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Bug 384715 - dev-lang/R-2.13.1-r1: potentially using java without the proper eclasses
Summary: dev-lang/R-2.13.1-r1: potentially using java without the proper eclasses
Status: RESOLVED INVALID
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Mathematics related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: 388937
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Reported: 2011-09-27 20:27 UTC by Ralph Sennhauser (RETIRED)
Modified: 2015-08-13 18:15 UTC (History)
0 users

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


Attachments
build.log with sandbox violations (R-2.13.1-r1.build.log,36.63 KB, text/plain)
2011-09-27 20:29 UTC, Ralph Sennhauser (RETIRED)
Details
patch agains R-2.13.1-r1.ebuild (R-2.13.1-r1.ebuild.patch,1.51 KB, text/plain)
2011-09-27 20:30 UTC, Ralph Sennhauser (RETIRED)
Details

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Description Ralph Sennhauser (RETIRED) gentoo-dev 2011-09-27 20:27:25 UTC
R fails to build due to sandbox violations during configure when running JVM tools. See attached build.log.

Steps to reproduce:
1) emerge oracle-jdk-bin:1.7
2) eselect java-vm set system oracle-jdk-bin-1.7
3) . /etc/profile
4) emerge R

A bit hard for me to tell how optional java is for R so I'm going to attach an ebuild which adds optional java support as other packages would do. This fixes the sandbox issue for when the java flag is enabled. Still fails if disabled.
Comment 1 Ralph Sennhauser (RETIRED) gentoo-dev 2011-09-27 20:29:34 UTC
Created attachment 287979 [details]
build.log with sandbox violations
Comment 2 Ralph Sennhauser (RETIRED) gentoo-dev 2011-09-27 20:30:39 UTC
Created attachment 287983 [details]
patch agains R-2.13.1-r1.ebuild
Comment 3 Vlastimil Babka (Caster) (RETIRED) gentoo-dev 2011-11-04 09:29:58 UTC
Since the original sandbox issue was workaround system-wide, the remaining question is what is R using java for, and what e.g. java jars, or JNI bindings it installs ? If there is really some java support, and not just spurious configure checks, java eclasses should be used.
Comment 4 Sébastien Fabbro (RETIRED) gentoo-dev 2012-01-02 20:02:37 UTC
It seems that Java is only needed for CRAN packages which are written in Java, meaning once R is installed. During configuration, it is only needed to get the java path for proper conafiguration of the R package installer.

@java team: please apply the patch to >= dev-lang/R-2.14.1 if you feel it is necessary.
Comment 5 Patrice Clement gentoo-dev 2015-07-27 13:48:01 UTC
What's the status of this bug? Is it still reproducible with recent versions of R?

The version listed in this bug is no more (dev-lang/R-2.13.1-r1). I have managed to install =dev-lang/R-3.0.1 (which is the only stabilised version available) without a hitch (no sandbox violations nor warnings occured).

@sci-maths: feel free to close it.
Comment 6 Patrice Clement gentoo-dev 2015-07-30 09:41:33 UTC
Taking @java off CC.
Comment 7 Patrice Clement gentoo-dev 2015-08-13 18:15:01 UTC
Closing this bug as per comment #5.