.Fortran successful, R locks up.

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]]
[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
library.dynam("rswat","EcoHydrology")
for (i in 0:5){
.Fortran("junk",i)
print(paste("success",i))
}
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

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

GFORTRAN_STDOUT_UNIT
GFORTRAN_STDERR_UNIT

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, ? ? ? ? ? ? ? ? ?ripley at stats.ox.ac.uk
Professor of Applied Statistics, ?http://www.stats.ox.ac.uk/~ripley/
University of Oxford, ? ? ? ? ? ? Tel: ?+44 1865 272861 (self)
1 South Parks Road, ? ? ? ? ? ? ? ? ? ? +44 1865 272866 (PA)
Oxford OX1 3TG, UK ? ? ? ? ? ? ? ?Fax: ?+44 1865 272595