[Rd] dyn.load error -- undefined symbol: ...

2005-09-11 Thread nwew 
Dear R-developers,

I am working on an C interface to some c functions.
I compiled the c file using R CMD SHLIB without any compilation errors. All 
libs used are added to the LD_LIBRARY_PATH.

However dyn.load("interface.so")
produces  undefined symbol: N_VNew_Serial;

which is defined in one of the libs I link against.
Where, and how to start searching for the error?

Eryk

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[Rd] NUMERIC_POINTER question

2005-09-13 Thread nwew 
Dear R-developers,

Using .Call I pass a S4 class with e.g. the following class definition:

setClass("mmatrix",representation(
   data="matrix")
)

On the "C side" i do
mat = GET_SLOT(vs,install("data"));
and then:
printf("%f\n",NUMERIC_POINTER(mat)[1]);


The above print statement produces the correct output if 
xx<- new("mmatrix")
[EMAIL PROTECTED]<-matrix(1:12+0.1,3,4). (data is double)

However it prints 
0. 
if [EMAIL PROTECTED] are integers ( [EMAIL PROTECTED]<-matrix(1:12,3,4) ).

Can anyone explain it to me why? 
I thought that NUMERIC_POINTER makes it clear that i expect datatype numeric.
(Why otherwise the distinction with INTEGER_POINTER)


cheers
Eryk

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[Rd] Problems with autoconf example from r-ext.

2005-10-05 Thread nwew 
Dear R-developers,

I am trying to reproduce the autoconf.ac example from R-ext and fail.

My autoconf file looks like this

[autoconf.ac]
# original by Friedrich Leisch, much changed by BDR

AC_INIT([SBMLodeSolveR])

dnl Select an optional include path, from a configure option
dnl or from an environment variable.
AC_ARG_WITH([sbmlode-include],
AC_HELP_STRING([--with-sbmlode-include=INCLUDE_PATH],
   [the location of SBMLODE header files]),
[sbmlode_include_path=$withval])
if test [ -n "$sbmlode_include_path" ] ; then
   AC_SUBST([CPPFLAGS],["-I${sbmlode_include_path} ${CPPFLAGS}"])
else
  if test [ -n "${SBMLODE_INCLUDE}" ] ; then
 AC_SUBST([CPPFLAGS],["-I${SBMLODE_INCLUDE} ${CPPFLAGS}"])
  fi
fi


dnl ditto for a library path
AC_ARG_WITH([sbmlode-lib],AC_HELP_STRING([--with-sbmlode-lib=LIB_PATH],[the 
location of libsbmlode libraries]),[sbmlode_lib_path=$withval])

  if test [ -n "$sbmlode_lib_path" ] ; then
 AC_SUBST([LIBS],[" -L${sbmlode_lib_path} ${LIBS}"])
  else
if test [ -n "${SBMLODE_LIBS}" ] ; then
   AC_SUBST([LIBS],["-I${SBMLODE_LIBS} ${LIBS}"])
fi
  fi

dnl Now find the compiler and compiler flags to use
  : ${R_HOME=`R RHOME`}
  if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
  fi
  CC=`"${R_HOME}/bin/R" CMD config CC`
  CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`

  
dnl substitute CPPFLAGS and LIBS
  AC_SUBST(CPPFLAGS)
  AC_SUBST(LIBS)
dnl and do subsitution in the src/Makevars.in
  AC_OUTPUT(src/Makevars)

[end autoconf.ac]

I rund autoconf..

[Makevars.in]
[EMAIL PROTECTED]@
[EMAIL PROTECTED]@
[end-Makevars.in]

I rund R CMD with

R CMD INSTALL 
--configure-args='--with-sbmlode-lib=/data/opt/sbmlodesolve/include \
--with-sbmlode-include=/data/opt/sbmlodesolve/lib' \
 SBMLodeSolveR


What I am getting is a

[Makvars]
PKG_CFLAGS=
PKG_LIBS= -L/data/opt/sbmlodesolve/include
[end-Makevars]


and the following warnings

[warnings]
* Installing *source* package 'SBMLodeSolveR' ...
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: /data/opt/sbmlodesolve/lib
configure: creating ./config.status
config.status: creating src/Makevars
*
[end-warnings]

Any suggestions?

Eryk

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[Rd] Error: .First.lib failed for 'SBMLodeSolveR'

2005-10-11 Thread nwew 
Dear R-developers,

I am getting the following error message (see bottom of e-mail) and can't make 
a clue out of it.

The zzz.R file contains 
.First.lib <- function(lib, pkg) library.dynam("SBMLodeSolveR",pkg,lib)
.Last.lib <- function(libpath) library.dynam.unload("SBMLodeSolveR", libpath)

There is a SBMLodeSolveR.so file in the src directory which works if loaded 
with 
dyn.load("/data/devel/SBMLodeSolveR/SBMLodeSolveR/src/SBMLodeSolveR.so")

The error/warning messages are:

* checking S3 generic/method consistency ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
*


Eryk

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[Rd] Problem with C code under R2.2 only.

2005-11-10 Thread nwew 
Dear R developers,

Running a R CMD check under R2.2 gives me the error messages (appended to this 
e-mail) while the with R2.1 the check on the same package directory runs fine. 
To my knowledge the configuration of R2.2 and R2.1 on my machine are 
identical.


* checking S3 generic/method consistency ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error: .First.lib failed for 'SBMLodeSolveR'
Call sequence:
2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
   domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error: .First.lib failed for 'SBMLodeSolveR'



Help is highly appreciated.

Eryk

Witold Eryk Wolski

University of Newcastle upon Tyne
School of Mathematics and Statistics
Merz Court
http://www.mas.ncl.ac.uk/~nwew
http://www.northeasttango.org.uk

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