* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘SOMMD’ ...
** package ‘SOMMD’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgrqinT/R.INSTALL8ef874dc0a6f8/SOMMD/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c rio_xtc.c -o rio_xtc.o
rio_xtc.c: In function ‘file_exists’:
rio_xtc.c:14:5: warning: argument 1 null where non-null expected [-Wnonnull]
   14 |     fclose(file);
      |     ^~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/include/R.h:44,
                 from rio_xtc.c:1:
/usr/include/stdio.h:184:12: note: in a call to function ‘fclose’ declared ‘nonnull’
  184 | extern int fclose (FILE *__stream) __nonnull ((1));
      |            ^~~~~~
rio_xtc.c: In function ‘rio_write_xtc_’:
rio_xtc.c:252:29: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized]
  252 |   INTEGER(return_status)[0] = status;
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
rio_xtc.c:209:7: note: ‘status’ was declared here
  209 |   int status;
      |       ^~~~~~
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c xdrfile/xdrfile.c -o xdrfile/xdrfile.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c xdrfile/xdrfile_trr.c -o xdrfile/xdrfile_trr.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c xdrfile/xdrfile_xtc.c -o xdrfile/xdrfile_xtc.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o SOMMD.so rio_xtc.o init.o xdrfile/xdrfile.o xdrfile/xdrfile_trr.o xdrfile/xdrfile_xtc.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgrqinT/R.INSTALL8ef874dc0a6f8/SOMMD/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgrqinT/R.INSTALL8ef874dc0a6f8/SOMMD/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgrqinT/R.INSTALL8ef874dc0a6f8/SOMMD/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-SOMMD/00new/SOMMD/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘SOMMD’
    finding HTML links ... done
    average.neur.property                   html  
    calc.distances                          html  
    calc.dists                              html  
    cat.trj                                 html  
    cluster.pathways                        html  
    cluster.representatives                 html  
    comp.trans.mat                          html  
    fit.trj                                 html  
    map.color                               html  
    matrix2graph                            html  
    native.cont                             html  
    neur.population                         html  
    neur.representatives                    html  
    print.struct                            html  
    print.trj                               html  
    read.gro                                html  
    read.struct                             html  
    read.trj                                html  
    remap.data                              html  
    rio_read_xtc                            html  
    rio_read_xtc2xyz                        html  
    rio_read_xtc_natoms                     html  
    rio_read_xtc_nframes                    html  
    rio_write_xtc                           html  
    silhouette.profile                      html  
    silhouette.score                        html  
    som.add.circles                         html  
    som.add.clusters.legend                 html  
    som.add.numbers                         html  
    stride.trj                              html  
    struct2pdb                              html  
    summary.struct                          html  
    summary.trj                             html  
    trace.path                              html  
    trj2pdb                                 html  
    trj2xyz                                 html  
** building package indices
** 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 (SOMMD)