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Bug 418625 - sci-biology/gatk-1.5: error: name clash: sum(Collection<Integer>) and sum(Collection<Number>) have the same erasure
Summary: sci-biology/gatk-1.5: error: name clash: sum(Collection<Integer>) and sum(Col...
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2012-06-01 09:18 UTC by Martin Mokrejš
Modified: 2013-02-17 08:28 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,88.54 KB, text/plain)
2012-06-01 09:18 UTC, Martin Mokrejš
Details

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Description Martin Mokrejš 2012-06-01 09:18:15 UTC
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"
 *
Comment 1 Martin Mokrejš 2012-06-01 09:18:40 UTC
Created attachment 313797 [details]
build.log
Comment 2 Martin Mokrejš 2012-06-01 09:20:00 UTC
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.