From: Johannes Rainer <johannes.rainer@gmail.com>
To: Rasmus <rasmus@gmx.us>
Cc: emacs-orgmode@gnu.org
Subject: Re: passing LC_ALL environment variable to org export call
Date: Mon, 29 Sep 2014 14:51:53 +0200 [thread overview]
Message-ID: <113D8AEB-BFB6-48D2-B473-EE2055C8C70D@gmail.com> (raw)
In-Reply-To: <87y4t2ws06.fsf@gmx.us>
On 29 Sep 2014, at 14:06, Rasmus <rasmus@gmx.us> wrote:
> Johannes Rainer <johannes.rainer@gmail.com> writes:
>
>> thanks for your hint. I checked Sys.getenv before and after the
>> failing code, but LC_ALL was always properly set. I’m afraid my
>> problem relates to some Mac LLVM and GCC gfortran compiler thing,
>> since I’m using a R version compiled against the Mac Accelerate
>> framework (vecLib)… it is just so strange that I only get the error in
>> Emacs org-mode upon exporting the org file, but not, if I evaluate
>> each code chunk separately.
>
> But are you using .C, .Fortran or Rcpp in your code-block? If not,
> why would your compilers matter? (I'm not an expert on R internals,
> so my comment may be naïve).
>
no I’m not using .C in the code-block, the code block contains only R-code, however, one of the R functions is using (like most R functions) either C or fortran code to do the actual calculation. I suspect the loess function in R causing the problem and that this function uses some code from the optimized BLAS (i.e. library for numeric calculation) library from Apple (i.e. the Accelerate, or vecLib framework).
So, if I run the code (exporting the org buffer to latex) in parallel processing mode I get a segfault. the same without parallel processing is fine. Strangely enough, the code block evaluated (C-c C-c) in parallel processing mode runs also fine. also, if I tangle the R-code and run the R-code in R it also works fine. It just doesn’t with org-mode export...
so, in the end I give up. I think there is some very mystic thing going on. I also tried to understand what the difference between org-mode export and org-mode eval is... without success. I thought that the R-process is somehow started differently, but that doesn’t seem to be the case.
> As a short turn solution try to add this to the top of your file
>
> #+PROPERTY: session *R*
>
> These days you might even get away with just
>
> #+PROPERTY: session
>
> I'm not sure. This should run your code from the same session.
>
> [This should be equivalent to adding :session to babel blocks, but
> check the manual if it ain't working]
>
>> to set all environment variables I’m using the “exec-path-from-shell”
>> extension, so, all environment settings from the shell are available
>> in Emacs.
>
> Are you exporting async or "normally"? If async, do you get the error
> when exporting "normally"?
>
> —Rasmus
>
> --
> Hvor meget poesi tror De kommer ud af et glas isvand?
>
>
prev parent reply other threads:[~2014-09-29 12:52 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-09-26 9:14 passing LC_ALL environment variable to org export call Johannes Rainer
2014-09-26 13:56 ` Rasmus
2014-09-29 10:54 ` Johannes Rainer
2014-09-29 12:06 ` Rasmus
2014-09-29 12:51 ` Johannes Rainer [this message]
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