* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘SOMMD’ ...
** this is package ‘SOMMD’ version ‘0.1.2’
** package ‘SOMMD’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9H5yV4/R.INSTALLaf527579d3ce2/SOMMD/src'
gcc-14 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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/Rtmp9H5yV4/R.INSTALLaf527579d3ce2/SOMMD/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9H5yV4/R.INSTALLaf527579d3ce2/SOMMD/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9H5yV4/R.INSTALLaf527579d3ce2/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)