* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘RNifti’ ...
** package ‘RNifti’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc-13
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc-13 accepts -g... yes
checking for gcc-13 option to enable C11 features... none needed
checking for library containing inflate... -lz
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-24) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/RtmpVMqp9a/R.INSTALL48a9f1663add0/RNifti/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c main.cpp -o main.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c zzz.c -o zzz.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c znzlib/znzlib.c -o znzlib/znzlib.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c niftilib/nifti1_io.c -o niftilib/nifti1_io.o
niftilib/nifti1_io.c:449:14: warning: ‘print_hex_vals’ declared ‘static’ but never defined [-Wunused-function]
449 | static int print_hex_vals (const char * data, size_t nbytes, FILE * fp);
| ^~~~~~~~~~~~~~
niftilib/nifti1_io.c:6135:14: warning: ‘escapize_string’ defined but not used [-Wunused-function]
6135 | static char *escapize_string( const char * str )
| ^~~~~~~~~~~~~~~
niftilib/nifti1_io.c:3337:12: warning: ‘compare_strlist’ defined but not used [-Wunused-function]
3337 | static int compare_strlist(const char * str, char ** strlist, int len)
| ^~~~~~~~~~~~~~~
niftilib/nifti1_io.c:3323:12: warning: ‘make_lowercase’ defined but not used [-Wunused-function]
3323 | static int make_lowercase(char * str)
| ^~~~~~~~~~~~~~
niftilib/nifti1_io.c:3310:12: warning: ‘make_uppercase’ defined but not used [-Wunused-function]
3310 | static int make_uppercase(char * str)
| ^~~~~~~~~~~~~~
niftilib/nifti1_io.c:3292:12: warning: ‘is_mixedcase’ defined but not used [-Wunused-function]
3292 | static int is_mixedcase(const char * str)
| ^~~~~~~~~~~~
niftilib/nifti1_io.c:3276:12: warning: ‘is_uppercase’ defined but not used [-Wunused-function]
3276 | static int is_uppercase(const char * str)
| ^~~~~~~~~~~~
niftilib/nifti1_io.c:363:29: warning: ‘nifti_type_list’ defined but not used [-Wunused-const-variable=]
363 | static const nifti_type_ele nifti_type_list[] = {
| ^~~~~~~~~~~~~~~
niftilib/nifti1_io.c:353:19: warning: ‘gni_version’ defined but not used [-Wunused-const-variable=]
353 | static const char gni_version[] = NIFTI1_IO_SOURCE_VERSION " (16 Jun, 2022)";
| ^~~~~~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c niftilib/nifti2_io.c -o niftilib/nifti2_io.o
niftilib/nifti2_io.c:8250:14: warning: ‘escapize_string’ defined but not used [-Wunused-function]
8250 | static char *escapize_string( const char * str )
| ^~~~~~~~~~~~~~~
niftilib/nifti2_io.c:4468:12: warning: ‘print_hex_vals’ defined but not used [-Wunused-function]
4468 | static int print_hex_vals( const char * data, size_t nbytes, FILE * fp )
| ^~~~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o RNifti.so main.o zzz.o znzlib/znzlib.o niftilib/nifti1_io.o niftilib/nifti2_io.o -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpVMqp9a/R.INSTALL48a9f1663add0/RNifti/src'
make[1]: Entering directory '/tmp/RtmpVMqp9a/R.INSTALL48a9f1663add0/RNifti/src'
make[1]: Leaving directory '/tmp/RtmpVMqp9a/R.INSTALL48a9f1663add0/RNifti/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-RNifti/00new/RNifti/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘RNifti’
finding HTML links ... done
ExtensionCodes html
asNifti html
channels html
defaultInfoPanel html
extensions html
indexing html
internalImage html
ndim html
niftiHeader html
niftiVersion html
pixdim html
readNifti html
rgbArray html
view html
voxelToWorld html
writeNifti html
xform 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
* creating tarball
packaged installation of ‘RNifti’ as ‘RNifti_1.6.1_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (RNifti)