From jgarcia at ija.csic.es  Tue Apr 13 22:20:33 2010
From: jgarcia at ija.csic.es (jgarcia at ija.csic.es)
Date: Tue, 13 Apr 2010 22:20:33 +0200 (CEST)
Subject: [Rd] .Fortran interface error
Message-ID: <42789.86.0.54.218.1271190033.squirrel@paleo.ija.csic.es>

Yes!!!!!!!! That's it! Thanks a lot!!!!!!
Changing UNIT=5 in the F95 code by UNIT=7 solves the collision.

Thank you very much Charlie, I've spent a lot of hours with this.

Still

R -d valgrind --vanilla < foofortran.Rcheck/foofortran-Ex.R

gives 3 errors (two "Invalid read of size 8" and one "Syscall param
write(buf) points to uninitialised byte(s)"), which are the same it gave
with UNIT=5. However, everything seems to work fine now in the normal
execution :-)

Thank you very much again

Javier
---

==25824== Memcheck, a memory error detector.
==25824== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
==25824== Using LibVEX rev 1732, a library for dynamic binary translation.
==25824== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
==25824== Using valgrind-3.2.3, a dynamic binary instrumentation framework.
==25824== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
==25824== For more details, rerun with: -v
==25824==

R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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> pkgname <- "foofortran"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('foofortran')
==25824== Invalid read of size 8
==25824==    at 0x401431B: (within /lib64/ld-2.6.1.so)
==25824==    by 0x4009631: (within /lib64/ld-2.6.1.so)
==25824==    by 0x5A9D804: (within /lib64/libc-2.6.1.so)
==25824==    by 0x57A3143: (within /lib64/libdl-2.6.1.so)
==25824==    by 0x400C8E5: (within /lib64/ld-2.6.1.so)
==25824==    by 0x57A336C: (within /lib64/libdl-2.6.1.so)
==25824==    by 0x57A30F9: dlsym (in /lib64/libdl-2.6.1.so)
==25824==    by 0x59871C: R_local_dlsym (dynload.c:216)
==25824==    by 0x4C9944: AddDLL (Rdynload.c:557)
==25824==    by 0x4CA073: do_dynload (Rdynload.c:893)
==25824==    by 0x428372: do_internal (names.c:1165)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==  Address 0x61BA068 is 16 bytes inside a block of size 18 alloc'd
==25824==    at 0x4C21D06: malloc (in
/usr/lib64/valgrind/amd64-linux/vgpreload_memcheck.so)
==25824==    by 0x4C9918: AddDLL (Rdynload.c:549)
==25824==    by 0x4CA073: do_dynload (Rdynload.c:893)
==25824==    by 0x428372: do_internal (names.c:1165)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==    by 0x54F6AF: Rf_applyClosure (eval.c:699)
==25824==    by 0x54D105: Rf_eval (eval.c:508)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==    by 0x54EE71: do_set (eval.c:1502)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==    by 0x55157B: do_begin (eval.c:1245)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==
==25824== Invalid read of size 8
==25824==    at 0x4014DCE: (within /lib64/ld-2.6.1.so)
==25824==    by 0x400967A: (within /lib64/ld-2.6.1.so)
==25824==    by 0x5A9D804: (within /lib64/libc-2.6.1.so)
==25824==    by 0x57A3143: (within /lib64/libdl-2.6.1.so)
==25824==    by 0x400C8E5: (within /lib64/ld-2.6.1.so)
==25824==    by 0x57A336C: (within /lib64/libdl-2.6.1.so)
==25824==    by 0x57A30F9: dlsym (in /lib64/libdl-2.6.1.so)
==25824==    by 0x59871C: R_local_dlsym (dynload.c:216)
==25824==    by 0x4C9944: AddDLL (Rdynload.c:557)
==25824==    by 0x4CA073: do_dynload (Rdynload.c:893)
==25824==    by 0x428372: do_internal (names.c:1165)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==  Address 0x61BA068 is 16 bytes inside a block of size 18 alloc'd
==25824==    at 0x4C21D06: malloc (in
/usr/lib64/valgrind/amd64-linux/vgpreload_memcheck.so)
==25824==    by 0x4C9918: AddDLL (Rdynload.c:549)
==25824==    by 0x4CA073: do_dynload (Rdynload.c:893)
==25824==    by 0x428372: do_internal (names.c:1165)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==    by 0x54F6AF: Rf_applyClosure (eval.c:699)
==25824==    by 0x54D105: Rf_eval (eval.c:508)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==    by 0x54EE71: do_set (eval.c:1502)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==    by 0x55157B: do_begin (eval.c:1245)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("fooRf90")
> ### * fooRf90
>
> flush(stderr()); flush(stdout())
>
> ### Name: fooRf90
> ### Title: Sample Call to FORTRAN 90
> ### Aliases: fooRf90
>
> ### ** Examples
>
> x <- c(1:10)
> filename <- "anystring"
> res <- fooRf90(x, filename)
==25824==
==25824== Syscall param write(buf) points to uninitialised byte(s)
==25824==    at 0x5A5DC40: write (in /lib64/libc-2.6.1.so)
==25824==    by 0x50E8000: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50E807D: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50E8817: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50E545C: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50E597B: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50E59D8: _gfortran_st_write_done (in
/usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x849CC02: foof90_ (ofoofunc.f90:18)
==25824==    by 0x5200FD: do_dotCode (dotcode.c:1724)
==25824==    by 0x54D3AB: Rf_eval (eval.c:490)
==25824==    by 0x54EE71: do_set (eval.c:1502)
==25824==    by 0x54D1E1: Rf_eval (eval.c:464)
==25824==  Address 0x404C3D3 is 171 bytes inside a block of size 8,344
alloc'd
==25824==    at 0x4C21D06: malloc (in
/usr/lib64/valgrind/amd64-linux/vgpreload_memcheck.so)
==25824==    by 0x5069D38: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50E8269: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50E7A73: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x5069B37: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x50F9241: (within /usr/lib64/libgfortran.so.2.0.0)
==25824==    by 0x5066CF2: (within /usr/lib64/libgfortran.so.2.0.0)
 runfile:   anystring !"#$%&'&#65533;&#65533;&#65533;&#65533;06
                                   &#65533;&#65533;&#65533;&#1075;&#65533;'


&#9618;&#9618;
orunfile:   anystring


>
> jgarcia-2 wrote:
>>
>> Hi,
>> I've stripped all the code, and it seems that any simple attempt to
>> open/close a file from fortran is the cause of the error, and the error
>> appears in f77 as well as in f95 code. Please, find attached a foo
>> package
>> that reproduce the errors, it should build/check/install without any
>> problem (it does in my computer). If the code
>>
>>  OPEN( UNIT=5, FILE=runfile, STATUS='OLD', ACTION='READ', &
>>        IOSTAT=status)
>>  WRITE (*,*) 'status:   ', status
>>  IF ( status == 0 ) THEN
>>    READ(5,'(A)') modelsel
>>    READ(5,'(A)') modelfile
>>    READ(5,'(A)') datdirpid
>>    CLOSE(5)
>>
>>    WRITE (*,*) 'selected model:   ', modelsel
>>    WRITE (*,*) 'model input file: ', modelfile
>>    WRITE (*,*) 'datdirpid: ', datdirpid
>>  ELSE
>>    WRITE (*,1002) status
>>     1002 FORMAT (1X,'open runfile failed--status = ', I6)
>>    STOP
>>  END IF
>>
>> is commented out in any of the two sources files (the f77 or the f95
>> one),
>> none of the two corresponding wrappers (as they appear in the examples)
>> give an error. Thus it seems clear that the operation causing it is the
>> OPEN/CLOSE. Without commenting out these pieces of code, everything
>> seems
>> to work right but R halts after a call to the wrapper functions. I
>> cannot
>> find any comment about this in the documentation. Please, could you tell
>> me if this is a known error?
>>
>> Thanks,
>>
>> Javier
>>
>
> It looks like you may have some I/O collisions occurring.  Some Fortran
> compilers treat unit 5 as being STDIN, so attempting to read from that
> stream when the Fortran program is embedded may be giving R a headache.  I
> would recommend either passing "modelsel", "modelfile" and "datadirpid" as
> parameters from R, or reading from a file using a different unit number.
>
> For output, instead of using write(*,*) you may need to use some of the R
> output callbacks described in section 6.5.1 of "Writing R Extensions".
>
> Hope this helps!
>
> -Charlie
>
>
>
> -----
> Charlie Sharpsteen
> Undergraduate-- Environmental Resources Engineering
> Humboldt State University
> --
> View this message in context:
> http://n4.nabble.com/Fortran-interface-error-tp1838225p1838888.html
> Sent from the R devel mailing list archive at Nabble.com.
>
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>



[Rd] .Fortran interface error
jgarcia at ija.csic.es