installing dependencies ‘maftools’, ‘PoissonBinomial’, ‘ShiftConvolvePoibin’ begin installing package ‘PoissonBinomial’ begin installing package ‘ShiftConvolvePoibin’ begin installing package ‘maftools’ * installing *source* package ‘ShiftConvolvePoibin’ ... ** this is package ‘ShiftConvolvePoibin’ version ‘1.0.0’ ** package ‘ShiftConvolvePoibin’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJgXZij/R.INSTALL2ad5bd766e826b/ShiftConvolvePoibin/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dcpaired.c -o dcpaired.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dcpaired_log.c -o dcpaired_log.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fftconv_min.c -o fftconv_min.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c logsum.c -o logsum.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c minfft.c -o minfft.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o ShiftConvolvePoibin.so dcpaired.o dcpaired_log.o fftconv_min.o init.o logsum.o minfft.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJgXZij/R.INSTALL2ad5bd766e826b/ShiftConvolvePoibin/src' installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-ShiftConvolvePoibin/00new/ShiftConvolvePoibin/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (ShiftConvolvePoibin) * installing *source* package ‘PoissonBinomial’ ... ** this is package ‘PoissonBinomial’ version ‘1.2.7’ ** package ‘PoissonBinomial’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpy4Hk8f/R.INSTALL2ad5c145a8d2/PoissonBinomial/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PoissonBinomial.cpp -o PoissonBinomial.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o PoissonBinomial.so PoissonBinomial.o RcppExports.o -lfftw3 -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpy4Hk8f/R.INSTALL2ad5c145a8d2/PoissonBinomial/src' installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-PoissonBinomial/00new/PoissonBinomial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PoissonBinomial) * installing *source* package ‘maftools’ ... ** this is package ‘maftools’ version ‘2.26.0’ ** package ‘maftools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpnvj8tn/R.INSTALL2ad5bf779c5c2b/maftools/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ntcounts.c -o ntcounts.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c snpcounts.c -o snpcounts.o snpcounts.c: In function ‘snpcounts’: snpcounts.c:89:47: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 89 | fprintf(tsv_fp, "#idxstats_mapped_reads\t%llu\n", tot_mapped); | ~~~^ ~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c somaticfreq.c -o somaticfreq.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpnvj8tn/R.INSTALL2ad5bf779c5c2b/maftools/src' installing to /home/hornik/tmp/CRAN_special_noSuggests/Library/00LOCK-maftools/00new/maftools/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maftools) checking Rediscover_0.3.3.tar.gz ... Depends: Package: Rediscover Depends: R (>= 4.0), Matrix, PoissonBinomial, ShiftConvolvePoibin, utils, matrixStats Imports: maftools, data.table, parallel, RColorBrewer, methods Timings: user system elapsed Rediscover 76.005 7.625 83.981 Results: Check status summary: NOTE Source packages 1 Check results summary: Rediscover ... NOTE * checking CRAN incoming feasibility ... [4s/4s] NOTE