons-math-java,
- libcommons-cli-java,
- libdistlib-java,
- liblog4j1.2-java,
- libexec-maven-plugin-java,
- libjaxb-api-java,
- libmaven-assembly-plugin-java,
- libmaven-antrun-plugin-java,
- libbuild-helper-maven-plugin-java,
- libmaven-dependency-plugin-java,
- libmaven-source-plugin-java,
- libmaven-javadoc-plugin-java,
- libprotobuf-java,
- libhtsjdk-java,
- libfastutil-java,
- protobuf-compiler,
- libjsap-java,
- libdsiutils-java,
- libicb-utils-java,
- libreflections-java,
- libpj-java,
- libprotobuf-dev,
- pkg-config,
- r-cran-rjava,
- libeasymock-java <!nocheck>,
- junit4 <!nocheck>,
- testng <!nocheck>,
- libpicard-java <!nocheck>
+ default-jdk
+Build-Depends-Indep: ant,
+ ant-contrib,
+ libjbzip2-java,
+ libcommons-collections3-java,
+ libcommons-configuration-java,
+ libcommons-exec-java,
+ libcommons-io-java,
+ libcommons-lang-java,
+ libcommons-logging-java,
+ libcommons-math-java,
+ libcommons-cli-java,
+ libdistlib-java,
+ liblog4j1.2-java,
+ libexec-maven-plugin-java,
+ libjaxb-api-java,
+ libmaven-assembly-plugin-java,
+ libmaven-antrun-plugin-java,
+ libbuild-helper-maven-plugin-java,
+ libmaven-dependency-plugin-java,
+ libmaven-source-plugin-java,
+ libmaven-javadoc-plugin-java,
+ libprotobuf-java,
+ libhtsjdk-java,
+ libfastutil-java,
+ protobuf-compiler,
+ libjsap-java,
+ libdsiutils-java,
+ libicb-utils-java,
+ libreflections-java,
+ libpj-java,
+ libprotobuf-dev,
+ pkg-config,
+ r-cran-rjava,
+ libeasymock-java <!nocheck>,
+ junit4 <!nocheck>,
+ testng <!nocheck>,
+ libpicard-java <!nocheck>
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/libgoby-java/
Vcs-Git: https://salsa.debian.org/med-team/libgoby-java.git
-Homepage: http://campagnelab.org/software/goby/
+Homepage: https://campagnelab.org/software/goby/
Rules-Requires-Root: no
Package: libgoby-io-java
=====================================
debian/maven.rules
=====================================
@@ -5,10 +5,5 @@ org.apache.maven.plugins maven-antrun-plugin jar s/.*/1.8/ * *
org.codehaus.mojo build-helper-maven-plugin jar s/.*/3.0.0/ * *
org.apache.maven.plugins maven-dependency-plugin jar s/.*/3.1.1/ * *
org.apache.maven.plugins maven-javadoc-plugin jar s/.*/3.0.1/ * *
-it.unimi.dsi dsiutils jar s/.*/debian/ * *
-org.campagnelab.icb icb-utils jar s/.*/debian/ * *
-org.reflections reflections jar s/.*/debian/ * *
s/org.campagnelab.ext/com.martiansoftware/ jsap jar s/.*/debian/ * *
junit junit jar s/.*/4.x/ * *
-org.easymock easymock jar s/.*/debian/ * *
-com.github.samtools htsjdk jar s/.*/debian/ * *
=====================================
debian/patches/adding_opens_arg_for_tests.patch
=====================================
@@ -0,0 +1,16 @@
+Description: adding a --add-opens argument needed to run the tests, starting
+ from OpenJDK17.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: no
+Last-Update: 2022-11-18
+
+--- a/goby-distribution/pom.xml
++++ b/goby-distribution/pom.xml
+@@ -81,6 +81,7 @@
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>debian</version>
+ <configuration>
++ <argLine>--add-opens=java.base/java.lang=ALL-UNNAMED</argLine>
+ <excludes>
+ <exclude>**/TestGobyPaperTop5000s.java</exclude>
+ <exclude>**/TestIterateSortedAlignment.java</exclude>
=====================================
debian/patches/series
=====================================
@@ -14,3 +14,4 @@ path_of_goby_jar_for_Debian.patch
jaxb_dependency.patch
using_pcre2.patch
omit_test_failing_randomly.patch
+adding_opens_arg_for_tests.patch
=====================================
debian/tests/test-fasta-to-compact
=====================================
@@ -16,6 +16,8 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
+TEMP_HOME=$(mktemp -d)
+
cp -a test-data/ "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}/test-data/seq-var-test"
@@ -23,21 +25,11 @@ cd "${AUTOPKGTEST_TMP}/test-data/seq-var-test"
# We launch a command in fasta-to-compact mode without the wrapper.
java -Xmx100m -jar /usr/share/java/goby.jar -m fasta-to-compact -d -o small-synth.compact-reads small-synth.fa | grep "Total logical entries written: 1"
-if [ $? -eq 0 ]; then
- echo "Result file correctly outputted by the java invocation"
-else
- echo "Failed to generate output"
- exit 1
-fi
+echo "Result file correctly outputted by the java invocation"
# Now we delete the output and try to launch a command in fasta-to-compact mode
# by invoking the shell launcher.
rm small-synth.compact-reads
-goby 100m fasta-to-compact -d -o small-synth.compact-reads small-synth.fa | grep "Total logical entries written: 1"
+HOME="${TEMP_HOME}" goby 100m fasta-to-compact -d -o small-synth.compact-reads small-synth.fa | grep "Total logical entries written: 1"
-if [ $? -eq 0 ]; then
- echo "Result file correctly outputted by the goby call"
-else
- echo "Failed to generate output"
- exit 1
-fi
+echo "Result file correctly outputted by the goby call"
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/02e249016fe09e204444fc5e5b8b6ffe388322b2...8b772a2356cd852343e06dcdf77fb19f0eb20573
--
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/02e249016fe09e204444fc5e5b8b6ffe388322b2...8b772a2356cd852343e06dcdf77fb19f0eb20573
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