Dear all,
I recently uploaded a new package Rlibeemd to CRAN
(http://cran.r-project.org/web/packages/Rlibeemd/index.html, and in github:
https://github.com/helske/Rlibeemd), and simple example in help files seems to
throw an error on Solaris:
Version: 1.3.1
Check: examples
Result: ERROR
Running examples in �Rlibeemd-Ex.R� failed
The error most likely occurred in:
> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
>
> ### ** Examples
>
> imfs <- ceemdan(UKgas, threads = 1)
gsl: tridiag.c:191: ERROR: matrix must be positive definite
Default GSL error handler invoked.
The package is structured in such way that the underlying C library uses GSL
for performing complete ensemble empirical mode decomposition, and I have
written Rcpp/R wrappers around those functions. In eemd.c there are lines
const int status = gsl_linalg_solve_tridiag(&diag_vec.vector,
&supdiag_vec.vector,
&subdiag_vec.vector,
&g_vec.vector,
&solution_vec.vector);
if (status) { // we never get to this point if above function fails!
REprintf("Error reported by gsl_linalg_solve_tridiag: %s\n",
gsl_strerror(status));
return EMD_GSL_ERROR;
}
So first I need to add gsl_set_error_handler_off() to some point of the code so
the GSL does not abort R. But what I wonder is why does the error happen at
all. The same example works fine wih Windows, Linux and OSX. After googling a
bit I saw that there are other packages with problems related to Solaris and
GSL (such as http://cran.r-project.org/web/checks/check_results_RcppGSL.html),
so I wonder if the issue is related to incorrect Makevars and/or configure or
something like that?
This is the first project where I needed configure script. This is my
configure.ac which I copied from RcppGSL packages example:
AC_INIT([Rlibeemd], 1.3.0)
## Use gsl-config to find arguments for compiler and linker flags
##
## Check for non-standard programs: gsl-config(1)
AC_PATH_PROG([GSL_CONFIG], [gsl-config])
## If gsl-config was found, let's use it
if test "${GSL_CONFIG}" != ""; then
# Use gsl-config for header and linker arguments (without BLAS which we get
from R)
GSL_CFLAGS=`${GSL_CONFIG} --cflags`
GSL_LIBS=`${GSL_CONFIG} --libs`
else
AC_MSG_ERROR([gsl-config not found, is GSL installed?])
fi
# Now substitute these variables in src/Makevars.in to create src/Makevars
AC_SUBST(GSL_CFLAGS)
AC_SUBST(GSL_LIBS)
AC_OUTPUT(src/Makevars)
And here is Makevars.in:
GSL_CFLAGS = @GSL_CFLAGS@
GSL_LIBS = @GSL_LIBS@
PKG_LIBS=$(GSL_LIBS) $(SHLIB_OPENMP_CFLAGS) $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(GSL_CFLAGS) $(SHLIB_OPENMP_CFLAGS)
PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS)
Any help would be greatly appreciated. I don't have access to Solaris which
makes the debugging rather hard.
Best regards,
Jouni Helske
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