Re: [O] passing LC_ALL environment variable to org export call
hi Rasmus, 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. 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. On 26 Sep 2014, at 15:56, Rasmus ras...@gmx.us wrote: Hi Johannes, Johannes Rainer johannes.rai...@gmail.com writes: I stumbled across a strange problem. I’m using org-mode to perform analyses in R and I have one block of R-code in which I use mclapply to perform parallel calculations. evaluating this code block using C-c C-c works fine, but I get a segfault error when I export the org file. This has to do something with the LC_ALL environment variable as I can reproduce the same error above in R in a terminal after “unset LC_ALL”. Is there a way to pass environment variables to the export call? Check the two functions `getenv' and `setenv' and the variable `org-export-async-init-file'. You should be able to cook something up. It sound like there's an issue with your system-setup. I'd look into that before. Hope it helps, Rasmus -- Lasciate ogni speranza, voi che leggete questo.
Re: [O] passing LC_ALL environment variable to org export call
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). 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?
Re: [O] passing LC_ALL environment variable to org export call
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?
[O] passing LC_ALL environment variable to org export call
dear all, I stumbled across a strange problem. I’m using org-mode to perform analyses in R and I have one block of R-code in which I use mclapply to perform parallel calculations. evaluating this code block using C-c C-c works fine, but I get a segfault error when I export the org file. This has to do something with the LC_ALL environment variable as I can reproduce the same error above in R in a terminal after “unset LC_ALL”. Is there a way to pass environment variables to the export call? thanks!
Re: [O] passing LC_ALL environment variable to org export call
Hi Johannes, Johannes Rainer johannes.rai...@gmail.com writes: I stumbled across a strange problem. I’m using org-mode to perform analyses in R and I have one block of R-code in which I use mclapply to perform parallel calculations. evaluating this code block using C-c C-c works fine, but I get a segfault error when I export the org file. This has to do something with the LC_ALL environment variable as I can reproduce the same error above in R in a terminal after “unset LC_ALL”. Is there a way to pass environment variables to the export call? Check the two functions `getenv' and `setenv' and the variable `org-export-async-init-file'. You should be able to cook something up. It sound like there's an issue with your system-setup. I'd look into that before. Hope it helps, Rasmus -- Lasciate ogni speranza, voi che leggete questo.
