* installing to library '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages'
* installing *source* package 'vcfR' ...
** package 'vcfR' successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/tmp/RtmpFUB3ow/R.INSTALL2a879a5f7fcb77/vcfR/src'
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c NM2winNM.cpp -o NM2winNM.o
NM2winNM.cpp:145:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
    if( ( x[i] != NA_REAL ) | ( x[i] != NA_INTEGER ) ){
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                            ||
NM2winNM.cpp:145:9: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c ad_frequency.cpp -o ad_frequency.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c deprecated_funcs.cpp -o deprecated_funcs.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c extract_gt.cpp -o extract_gt.o
extract_gt.cpp:362:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
    if( ( temp[i] == '|' ) | ( temp[i] == '/' ) ){ploidy++;}
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                           ||
extract_gt.cpp:362:9: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c freq_peak.cpp -o freq_peak.o
freq_peak.cpp:400:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
      if( ( intQuery >= intBreaks(j,0) ) & ( intQuery <= intBreaks(j,2) ) ){
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                         &&
freq_peak.cpp:400:11: note: cast one or both operands to int to silence this warning
freq_peak.cpp:405:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
        if( ( intQuery > intBreaks(j,0) ) & ( intQuery <= intBreaks(j,2) ) ){
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                          &&
freq_peak.cpp:405:13: note: cast one or both operands to int to silence this warning
2 warnings generated.
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c gt_to_popsum.cpp -o gt_to_popsum.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c is_het.cpp -o is_het.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c masplit.cpp -o masplit.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c pair_sort.cpp -o pair_sort.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c rank_variants.cpp -o rank_variants.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c read_vcfR.cpp -o read_vcfR.o
read_vcfR.cpp:497:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
    if( ( row_num >= nrows ) & ( lastline[0] != '#' ) & ( lastline.size() > 0 ) ){
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                      &&
read_vcfR.cpp:497:9: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c seq_to_rects.cpp -o seq_to_rects.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c var_window.cpp -o var_window.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c vcfRCommon.cpp -o vcfRCommon.o
vcfRCommon.cpp:112:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
    if( ( mystring[i] == split1 ) | ( mystring[i] == split2 ) ){
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                  ||
vcfRCommon.cpp:112:9: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=2   -fpic  -g -O3 -Wall -pedantic -mtune=native -c write_vcfR.cpp -o write_vcfR.o
clang++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o vcfR.so NM2winNM.o RcppExports.o ad_frequency.o deprecated_funcs.o extract_gt.o freq_peak.o gt_to_popsum.o is_het.o masplit.o pair_sort.o rank_variants.o read_vcfR.o seq_to_rects.o var_window.o vcfRCommon.o write_vcfR.o -lz -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpFUB3ow/R.INSTALL2a879a5f7fcb77/vcfR/src'
make[1]: Entering directory '/tmp/RtmpFUB3ow/R.INSTALL2a879a5f7fcb77/vcfR/src'
make[1]: Leaving directory '/tmp/RtmpFUB3ow/R.INSTALL2a879a5f7fcb77/vcfR/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-vcfR/00new/vcfR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'rbind' from package 'base' in package 'vcfR'
Creating a generic function for 'nrow' from package 'base' in package 'vcfR'
** 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
readelf: Warning: Unrecognized form: 0x23
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Bogus end-of-siblings marker detected at offset 6a8d in .debug_info section
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Bogus end-of-siblings marker detected at offset 6a98 in .debug_info section
readelf: Warning: Unrecognized form: 0x23
readelf: Warning: Bogus end-of-siblings marker detected at offset 6c12 in .debug_info section
readelf: Warning: Further warnings about bogus end-of-sibling markers suppressed
readelf: Warning: Unrecognized form: 0x23
readelf: Warning: Unrecognized form: 0x23
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x23
readelf: Warning: Unrecognized form: 0x22
readelf: Warning: Unrecognized form: 0x23
readelf: Warning: DIE at offset 0x8c8e refers to abbreviation number 6031 which does not exist
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vcfR)