sra-tools: Regenerate PLIST with Java disabled

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Aug 13 17:07:04 2023 -0500
Changeset:	723680b4635752838999404d3ef9342cc2b6faee

Modified Files:
	sra-tools/Makefile
	sra-tools/PLIST

Log Message:
sra-tools: Regenerate PLIST with Java disabled

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=723680b4635752838999404d3ef9342cc2b6faee

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 sra-tools/Makefile |  7 ++---
 sra-tools/PLIST    | 80 ------------------------------------------------------
 2 files changed, 3 insertions(+), 84 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index ceb227a5db..f8e6ba6210 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -84,7 +84,6 @@ post-install:
 	${MKDIR} ${DESTDIR}${EXAMPLESDIR}
 	${MV} ${DESTDIR}${PREFIX}/share/examples-sratools/* ${DESTDIR}${EXAMPLESDIR}
 	${RMDIR} ${DESTDIR}${PREFIX}/share/examples-sratools
-	${MV} ${DESTDIR}${PREFIX}/share/examples-java ${DESTDIR}${EXAMPLESDIR}/java
 	${MV} ${DESTDIR}${PREFIX}/share/examples-python ${DESTDIR}${EXAMPLESDIR}/python
 
 # Shouldn't epoll bl3 check this?
@@ -94,9 +93,9 @@ post-install:
 
 # Triggers openjdk install on Linux even if installed via Yum
 # FIXME: Should we just build without Java to avoid these issues?
-.if ${OPSYS} == NetBSD
-.include "../../mk/java-vm.mk"
-.endif
+# .if ${OPSYS} == NetBSD
+# .include "../../mk/java-vm.mk"
+# .endif
 .include "../../mk/pthread.buildlink3.mk"
 .include "../../devel/cmake/build.mk"
 .include "../../textproc/libxml2/buildlink3.mk"
diff --git a/sra-tools/PLIST b/sra-tools/PLIST
index f71e0b24c4..b6a6bb584c 100644
--- a/sra-tools/PLIST
+++ b/sra-tools/PLIST
@@ -178,10 +178,6 @@ include/ngs/unix/i386/atomic32.h
 include/ngs/unix/x86_64/atomic32.h
 include/ngs/win/atomic32.h
 include/ngs/win/stdbool.h
-jar/ngs-doc.jar
-jar/ngs-examples.jar
-jar/ngs-java.jar
-jar/ngs-src.jar
 lib/libncbi-ngs-c++-static.a
 lib/libncbi-ngs-c++.a
 lib/libncbi-ngs-c++.a.3
@@ -209,16 +205,6 @@ share/examples/sra-tools/PileupTest.cpp
 share/examples/sra-tools/README.txt
 share/examples/sra-tools/RefTest.cpp
 share/examples/sra-tools/expected.txt
-share/examples/sra-tools/java/Makefile
-share/examples/sra-tools/java/README.txt
-share/examples/sra-tools/java/examples/AlignSliceTest.java
-share/examples/sra-tools/java/examples/AlignTest.java
-share/examples/sra-tools/java/examples/DumpReferenceFASTA.java
-share/examples/sra-tools/java/examples/FragTest.java
-share/examples/sra-tools/java/examples/PileupTest.java
-share/examples/sra-tools/java/examples/ReadGroupTest.java
-share/examples/sra-tools/java/examples/RefTest.java
-share/examples/sra-tools/java/expected.txt
 share/examples/sra-tools/python/AlignSliceTest.py
 share/examples/sra-tools/python/AlignTest.py
 share/examples/sra-tools/python/FragTest.py
@@ -227,69 +213,3 @@ share/examples/sra-tools/python/PileupTest.py
 share/examples/sra-tools/python/README.txt
 share/examples/sra-tools/python/RefTest.py
 share/examples/sra-tools/python/expected.txt
-share/javadoc/ngs-doc/allclasses-index.html
-share/javadoc/ngs-doc/allclasses.html
-share/javadoc/ngs-doc/allpackages-index.html
-share/javadoc/ngs-doc/constant-values.html
-share/javadoc/ngs-doc/deprecated-list.html
-share/javadoc/ngs-doc/element-list
-share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
-share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
-share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html
-share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
-share/javadoc/ngs-doc/help-doc.html
-share/javadoc/ngs-doc/index-all.html
-share/javadoc/ngs-doc/index.html
-share/javadoc/ngs-doc/jquery-ui.overrides.css
-share/javadoc/ngs-doc/jquery/external/jquery/jquery.js
-share/javadoc/ngs-doc/jquery/jquery-3.6.1.min.js
-share/javadoc/ngs-doc/jquery/jquery-ui.min.css
-share/javadoc/ngs-doc/jquery/jquery-ui.min.js
-share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils-ie.js
-share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils-ie.min.js
-share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils.js
-share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils.min.js
-share/javadoc/ngs-doc/jquery/jszip/dist/jszip.js
-share/javadoc/ngs-doc/jquery/jszip/dist/jszip.min.js
-share/javadoc/ngs-doc/legal/ADDITIONAL_LICENSE_INFO
-share/javadoc/ngs-doc/legal/ASSEMBLY_EXCEPTION
-share/javadoc/ngs-doc/legal/LICENSE
-share/javadoc/ngs-doc/legal/jquery.md
-share/javadoc/ngs-doc/legal/jqueryUI.md
-share/javadoc/ngs-doc/legal/jszip.md
-share/javadoc/ngs-doc/legal/pako.md
-share/javadoc/ngs-doc/member-search-index.js
-share/javadoc/ngs-doc/member-search-index.zip
-share/javadoc/ngs-doc/ngs/Alignment.html
-share/javadoc/ngs-doc/ngs/AlignmentIterator.html
-share/javadoc/ngs-doc/ngs/ErrorMsg.html
-share/javadoc/ngs-doc/ngs/Fragment.html
-share/javadoc/ngs-doc/ngs/FragmentIterator.html
-share/javadoc/ngs-doc/ngs/Package.html
-share/javadoc/ngs-doc/ngs/Pileup.html
-share/javadoc/ngs-doc/ngs/PileupEvent.html
-share/javadoc/ngs-doc/ngs/PileupEventIterator.html
-share/javadoc/ngs-doc/ngs/PileupIterator.html
-share/javadoc/ngs-doc/ngs/Read.html
-share/javadoc/ngs-doc/ngs/ReadCollection.html
-share/javadoc/ngs-doc/ngs/ReadGroup.html
-share/javadoc/ngs-doc/ngs/ReadGroupIterator.html
-share/javadoc/ngs-doc/ngs/ReadIterator.html
-share/javadoc/ngs-doc/ngs/Reference.html
-share/javadoc/ngs-doc/ngs/ReferenceIterator.html
-share/javadoc/ngs-doc/ngs/ReferenceSequence.html
-share/javadoc/ngs-doc/ngs/Statistics.html
-share/javadoc/ngs-doc/ngs/package-summary.html
-share/javadoc/ngs-doc/ngs/package-tree.html
-share/javadoc/ngs-doc/overview-summary.html
-share/javadoc/ngs-doc/overview-tree.html
-share/javadoc/ngs-doc/package-search-index.js
-share/javadoc/ngs-doc/package-search-index.zip
-share/javadoc/ngs-doc/resources/glass.png
-share/javadoc/ngs-doc/resources/x.png
-share/javadoc/ngs-doc/script.js
-share/javadoc/ngs-doc/search.js
-share/javadoc/ngs-doc/serialized-form.html
-share/javadoc/ngs-doc/stylesheet.css
-share/javadoc/ngs-doc/type-search-index.js
-share/javadoc/ngs-doc/type-search-index.zip