Your message dated Thu, 14 Dec 2023 13:34:56 +0000 with message-id <e1rdlrc-000xgp...@fasolo.debian.org> and subject line Bug#1058683: fixed in igv 2.16.2+dfsg-2 has caused the Debian Bug report #1058683, regarding FTBFS against htsjdk/4.0.2+dfsg-1 now in unstable to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1058683: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1058683 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: igv Version: 2.16.2+dfsg-1 Severity: serious Tags: patch Hello, igv fails to build against new htsjdk/4.0.2+dfsg-1: /<<PKGBUILDDIR>>/src/main/java/org/broad/igv/track/TribbleFeatureSource.java:352: error: reference to NamedFeature is ambiguous if (f instanceof NamedFeature) FeatureDB.addFeature((NamedFeature) f, genome); ^ both interface org.broad.igv.feature.NamedFeature in org.broad.igv.feature and interface htsjdk.tribble.NamedFeature in htsjdk.tribble match /<<PKGBUILDDIR>>/src/main/java/org/broad/igv/track/TribbleFeatureSource.java:352: error: reference to NamedFeature is ambiguous if (f instanceof NamedFeature) FeatureDB.addFeature((NamedFeature) f, genome); ^ both interface org.broad.igv.feature.NamedFeature in org.broad.igv.feature and interface htsjdk.tribble.NamedFeature in htsjdk.tribble match There is some ambiguity to be removed, which is solved by the enclosed patch. Best, -- PierreDescription: solving an ambiguity in the tests due to a new class in htsjdk/4.0.2+dfsg Author: Pierre Gruet <p...@debian.org> Forwarded: no Last-Update: 2023-12-14 --- a/src/main/java/org/broad/igv/track/TribbleFeatureSource.java +++ b/src/main/java/org/broad/igv/track/TribbleFeatureSource.java @@ -349,7 +349,7 @@ featureMap.put(igvChr, featureList); } featureList.add(f); - if (f instanceof NamedFeature) FeatureDB.addFeature((NamedFeature) f, genome); + if (f instanceof org.broad.igv.feature.NamedFeature) FeatureDB.addFeature((org.broad.igv.feature.NamedFeature) f, genome); if (this.isVCF && f instanceof Variant) { Variant v = (Variant) f;
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--- Begin Message ---Source: igv Source-Version: 2.16.2+dfsg-2 Done: Pierre Gruet <p...@debian.org> We believe that the bug you reported is fixed in the latest version of igv, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1058...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Pierre Gruet <p...@debian.org> (supplier of updated igv package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 14 Dec 2023 14:09:05 +0100 Source: igv Architecture: source Version: 2.16.2+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Pierre Gruet <p...@debian.org> Closes: 1058683 Changes: igv (2.16.2+dfsg-2) unstable; urgency=medium . * Solving ambiguity to build against htsjdk/4.0.2+dfsg (Closes: #1058683) Checksums-Sha1: 0d0fab13758b4434268de8c3cb96ec48627774b2 2544 igv_2.16.2+dfsg-2.dsc d2f30730793ac44c770ae5d91713dcd435b3fc28 31036 igv_2.16.2+dfsg-2.debian.tar.xz 30307534606afa213d566ae468cfc7b0fcdee89d 17257 igv_2.16.2+dfsg-2_source.buildinfo Checksums-Sha256: 76bafe701ef897da0f87c5f5d64f5081d8468647896f23d93703927c17bd7d38 2544 igv_2.16.2+dfsg-2.dsc 3dc6143dd9c2925de4b3e11a0b99a7a92b8793e23b075ee0ae18bf2f786d99a4 31036 igv_2.16.2+dfsg-2.debian.tar.xz 1f10df17c35041b4d7cc54a3050027e025a60ad99a27bf7451880be3da5cb219 17257 igv_2.16.2+dfsg-2_source.buildinfo Files: 170223ab614c88c611838600a44dd396 2544 science optional igv_2.16.2+dfsg-2.dsc 663c08465b93348ca2c1dfe047e9f63f 31036 science optional igv_2.16.2+dfsg-2.debian.tar.xz 74d5f5326fc833e6fffa58a46adfe6b7 17257 science optional igv_2.16.2+dfsg-2_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmV6/o8ACgkQYAMWptwn dHbuxA//duLfPJRkKoobUh59cUxSeIlXEuQrfkAGFfITKZ8iNK69+4K3SE9iyhzB HvdZfxVktCcGXeOewt4G2DA6zibK/5O0DnSxQqKIntkiRBcbp7XkkHnE76Nc23vo 6/pz0BzFYOyVQ9RTVlyY092ooFFXSLVo/5pfksr2qGNa2Q5SIU2oKcnh58myUmX4 KeGqn88BRpa++Wz6ROlzP5Bzp3P6Ar5hLhVwdtBrDnqF4c49JIAMWdGQ4iQZSPfP TOpkbOtKRcuOnU44H/uM2/yHODtNNufVd21ezW/pV5IAHUxEASRtImTAnVu0fbPp BbwoA+bQcTIhOjg2L5z9W33rLXJzoybKlo412gCHhZPN7mderVskTCmpYVXTtBBQ MXgyQm082rcdoAY03MpDjubL7sCz5UBqAheWawBP4Bzkvq4ClycP3unYx5KaYAYG fgciC03PLWrbbKNp1lUtJOzP0Av5LN+j3qduPjVNe6pjbFQEhqhmqJwSylFlS9bv uFvTX74TuDunJ0eDXD+gCoQ7BbHKNOkH6kpVRhcJSSNUb23WssdFI73PQOcjed3X FZS4ZsTRJTo1xTGv8eWdO1K8I3cBdDSSkomT1imrGmYR8RlolNFvRw1G7hLwkk8v rO1GYacerA79KR47PC+a1BPU/nDqgp5nh5ijs2FtDweaVMZVrp4= =aAZ0 -----END PGP SIGNATURE-----
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