##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CardinalIO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CardinalIO’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c CardinalIO.cpp -o CardinalIO.o
In file included from CardinalIO.h:5,
                 from CardinalIO.cpp:2:
imzML.h:5: warning: "R_NO_REMAP" redefined
    5 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
imzML.h: In member function ‘int imzML::get_params(pugi::xml_node, int, SEXP, SEXP)’:
imzML.h:348:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  348 |                         while ( node && i < count ) {
      |                                         ~~^~~~~~~
imzML.h:369:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  369 |                         if ( i != count )
      |                              ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c init.cpp -o init.o
In file included from CardinalIO.h:5,
                 from init.cpp:3:
imzML.h:5: warning: "R_NO_REMAP" redefined
    5 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
imzML.h: In member function ‘int imzML::get_params(pugi::xml_node, int, SEXP, SEXP)’:
imzML.h:348:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  348 |                         while ( node && i < count ) {
      |                                         ~~^~~~~~~
imzML.h:369:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  369 |                         if ( i != count )
      |                              ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c pugixml.cpp -o pugixml.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o CardinalIO.so CardinalIO.o init.o pugixml.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-CardinalIO/00new/CardinalIO/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CardinalIO)