Pierre Gruet pushed to branch master at Debian Med / biojava4-live
Commits: 080b624d by Pierre Gruet at 2022-12-11T21:52:11+01:00 Fixing ambiguous call to newFileSystem - - - - - 51dcbc97 by Pierre Gruet at 2022-12-11T22:19:07+01:00 Corrrecting the Lintian override for embedded JS after a change in Lintian syntax - - - - - f519396c by Pierre Gruet at 2022-12-11T22:19:35+01:00 Upload to unstable - - - - - 4 changed files: - debian/changelog - debian/libbiojava4-java-doc.lintian-overrides - + debian/patches/fix_ambiguous_method_call.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +biojava4-live (4.2.12+dfsg-8) unstable; urgency=medium + + * Fixing ambiguous method call to newFileSystem, thanks to Hans Joachim + Desserud! (Closes: #1025887) + * Correcting the Lintian override for embedded JS after a change in Lintian + syntax + + -- Pierre Gruet <[email protected]> Sun, 11 Dec 2022 22:19:23 +0100 + biojava4-live (4.2.12+dfsg-7) unstable; urgency=medium * Moving javahelper from B-D-Indep to B-D to avoid clean failure in source ===================================== debian/libbiojava4-java-doc.lintian-overrides ===================================== @@ -2,4 +2,4 @@ # javadocs, see the discussion on Debian Java mailing list starting at # https://lists.debian.org/debian-java/2018/06/msg00020.html. # See also https://bugs.debian.org/988846 -embedded-javascript-library usr/share/doc/libbiojava4-java/api/jquery/* +embedded-javascript-library please use * [usr/share/doc/libbiojava4-java/api/script-dir/*s] ===================================== debian/patches/fix_ambiguous_method_call.patch ===================================== @@ -0,0 +1,31 @@ +Description: Add explicit cast to fix ambiguos method call error + +Taken from upstream to match expected method call +https://github.com/biojava/biojava/blob/master/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java + +--- + +Origin: upstream +Forwarded: not-needed +Last-Update: 2022-12-11 + +--- biojava4-live-4.2.12+dfsg.orig/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java ++++ biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java +@@ -236,7 +236,7 @@ public class ZipChemCompProvider impleme + final String filename = "chemcomp/" + recordName+".cif.gz"; + + // try with resources block to read from the filesystem. +- try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, null)) { ++ try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, (ClassLoader)null)) { + Path cif = fs.getPath(filename); + + if (Files.exists(cif)) { +@@ -293,7 +293,7 @@ public class ZipChemCompProvider impleme + */ + + // Copy in each file. +- try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, null)) { ++ try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, (ClassLoader)null)) { + Files.createDirectories(pathWithinArchive); + for (File f : files) { + if (!f.isDirectory() && f.exists()) { ===================================== debian/patches/series ===================================== @@ -6,3 +6,4 @@ fix_ascii_characters_mapping skip_network_related_tests remove_openchart_use ignore_fake_tests +fix_ambiguous_method_call.patch View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/459bfd75d783d68ebfadc0b6115e1d21c4c06160...f519396c8de49b2a6b219203554df7d1b2d02396 -- View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/459bfd75d783d68ebfadc0b6115e1d21c4c06160...f519396c8de49b2a6b219203554df7d1b2d02396 You're receiving this email because of your account on salsa.debian.org.
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