R devel - Apr 2008 - getNativeSymbolInfo fails with Fortran symbol.

In the following code routine 'initaquaphy' is defined in Fortran,
and dynamically loaded into R.:

test.f:


      subroutine initaquaphy(odeparms)

      external odeparms
      double precision pars(19)
      common /myparms/pars

       call odeparms(19, pars)

      return
      end

$ R CMD SHLIB Aquaphy.f
gfortran   -fpic  -g -O2 -c test.f -o test.o
gcc -std=gnu99 -shared -L/usr/local/lib -o test.so test.o  -lgfortran -lm


and linked into the package dll (or so).  Help for is.loaded() and
getNativeSymbolInfo() say not to use symbol.For() to convert
to Fortran-specific symbols.  However, on Linux, getNativeSymbolInfo
is unable to find 'initaquaphy' in 'test.so', but does find
'initaquaphy_'.  Note that is.loaded() works as advertised. 
Furthermore,
this code works in Windows, R-2.6.2patched44759.

triggerbug.R:

system("R CMD SHLIB test.f")
dyn.load(paste("test",.Platform$dynlib.ext,sep=""))
is.loaded("initaquaphy", PACKAGE="test")
getNativeSymbolInfo("initaquaphy_", PACKAGE="test")
getNativeSymbolInfo("initaquaphy", PACKAGE="test")
cat("All Done")

Resulting in:
> source("triggerbug.R", echo=TRUE, print.eval=TRUE)
> system("R CMD SHLIB test.f")
gfortran   -fpic  -g -O2 -c test.f -o test.o
gcc -std=gnu99 -shared -L/usr/local/lib -o test.so test.o  -lgfortran -lm
> dyn.load(paste("test",.Platform$dynlib.ext,sep=""))
> is.loaded("initaquaphy", PACKAGE="test")
[1] TRUE
> getNativeSymbolInfo("initaquaphy_", PACKAGE="test")
$name
[1] "initaquaphy_"

$address
<pointer: 0x1c03f0>
attr(,"class")
[1] "NativeSymbol"

$package
DLL name: test
Filename: /home/setzer/tasks/Programming_Projects/test.so
Dynamic lookup: TRUE

attr(,"class")
[1] "NativeSymbolInfo"
> getNativeSymbolInfo("initaquaphy", PACKAGE="test")
Error in FUN("initaquaphy"[[1L]], ...) :
  no such symbol initaquaphy in package test
>
Have I misunderstood the help page, or is this a bug?

--please do not edit the information below--

Version:
 platform = i686-pc-linux-gnu
 arch = i686
 os = linux-gnu
 system = i686, linux-gnu
 status = beta
 major = 2
 minor = 7.0
 year = 2008
 month = 04
 day = 07
 svn rev = 45159
 language = R
 version.string = R version 2.7.0 beta (2008-04-07 r45159)

Locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

Search Path:
 .GlobalEnv, package:deSolve, package:stats, package:graphics,
package:grDevices, package:utils, package:datasets, package:methods, Autoloads,
package:base

R. Woodrow Setzer, Ph. D.
National Center for Computational Toxicology
http://www.epa.gov/comptox
US Environmental Protection Agency
Mail Drop B205-01/US EPA/RTP, NC 27711
Ph: (919) 541-0128    Fax: (919) 541-1194

It's a bug -- unlike is.loaded, getNativeSymbolInfo seems unaware of 
Fortran names unless registered.

Will be fixed in 2.7.0.

On Wed, 9 Apr 2008, Setzer.Woodrow at epamail.epa.gov wrote:
>
>
> In the following code routine 'initaquaphy' is defined in Fortran,
> and dynamically loaded into R.:
>
> test.f:
>
>
>      subroutine initaquaphy(odeparms)
>
>      external odeparms
>      double precision pars(19)
>      common /myparms/pars
>
>       call odeparms(19, pars)
>
>      return
>      end
>
> $ R CMD SHLIB Aquaphy.f
> gfortran   -fpic  -g -O2 -c test.f -o test.o
> gcc -std=gnu99 -shared -L/usr/local/lib -o test.so test.o  -lgfortran -lm
>
>
> and linked into the package dll (or so).  Help for is.loaded() and
> getNativeSymbolInfo() say not to use symbol.For() to convert
> to Fortran-specific symbols.  However, on Linux, getNativeSymbolInfo
> is unable to find 'initaquaphy' in 'test.so', but does find
> 'initaquaphy_'.  Note that is.loaded() works as advertised. 
Furthermore,
> this code works in Windows, R-2.6.2patched44759.
>
> triggerbug.R:
>
> system("R CMD SHLIB test.f")
> dyn.load(paste("test",.Platform$dynlib.ext,sep=""))
> is.loaded("initaquaphy", PACKAGE="test")
> getNativeSymbolInfo("initaquaphy_", PACKAGE="test")
> getNativeSymbolInfo("initaquaphy", PACKAGE="test")
> cat("All Done")
>
> Resulting in:
>
>> source("triggerbug.R", echo=TRUE, print.eval=TRUE)
>
>> system("R CMD SHLIB test.f")
> gfortran   -fpic  -g -O2 -c test.f -o test.o
> gcc -std=gnu99 -shared -L/usr/local/lib -o test.so test.o  -lgfortran -lm
>
>> dyn.load(paste("test",.Platform$dynlib.ext,sep=""))
>
>> is.loaded("initaquaphy", PACKAGE="test")
> [1] TRUE
>
>> getNativeSymbolInfo("initaquaphy_", PACKAGE="test")
> $name
> [1] "initaquaphy_"
>
> $address
> <pointer: 0x1c03f0>
> attr(,"class")
> [1] "NativeSymbol"
>
> $package
> DLL name: test
> Filename: /home/setzer/tasks/Programming_Projects/test.so
> Dynamic lookup: TRUE
>
> attr(,"class")
> [1] "NativeSymbolInfo"
>
>> getNativeSymbolInfo("initaquaphy", PACKAGE="test")
> Error in FUN("initaquaphy"[[1L]], ...) :
>  no such symbol initaquaphy in package test
>>
>
> Have I misunderstood the help page, or is this a bug?
>
> --please do not edit the information below--
>
> Version:
> platform = i686-pc-linux-gnu
> arch = i686
> os = linux-gnu
> system = i686, linux-gnu
> status = beta
> major = 2
> minor = 7.0
> year = 2008
> month = 04
> day = 07
> svn rev = 45159
> language = R
> version.string = R version 2.7.0 beta (2008-04-07 r45159)
>
> Locale:
>
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> Search Path:
> .GlobalEnv, package:deSolve, package:stats, package:graphics,
package:grDevices, package:utils, package:datasets, package:methods, Autoloads,
> package:base
>
> R. Woodrow Setzer, Ph. D.
> National Center for Computational Toxicology
> http://www.epa.gov/comptox
> US Environmental Protection Agency
> Mail Drop B205-01/US EPA/RTP, NC 27711
> Ph: (919) 541-0128    Fax: (919) 541-1194
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
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