Re: [Rd] .Fortran successful, R locks up.

From: Daniel Fuka <>
Date: Sun, 27 Mar 2011 15:31:11 -0400

Duncan and Brian,

Thanks again for the help with this. As it turns out the suggestion of setting the GFORTRAN_STDIN_UNIT=-1 has the library working for Mac, Linux, and Windows, so it appears to be in a STDIN read somewhere. Of the 1100 read statements in the code, none are from stdin, or unit 5. Oddly enough, without the environment variable set, everything runs fine looping within a script called from command line (-f) which I delve into a bit below. So, we are functional on repo binaries, and standard linux distros, but intel fortran and xlf appear to have issues still... not a big deal, but if anyone is willing to give me suggestions on other things I can use to try to debug this issue, I would love to clear it up.

Sorry for not giving all the background information. I am working/testing on Mac OSX(gfortran 4.2.3, intel fortran 11), Linux (gfortran 4.1.2, intel fortran 11) , WindowsXP (gfortran 4.5), and AIX(xlf v12.1). Right now the environment variable will work I believe since we are just trying to get the standard r-forge distro binaries to work with the package, though I shall keep looking for the STDIN that appears to have been opened.

> Sys.setenv(GFORTRAN_STDIN_UNIT=-1)
> library.dynam("rswat","EcoHydrology")
> .Fortran("junk",3)

SWAT Run Successful

[1] 0
[1] 3


Just a bit more information here on this issue. Without the Sys.setenv(GFORTRAN_STDIN_UNIT=-1) function, the .Fortran call runs fine in a loop when called from command line script file (-f) call. When called from interactive session, it runs successfully, then gets stuck in an endless loop of lines 911, 912, 904 in in ../../../../R-2.12.1/src/unix/sys-std.c . There appears to be no STDIO in the routines, and to make sure, I am now closing all the stdio units at the end of the run.

DRF28: dan$ cat test.R
for (i in 0:5){
DRF28: dan$ r -q -f test.R
> library.dynam("rswat","EcoHydrology")
> for (i in 0:5){

+ .Fortran("junk",i)
+ print(paste("success",i))
+ }

SWAT Run Successful
[1] 0
[1] "success 0"
SWAT Run Successful
[1] 1
[1] "success 1"
SWAT Run Successful
[1] 2
[1] "success 2"
----SNIP---- On Sat, Mar 26, 2011 at 11:49 PM, Prof Brian Ripley <> wrote:
> You seem to have missed the force of the warning in 'Writing R Extensions'.
> If you include *any* Fortrann I/O in your package code, you are at risk from
> it interfering with C I/O, whether or not that Fortran I/O is called.
> On some platforms with gfortran, merely loading such a package's DSO/DLL
> calls the libgfortran initialization functions and they reset the process'
> stdin, causing the behaviour you saw.
> You have not told us what compilers etc you are using.  On some versions of
> gfortran you can avoid this by setting the environment variables
> to -1: these tell gfortran not to use C stdout/stderr (and because of what I
> can only see is a bug, it was the use of those which resets stdin).
> On Fri, 25 Mar 2011, Daniel Fuka wrote:
>> Thanks Duncan for helping me along the way. I am working in OSX,
>> Linux, and Windows, and gdb is helping me trace it along to what
>> appears to be an endless processor intensive loop in sys-std.c .
>> Below, I have pasted the output. All files are closed as verified by
>> lsof. There is absolutely no stdio other than what I have put in a
>> call to R library's subroutine intpr, all other io is routed to files,
>> which are all successfully closed. The entire routine successfully
>> runs, and spits out the output from intpr. Is there supposed to be
>> something returned from the Fortran routine that Rstd_ReadConsole is
>> looking for? I have attached the final lines of the fortran
>> subroutine, as well as the gdb steps post fortran routine. Any
>> additional help is greatly appreciated!
> ...
> --
> Brian D. Ripley,        
> Professor of Applied Statistics,
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> mailing list Received on Sun 27 Mar 2011 - 20:02:55 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Mon 28 Mar 2011 - 01:40:36 GMT.

Mailing list information is available at Please read the posting guide before posting to the list.

list of date sections of archive