Install log for 'jackalope'

* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘jackalope’ ...
** package ‘jackalope’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp8nww8j/R.INSTALL2d541a42e2e8b9/jackalope/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c alter_reference.cpp -o alter_reference.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c create_sequences.cpp -o create_sequences.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hap_classes.cpp -o hap_classes.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c haps_ssites.cpp -o haps_ssites.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hts_illumina.cpp -o hts_illumina.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hts_pacbio.cpp -o hts_pacbio.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c io_fasta.cpp -o io_fasta.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c io_ms.cpp -o io_ms.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c io_vcf.cpp -o io_vcf.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mutator.cpp -o mutator.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mutator_indels.cpp -o mutator_indels.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mutator_subs.cpp -o mutator_subs.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c phylogenomics.cpp -o phylogenomics.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ref_hap_access.cpp -o ref_hap_access.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sub_models.cpp -o sub_models.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c util.cpp -o util.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o jackalope.so RcppExports.o alter_reference.o create_sequences.o hap_classes.o haps_ssites.o hts_illumina.o hts_pacbio.o io_fasta.o io_ms.o io_vcf.o mutator.o mutator_indels.o mutator_subs.o phylogenomics.o ref_hap_access.o sub_models.o util.o -lz -llzma -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp8nww8j/R.INSTALL2d541a42e2e8b9/jackalope/src'
make[1]: Entering directory '/tmp/Rtmp8nww8j/R.INSTALL2d541a42e2e8b9/jackalope/src'
make[1]: Leaving directory '/tmp/Rtmp8nww8j/R.INSTALL2d541a42e2e8b9/jackalope/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-jackalope/00new/jackalope/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 ‘jackalope’
    finding HTML links ... done
    create_genome                           html  
    create_haplotypes                       html  
    evo_rates                               html  
    haplotypes                              html  
    haps_functions                          html  
    haps_gtrees                             html  
    haps_phylo                              html  
    haps_ssites                             html  
    haps_theta                              html  
    haps_vcf                                html  
    illumina                                html  
    indels                                  html  
    jackalope-package                       html  
    pacbio                                  html  
    read_fasta                              html  
    ref_genome                              html  
    sub_models                              html  
    write_fasta                             html  
    write_vcf                               html  
*** copying figures
** 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 (jackalope)