gatk.compile.public.source: [javac] Compiling 738 source files to /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build/java/classes [javac] /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/public/java/src/org/broadinstitute/sting/utils/MathUtils.java:1103: error: name clash: sum(Collection<Integer>) and sum(Collection<Number>) have the same erasure [javac] public static long sum(Collection<Integer> x) { [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 error BUILD FAILED /var/tmp/portage/sci-biology/gatk-1.5/work/broadgsa-gatk-c981d24/build.xml:292: Compile failed; see the compiler error output for details. Total time: 4 minutes 41 seconds * ERROR: sci-biology/gatk-1.5 failed (compile phase): * eant failed * * Call stack: * ebuild.sh, line 85: Called src_compile * environment, line 3860: Called java-pkg-2_src_compile * environment, line 1911: Called eant 'dist' '-f' 'build.xml' * environment, line 523: Called die * The specific snippet of code: * ant ${antflags} "${@}" || die "eant failed" *
Created attachment 313797 [details] build.log
BTW, it is ugly that the build system fetches some stuff directly via instead of using /usr/portage/distfiles/. See the build.log but I am aware we are all short on time.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=07bea2652d449ecfd5bae8ca97e28e66272d902d commit 07bea2652d449ecfd5bae8ca97e28e66272d902d Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-04-05 16:48:21 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-04-05 16:48:21 +0000 package.mask: last-rite sci-biology/gatk Bug: https://bugs.gentoo.org/418625 Bug: https://bugs.gentoo.org/431644 Bug: https://bugs.gentoo.org/515816 Bug: https://bugs.gentoo.org/542940 Bug: https://bugs.gentoo.org/574632 Bug: https://bugs.gentoo.org/780396 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 ++++++ 1 file changed, 6 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92cb6e9daf7c9865bfc003d4968b56501d5d00c6 commit 92cb6e9daf7c9865bfc003d4968b56501d5d00c6 Author: Jakov Smolic <jakov.smolic@sartura.hr> AuthorDate: 2021-05-04 21:57:13 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-05-04 22:29:36 +0000 sci-biology/gatk: Remove last-rited pkg Closes: https://bugs.gentoo.org/780396 Closes: https://bugs.gentoo.org/574632 Closes: https://bugs.gentoo.org/542940 Closes: https://bugs.gentoo.org/515816 Closes: https://bugs.gentoo.org/431644 Closes: https://bugs.gentoo.org/418625 Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Closes: https://github.com/gentoo/gentoo/pull/20667 Signed-off-by: Sam James <sam@gentoo.org> profiles/package.mask | 6 ------ sci-biology/gatk/Manifest | 1 - sci-biology/gatk/gatk-2.4.ebuild | 32 -------------------------------- sci-biology/gatk/metadata.xml | 11 ----------- 4 files changed, 50 deletions(-)
