* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘kmeRtone’ ...
** package ‘kmeRtone’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfUK5uw/R.INSTALL12b4c71f812e1d/kmeRtone/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countKmers.cpp -o countKmers.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countMidPatternContext.cpp -o countMidPatternContext.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countMidPatternContext2.cpp -o countMidPatternContext2.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countMidPatternKmers.cpp -o countMidPatternKmers.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countMidPatternRangedKmers.cpp -o countMidPatternRangedKmers.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countPointContext.cpp -o countPointContext.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countPointContext2.cpp -o countPointContext2.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countRangedKmers.cpp -o countRangedKmers.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countSlidingWindow.cpp -o countSlidingWindow.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c countSlidingWindow2.cpp -o countSlidingWindow2.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_substring_fixed.cpp -o count_substring_fixed.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_substring_regex.cpp -o count_substring_regex.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c import_stringi.cpp -o import_stringi.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/stringi/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simulatePopulation.cpp -o simulatePopulation.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o kmeRtone.so RcppExports.o countKmers.o countMidPatternContext.o countMidPatternContext2.o countMidPatternKmers.o countMidPatternRangedKmers.o countPointContext.o countPointContext2.o countRangedKmers.o countSlidingWindow.o countSlidingWindow2.o count_substring_fixed.o count_substring_regex.o import_stringi.o simulatePopulation.o /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfUK5uw/R.INSTALL12b4c71f812e1d/kmeRtone/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfUK5uw/R.INSTALL12b4c71f812e1d/kmeRtone/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfUK5uw/R.INSTALL12b4c71f812e1d/kmeRtone/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-kmeRtone/00new/kmeRtone/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘kmeRtone’
finding HTML links ... done
Coordinate html
EXPLORE html
Kmer_Table html
NCBI_Genome html
SCORE html
STUDY_ACROSS_POPULATIONS html
STUDY_ACROSS_SPECIES html
STUDY_CANCER_GENES html
STUDY_GENIC_ELEMENTS html
UCSC_Genome html
addAlphaCol html
bedToCoor html
buildControl html
buildKmerTable html
buildMidPatternKmerTable html
buildRESTurl html
buildRangedKmerTable html
calKmerSkew html
calPWM html
catHeader html
countBaseComposition html
countChoppedKmers html
countDistribution html
countKmers html
countMidPatternContext2 html
countMidPatternKmers html
countPointContext2 html
countRangedKmers html
countRevCompKmers html
countSlidingWindow html
countSlidingWindow2 html
count_substring_fixed html
count_substring_regex html
downloadNCBIGenomes html
downloadUCSCgenome html
example_genome_coor html
example_kmeRtone_score html
extractKmers html
generateGenicElementCoor html
generateIntergenicCoor html
getCOSMICauthURL html
getCOSMICcancerGeneCensus html
getCOSMIClatestVersion html
getCOSMICmutantExport html
getEnsemblData html
getEnsemblRegionFeatures html
getEnsemblVariantFeatures html
getEnsemblVariantFeatures_serial html
getGnomADvariants html
getICTVvirusMetadataResource html
getNCBIassemblySummary html
getScores html
getUCSCgenePredTable html
getVCFmetainfo html
initKmerTable html
kmeRtone html
loadCoordinate html
loadGenome html
loadGenomicContents html
mapKmers html
mergeCoordinate html
mixColors html
partitionCoordinate html
persistentDownload html
readBED html
readFASTA html
readVCF html
readVCF2 html
removeRegion html
reverseComplement html
scoreKmers html
selectGenomesForCrossSpeciesStudy html
selectRepresentativeFromASM html
simulatePopulation html
splitFASTA html
system3 html
trimCoordinate html
writeBED html
writeFASTA html
writeVCF html
*** copying figures
** 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 (kmeRtone)