* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘spgs’ ...
** this is package ‘spgs’ version ‘1.0-4’
** package ‘spgs’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc-14 -std=gnu23
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 we are using the GNU C compiler... yes
checking whether gcc-14 -std=gnu23 accepts -g... yes
checking for gcc-14 -std=gnu23 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-14 -std=gnu23 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for uint64_t... yes
checking for uint_least64_t... yes
checking for unsigned long long... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRpQFmz/R.INSTALL1a02823944afb/spgs/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  -DPACKAGE_NAME=\"spgs\" -DPACKAGE_TARNAME=\"spgs\" -DPACKAGE_VERSION=\"1.0.1\" -DPACKAGE_STRING=\"spgs\ 1.0.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_UINT64_T=1 -DHAVE_UINT_LEAST64_T=1 -DHAVE_UNSIGNED_LONG_LONG=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c spgs.c -o spgs.o
gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o spgs.so spgs.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRpQFmz/R.INSTALL1a02823944afb/spgs/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRpQFmz/R.INSTALL1a02823944afb/spgs/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRpQFmz/R.INSTALL1a02823944afb/spgs/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-spgs/00new/spgs/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘spgs’
    finding HTML links ... done
    ag.test                                 html  
    agct.test                               html  
    array2vector                            html  
    chargaff.gibbs.test                     html  
    chargaff0.test                          html  
    chargaff1.test                          html  
    chargaff2.test                          html  
    chisq.unif.test                         html  
    complement                              html  
    cylinder.counts                         html  
    diffsign.test                           html  
    diid.disturbance                        html  
    diid.test                               html  
    disambiguate                            html  
    estimateMarkovChain                     html  
    ks.unif.test                            html  
    lb.test                                 html  
    markov.disturbance                      html  
    markov.test                             html  
    nanoarchaeum                            html  
    oligoProfile                            html  
    pair.counts                             html  
    pieris                                  html  
    quadruple.counts                        html  
    rank.test                               html  
    rcspr2mat                               html  
    reverseComplement                       html  
    rstochmat                               html  
    rstochvec                               html  
    simulateMarkovChain                     html  
    spgs-package                            html  
    triple.counts                           html  
    turningpoint.test                       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 (spgs)