[med-svn] [Git][med-team/snpeff][master] 6 commits: Depending on biojava6 instead of biojava5
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Thu Jan 12 21:18:52 GMT 2023
Pierre Gruet pushed to branch master at Debian Med / snpeff
Commits:
adefbb8d by Pierre Gruet at 2023-01-12T17:46:19+01:00
Depending on biojava6 instead of biojava5
- - - - -
8718f0b7 by Pierre Gruet at 2023-01-12T17:46:43+01:00
Raising Standards version to 4.6.2 (no change)
- - - - -
c5ff7c31 by Pierre Gruet at 2023-01-12T17:47:00+01:00
Updating changelog
- - - - -
6097d0a6 by Pierre Gruet at 2023-01-12T17:48:04+01:00
Update lintian override info format in d/source/lintian-overrides on line 2.
Changes-By: lintian-brush
Fixes: lintian: mismatched-override
See-also: https://lintian.debian.org/tags/mismatched-override.html
- - - - -
c0857de8 by Pierre Gruet at 2023-01-12T21:21:54+01:00
Refreshing Lintian overrides
- - - - -
efe1f764 by Pierre Gruet at 2023-01-12T21:22:14+01:00
Upload to unstable
- - - - -
12 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/libsnpeff-java-doc.lintian-overrides
- + debian/libsnpeff-java.lintian-overrides
- debian/libsnpeff-java.manifest
- debian/maven.rules
- − debian/patches/alternatives_to_biojava6_classes_in_biojava5.patch
- debian/patches/series
- debian/patches/use_fastq_from_biojava5.patch → debian/patches/use_fastq_from_biojava6.patch
- debian/source/lintian-overrides
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+snpeff (5.1+d+dfsg-2) unstable; urgency=medium
+
+ * Depending on biojava6 instead of biojava5
+ * Raising Standards version to 4.6.2 (no change)
+ * Update Lintian override info format in d/source/lintian-overrides on line 2
+ * Adding a Lintian override for the bad-jar-name tag
+ * Correcting the mismatched Lintian overrride about embedded JS
+
+ -- Pierre Gruet <pgt at debian.org> Thu, 12 Jan 2023 21:21:57 +0100
+
snpeff (5.1+d+dfsg-1) unstable; urgency=medium
* New upstream version 5.1+d+dfsg
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
libmaven-assembly-plugin-java,
libtrove3-java,
libhtsjdk-java,
- libbiojava5-java,
+ libbiojava6-java,
junit5,
libcommons-codec-java,
libcommons-io-java,
@@ -21,12 +21,12 @@ Build-Depends: debhelper-compat (= 13),
libfreemarker-java,
libjaxb-api-java,
libmaven-javadoc-plugin-java,
- libbiojava5-java-doc,
+ libbiojava6-java-doc,
libtrove3-java-doc,
libcharts4j-java,
libapfloat-java,
libdistlib-java
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/snpeff
Vcs-Git: https://salsa.debian.org/med-team/snpeff.git
Homepage: https://pcingola.github.io/SnpEff/
@@ -36,7 +36,7 @@ Package: libsnpeff-java
Architecture: all
Depends: ${misc:Depends},
${maven:Depends},
- libbiojava5-java,
+ libbiojava6-java,
libhtsjdk-java
Suggests: ${maven:OptionalDepends},
libsnpeff-java-doc
@@ -100,7 +100,7 @@ Architecture: all
Section: doc
Depends: ${misc:Depends}
Recommends: default-jdk-doc,
- libbiojava5-java-doc,
+ libbiojava6-java-doc,
libtrove3-java-doc
Suggests: libsnpeff-java
Multi-Arch: foreign
=====================================
debian/copyright
=====================================
@@ -17,7 +17,7 @@ Files-Excluded: */config/OLD
src/main/java/org/snpeff/fastq/FastqBuilder.java
src/main/java/org/snpeff/fastq/FastqVariant.java
tests/old
-Comment: The three files in src/main/java/ are provided by biojava5-live..
+Comment: The three files in src/main/java/ are provided by biojava6-live..
Other files are useless or have unclear copyright.
Files: *
=====================================
debian/libsnpeff-java-doc.lintian-overrides
=====================================
@@ -1,4 +1,4 @@
# It would be too complicated to remove the javascript that is included in
# javadocs, see the discussion on Debian Java mailing list starting at
# https://lists.debian.org/debian-java/2018/06/msg00020.html.
-embedded-javascript-library usr/share/doc/libsnpeff-java/api/*/jquery*.*s *
+embedded-javascript-library please use * [usr/share/doc/libsnpeff-java/api/*s]
=====================================
debian/libsnpeff-java.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# The indicated file is the real jar and not a symlink, but this really does
+# not harm.
+bad-jar-name [usr/share/java/snpeff.jar]
=====================================
debian/libsnpeff-java.manifest
=====================================
@@ -1,3 +1,3 @@
/usr/share/java/snpeff.jar:
- Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar /usr/share/java/biojava5-core.jar /usr/share/java/biojava5-structure.jar
+ Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar /usr/share/java/biojava6-core.jar /usr/share/java/biojava6-structure.jar
Main-Class: org.snpeff.SnpEff
=====================================
debian/maven.rules
=====================================
@@ -9,6 +9,6 @@ org.freemarker freemarker jar s/.*/debian/ * *
org.apache.commons commons-math3 jar s/.*/debian/ * *
commons-io commons-io jar s/.*/debian/ * *
commons-codec commons-codec jar s/.*/debian/ * *
-org.biojava biojava-core jar s/.*/5.x/ * *
-org.biojava biojava-genome jar s/.*/5.x/ * *
-org.biojava biojava-structure jar s/.*/5.x/ * *
+org.biojava biojava-core jar s/.*/6.x/ * *
+org.biojava biojava-genome jar s/.*/6.x/ * *
+org.biojava biojava-structure jar s/.*/6.x/ * *
=====================================
debian/patches/alternatives_to_biojava6_classes_in_biojava5.patch deleted
=====================================
@@ -1,77 +0,0 @@
-Description: Modifying some calls to be compatible with biojava5-live, the
- software being written for biojava6.
-Author: Pierre Gruet <pgt at debian.org>
-Forwarded: not-needed
-Last-Update: 2022-02-23
-
---- a/src/main/java/org/snpeff/pdb/DistanceResult.java
-+++ b/src/main/java/org/snpeff/pdb/DistanceResult.java
-@@ -189,19 +189,19 @@
- }
-
- public void setAa1(AminoAcid aa) {
-- String pdbId = aa.getChain().getStructure().getPDBHeader().getPdbId().toString();
-+ String pdbId = aa.getChain().getParent().getPDBCode();
- setPdbId(pdbId);
- pdbChainId1 = aa.getChainId();
- aaPos1 = aa.getResidueNumber().getSeqNum() - 1;
-- aa1 = aa.getChemComp().getOneLetterCode().charAt(0);
-+ aa1 = aa.getChemComp().getOne_letter_code().charAt(0);
- }
-
- public void setAa2(AminoAcid aa) {
-- String pdbId = aa.getChain().getStructure().getPDBHeader().getPdbId().toString();
-+ String pdbId = aa.getChain().getParent().getPDBCode();
- setPdbId(pdbId);
- pdbChainId2 = aa.getChainId();
- aaPos2 = aa.getResidueNumber().getSeqNum() - 1;
-- aa2 = aa.getChemComp().getOneLetterCode().charAt(0);
-+ aa2 = aa.getChemComp().getOne_letter_code().charAt(0);
- }
-
- void setPdbId(String pdbId) {
---- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java
-+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java
-@@ -128,7 +128,7 @@
- */
- List<IdMapperEntry> checkSequencePdbGenome(Structure pdbStruct, Chain chain, String trId, List<IdMapperEntry> idmapsOri) {
- List<IdMapperEntry> idmapsNew = new ArrayList<>();
-- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();
-+ String pdbId = pdbStruct.getPDBCode();
-
- // Does chain pass filter criteria?
- if (!filterPdbChain(chain)) return idmapsNew;
-@@ -149,13 +149,13 @@
- int aaPos = aa.getResidueNumber().getSeqNum() - 1;
- if (aaPos < 0) continue; // I don't know why some PDB coordinates are negative...
-
-- char aaLetter = aa.getChemComp().getOneLetterCode().charAt(0);
-+ char aaLetter = aa.getChemComp().getOne_letter_code().charAt(0);
- if (prot.length() > aaPos) {
- char trAaLetter = prot.charAt(aaPos);
- if (aaLetter == trAaLetter) countMatch++;
- else countMismatch++;
- } else countMismatch++;
-- sb.append(aa.getChemComp().getOneLetterCode());
-+ sb.append(aa.getChemComp().getOne_letter_code());
- }
-
- // Only use mappings that have low error rate
-@@ -204,7 +204,7 @@
- * transcript)
- */
- List<IdMapperEntry> checkSequencePdbGenome(Structure pdbStruct, String trId) {
-- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();
-+ String pdbId = pdbStruct.getPDBCode();
- if (debug) System.err.println("\nChecking '" + trId + "'\t<->\t'" + pdbId + "'");
- List<IdMapperEntry> idmapsOri = idMapper.getByPdbId(pdbId);
- List<IdMapperEntry> idmapsNew = new ArrayList<>();
-@@ -461,7 +472,7 @@
- * Filter IdMaps for a specific chain
- */
- List<IdMapperEntry> idMapChain(Structure pdbStruct, Chain chain, List<IdMapperEntry> idMaps) {
-- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();
-+ String pdbId = pdbStruct.getPDBCode();
- List<IdMapperEntry> idMapChain = new ArrayList<>();
- for (IdMapperEntry idmap : idMaps) {
- if (idmap.pdbId.equals(pdbId) //
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,5 @@
alter_pom_for_debian_packaging.patch
update_launching_script_and_config_file_for_Debian.patch
-use_fastq_from_biojava5.patch
+use_fastq_from_biojava6.patch
omit_unused_junit_classes_and_integration_tests.patch
exclude_tests_with_missing_data.patch
-alternatives_to_biojava6_classes_in_biojava5.patch
=====================================
debian/patches/use_fastq_from_biojava5.patch → debian/patches/use_fastq_from_biojava6.patch
=====================================
@@ -1,7 +1,7 @@
-Description: Using Fastq* classes from biojava5-live
+Description: Using Fastq* classes from biojava6-live
Author: Pierre Gruet <pgt at debian.org>
Forwarded: not-needed
-Last-Update: 2022-02-22
+Last-Update: 2023-01-12
--- a/src/main/java/org/snpeff/Fastq2Fastq.java
+++ b/src/main/java/org/snpeff/Fastq2Fastq.java
=====================================
debian/source/lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# File with innocuous very-long-lines
-snpeff source: source-is-missing docs/se_tests/index.html
+snpeff source: source-is-missing [docs/se_tests/index.html]
=====================================
debian/tests/run-unit-test
=====================================
@@ -28,7 +28,7 @@ cp -a tests/ "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
mkdir classes/
-javac -d classes -cp /usr/share/java/junit-jupiter-api.jar:/usr/share/java/snpeff.jar:/usr/share/java/biojava5-core.jar:/usr/share/java/biojava5-genome.jar:/usr/share/java/biojava5-structure.jar org/snpeff/snpEffect/testCases/*/*.java
+javac -d classes -cp /usr/share/java/junit-jupiter-api.jar:/usr/share/java/snpeff.jar:/usr/share/java/biojava6-core.jar:/usr/share/java/biojava6-genome.jar:/usr/share/java/biojava6-structure.jar org/snpeff/snpEffect/testCases/*/*.java
# Only running unit tests, not integration ones (needing data from the Internet)
-java -jar /usr/share/java/junit-platform-console-standalone.jar --class-path /usr/share/java/snpeff.jar:/usr/share/java/biojava5-genome.jar:classes --select-package org.snpeff.snpEffect.testCases.unity
+java -jar /usr/share/java/junit-platform-console-standalone.jar --class-path /usr/share/java/snpeff.jar:/usr/share/java/biojava6-genome.jar:classes --select-package org.snpeff.snpEffect.testCases.unity
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/04d3e1ffd8c62ac80975c4f235f5559f2db04db1...efe1f764e9da32a3b38f9495d6ba8de27d9ee88f
--
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/04d3e1ffd8c62ac80975c4f235f5559f2db04db1...efe1f764e9da32a3b38f9495d6ba8de27d9ee88f
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