Three data points, some random musings and a couple questions :
1)
charpent@asus16-ec:/usr/local/sage-5.13$ echo $LD_LIBRARY_PATH
charpent@asus16-ec:/usr/local/sage-5.13$ ./sage -R
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.
R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.
Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.
> system("echo $LD_LIBRARY_PATH")
/usr/local/sage-5.13/local/lib/R//lib:/usr/local/sage-5.13/local/lib/:/usr/local/sage-5.13/local/lib:/usr/local/sage-5.13/local/lib:/usr/local/sage-5.13/local/lib/R/lib
>
So "the usual nightmare" does not seem to originate in my account's
configuration, but in sage's setting of this variable ?
2) An "in place" recompilation gives exactly the same result as before.
3) From cloud.sagemath.org (with manual removal of code decoration) :
r.version()
((2, 15, 2), 'R version 2.15.2 (2012-10-26)')
sage.version.version
'5.12'
r.capabilities()
jpeg png tiff tcltk X11 aqua http/ftp sockets
libxml fifo cledit
TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE
TRUE TRUE TRUE
iconv NLS profmem cairo
TRUE TRUE FALSE TRUE
I suspect that trac#14706 <http://trac.sagemath.org/ticket/14706> might be
responsible for this problem : this ticket, which was in the beginning a
pure port of the R 3.0 source, has been hijacked in order to solve related
DYLD_LIBRARY_PATH and (possibly related) readline issues in cygwin. I am
unable to follow the relevant discussion (no real experience with cygwin),
but I think that messing around might have been the source of this new bugn
that R-under-Sage users might consider as quite serious.
Since this ticket has been closed and the resulting package merged in
sage-5.13, what would be the "right" way to report this ?
More interesting : is there a workaround, i. e. a way to use sage's R
*without* the suspicious LD_LIBRARY_PATH ? Ditto from sage ?
Bonus question : is there a way to retrieve the "old" (<=5.12) spkg and use
it as a base for a "forked" R-3 spkg ?
Le mardi 17 décembre 2013 22:32:26 UTC+1, Volker Braun a écrit :
>
> Looks like the usual LD_LIBRARY_PATH nightmare. Whenever you use system
> shared libraries it is a bit of a gamble... The only correct solution is to
> not set LD_LIBRARY_PATH.
>
> Again : how do you do that ?
Anyway, thank you very much for your help !
--
Emmanuel Charpentier
>
>
> On Tuesday, December 17, 2013 8:41:52 PM UTC, Emmanuel Charpentier wrote:
>>
>> I compiled sage from sources on a debian amd64 system, on which sage 5.12
>> had no problems.
>>
>> Sage itself seems fine. But I had problems installng packages requiring
>> tcl/tk. After examonation, it seems that Sage's R has lost its graphics :
>>
>> charpent@asus16-ec:~$ sage -R
>>
>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>> Copyright (C) 2013 The R Foundation for Statistical Computing
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> R est un logiciel libre livré sans AUCUNE GARANTIE.
>> Vous pouvez le redistribuer sous certaines conditions.
>> Tapez 'license()' ou 'licence()' pour plus de détails.
>>
>> R est un projet collaboratif avec de nombreux contributeurs.
>> Tapez 'contributors()' pour plus d'information et
>> 'citation()' pour la façon de le citer dans les publications.
>>
>> Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
>> en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
>> Tapez 'q()' pour quitter R.
>>
>> [Sauvegarde de la session précédente restaurée]
>>
>> > capabilities()
>> jpeg png tiff tcltk X11 aqua http/ftp sockets
>> FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
>> libxml fifo cledit iconv NLS profmem cairo
>> TRUE TRUE TRUE TRUE TRUE FALSE FALSE
>> Message d'avis :
>> In doTryCatch(return(expr), name, parentenv, handler) :
>> impossible de charger l'objet partagé
>> '/usr/local/sage-5.13/local/lib/R//modules//R_X11.so':
>> /usr/lib/x86_64-linux-gnu/libharfbuzz.so.0: undefined symbol:
>> FT_Face_GetCharVariantIndex
>> >
>>
>> Same symptoms (minus the informative "Message d'avis" (warnings)) in the
>> notebook.
>>
>> R_X11.so *is* in the requested place. Bit the double slash in its path is
>> suspicious...
>>
>> Note : I compiled sage in my home directory, then moved it to its
>> intended location in /usr/local. I remember having had analogous problems
>> with such "moved" installations of sage (pertaining to other R packages
>> using C++ libraries).
>>
>> Questions :
>>
>> Is this a bug ? Worth a ticket ?
>> 2) if so, should I report it ? With which tags ?
>>
>> Sincerely,
>> --
>> Emmanuel Charpentier
>> PS : I'll try an "in place" recompilation.
>>
>
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