[R] Mysteriously vanishing LD_LIBRARY_PATH

[p_connolly at slingshot.co.nz]

Quoting Godmar Back <godmar at gmail.com>:

> R respects LD_LIBRARY_PATH, see /usr/lib/R/etc/ldpaths where it
> prepends its own path to any value in the environment when R is
> invoked:
>
> if test -z "${LD_LIBRARY_PATH}"; then
>   LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
> else
>   LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"
> fi
> export LD_LIBRARY_PATH
>
> =====
>
> Provide the output of
>
> echo $LD_LIBRARY_PATH
> or
> env | grep LD_LIBRARY_PATH
>
> to check that it's set correctly *BEFORE* you invoke R.

There's nothing there.  However, you might have got me onto a 
workaround.  When
I see this:


$ diff /home/hrapgc/local/R-2.8.1/etc/ldpaths
/home/hrapgc/local/R-2.9.1/etc/ldpaths
2c2
< :
${R_JAVA_LD_LIBRARY_PATH=/usr/lib/gcj-4.1.2:/home/hrapgc/Rstuff/library/asreml/libs}
---
> : ${R_JAVA_LD_LIBRARY_PATH=/usr/lib/gcj-4.1.2}


I think a little editing job will do the trick.  Presumably, that happened at
compilation time and something screwy is happening with CentOS which doesn't
happen with other OSs.

The gcj thing IS a red herring, can we assume?

Thanks






>
>  - Godmar
>
> On Wed, Jul 8, 2009 at 9:45 PM, <p_connolly at slingshot.co.nz> wrote:
>> Using R-2.8.0 and R-2.8.1, I get behaviour like this:
>>
>> R version 2.8.0 (2008-10-20)
>> Copyright (C) 2008 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> [....]
>>
>>> Sys.getenv("LD_LIBRARY_PATH")
>>
>>          LD_LIBRARY_PATH
>> "/home/hrapgc/local/R-2.8.0/lib:/usr/local/lib:/usr/lib/gcj-4.1.1:/home/hrapgc/Rstuff/library/asreml/libs"
>>> q()
>> Save workspace image? [y/n/c]: n
>>
>>
>> However:
>>
>> R version 2.9.1 (2009-06-26)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> [...]
>>
>>> Sys.getenv("LD_LIBRARY_PATH")
>>                                                   LD_LIBRARY_PATH
>> "/home/hrapgc/local/R-2.9.1/lib:/usr/local/lib:/usr/lib/gcj-4.1.2"
>>
>>
>> I'm particularly dismayed by the fact that there are now only three
>> parts to LD_LIBRARY_PATH, and slightly mystified by the appearance of
>> /usr/lib/gcj-4.1.2 in place of /usr/lib/gcj-4.1.1.  Maybe that's a red
>> herring since the former is a link to the latter.
>>
>> I would appreciate help getting the rest of LD_LIBRARY_PATH back.  I
>> set it in ~/.bash_profile in case that makes a difference to the
>> possible cause of the phenomenon.
>>
>> $ uname -r
>> 2.6.18-92.1.22.el5
>>
>> The problem doesn't seem to arise with Fedora 8 nor with Mepis 6.5.
>>
>> TIA
>>
>> --
>> Patrick Connolly
>> HortResearch
>> Mt Albert
>> Auckland
>> New Zealand
>> Ph: +64-9 925 7079
>> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~
>> I have the world`s largest collection of seashells. I keep it on all
>> the beaches of the world ... Perhaps you`ve seen it.  ---Steven Wright
>> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>