586034 – sys-devel/gcc-5.* and dev-java/icedtea-7.2.6.6 - libjvm.so => not found

Bug 586034 - sys-devel/gcc-5.* and dev-java/icedtea-7.2.6.6 - libjvm.so => not found

Summary: sys-devel/gcc-5.* and dev-java/icedtea-7.2.6.6 - libjvm.so => not found

Status:	RESOLVED INVALID

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	[OLD] Core system (show other bugs)
Hardware:	All Linux

Importance:	Normal normal (vote)
Assignee:	Gentoo Linux bug wranglers

URL:
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Depends on:
Blocks:

Reported:	2016-06-15 16:53 UTC by Juergen Rose
Modified:	2016-07-16 17:03 UTC (History)
CC List:	1 user (show)

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

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Description Juergen Rose 2016-06-15 16:53:31 UTC

Revdep-rebuild complains about broken R-packages:

root@lynx:/root(3)# revdep-rebuild -p
 * This is the new python coded version
...
!!! Broken orphaned files: No installed package was found for the following:
        * /usr/lib64/R/library/JavaGD/libs/JavaGD.so
        * /usr/lib64/R/library/rJava/libs/rJava.so
        * /usr/lib64/R/library/rJava/jri/libjri.so

ldd shows missing libjvm.so for these files, e.g.:

root@lynx:/root(4)# ldd /usr/lib64/R/library/JavaGD/libs/JavaGD.so
        linux-vdso.so.1 (0x00007fffc8de1000)
        libjvm.so => not found
        libR.so => /usr/lib64/R/lib/libR.so (0x00007ff869c77000)
        libc.so.6 => /lib64/libc.so.6 (0x00007ff8698de000)
        libf77blas.so.3 => /usr/lib64/libf77blas.so.3 (0x00007ff868e3c000)
...

But libjvm.so seems to be installed by gcc and icedtea:

root@lynx:/root(6)# find /usr/lib/ -name libjvm.so\*
/usr/lib/gcj-5.4.0-16/libjvm.so
/usr/lib/icedtea7/jre/lib/amd64/server/libjvm.so
/usr/lib/gcj-4.9.3-15/libjvm.so
/usr/lib/gcj-5.3.0-16/libjvm.so
root@lynx:/root(7)# qlist -Iv icedtea
dev-java/icedtea-7.2.6.6
dev-java/icedtea-bin-3.0.1
dev-java/icedtea-sound-1.0.1
dev-java/icedtea-web-1.6.1-r1

root@lynx:/root(9)# gcc-config -l
 [1] x86_64-pc-linux-gnu-4.9.3
 [2] x86_64-pc-linux-gnu-5.3.0
 [3] x86_64-pc-linux-gnu-5.4.0 *

root@lynx:/root(11)# java-config -L
The following VMs are available for generation-2:
*)      IcedTea JDK 7.2.6.6 [icedtea-7]
2)      IcedTea JDK 3.0.1 [icedtea-bin-8]


Any hint is apprecieated.

Comment 1 Thomas Deutschmann (RETIRED) gentoo-dev

2016-06-30 10:38:49 UTC

Have you tried to rebuild dev-lang/R?

Comment 2 Panagiotis Christopoulos (RETIRED) gentoo-dev

2016-07-14 15:39:56 UTC

Hi Juergen,

did what Thomas wrote help?

Comment 3 Mike Gilbert gentoo-dev

2016-07-16 17:03:47 UTC

> !!! Broken orphaned files

That means the files are not owned by any package installed by portage. No amount of revdep-rebuilding will fix them.