Bug 384715

Summary:	dev-lang/R-2.13.1-r1: potentially using java without the proper eclasses
Product:	Gentoo Linux	Reporter:	Ralph Sennhauser (RETIRED) <sera>
Component:	Current packages	Assignee:	Gentoo Science Mathematics related packages <sci-mathematics>
Status:	RESOLVED INVALID
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	388937
Attachments:	build.log with sandbox violations patch agains R-2.13.1-r1.ebuild

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 (RETIRED) 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 (RETIRED) gentoo-dev

2015-07-30 09:41:33 UTC

Taking @java off CC.

Comment 7 Patrice Clement (RETIRED) gentoo-dev

2015-08-13 18:15:01 UTC

Closing this bug as per comment #5.