On 29 Sep 2014, at 14:06, Rasmus <ras...@gmx.us> wrote: > Johannes Rainer <johannes.rai...@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? > >
