* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘strollur’ ...
** this is package ‘strollur’ version ‘0.1.3’
** package ‘strollur’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.3.0-1) 15.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpaIOaBF/R.INSTALL15111a2960f29f/strollur/src'
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c abundtable.cpp -o abundtable.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bintable.cpp -o bintable.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dataset.cpp -o dataset.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phylotree.cpp -o phylotree.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_dataset.cpp -o rcpp_dataset.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_xint_xdev_functions.cpp -o rcpp_xint_xdev_functions.o
rcpp_xint_xdev_functions.cpp: In function ‘Rcpp::Environment xdev_set_abundances(const Rcpp::Environment&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::vector<float> >&, const std::string&)’:
rcpp_xint_xdev_functions.cpp:1148:39: warning: comparison of integer expressions of different signedness: ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1148 | if (abundances[i].size() != numSamples) {
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c report.cpp -o report.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c seqreport.cpp -o seqreport.o
g++-15 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -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/cli/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcereal/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o strollur.so RcppExports.o abundtable.o bintable.o dataset.o phylotree.o rcpp_dataset.o rcpp_xint_xdev_functions.o report.o seqreport.o utils.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpaIOaBF/R.INSTALL15111a2960f29f/strollur/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpaIOaBF/R.INSTALL15111a2960f29f/strollur/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpaIOaBF/R.INSTALL15111a2960f29f/strollur/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-strollur/00new/strollur/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘strollur’
finding HTML links ... done
abundance html
add html
assign html
clear html
copy_dataset html
count html
export_dataset html
get_bin_types html
has_sample html
has_sequence_strings html
import_dataset html
is_aligned html
is_equal html
load_dataset html
miseq_sop_example html
names html
new_dataset html
new_reference html
read_dada2 html
read_fasta html
read_mothur html
read_mothur_cons_taxonomy html
read_mothur_count html
read_mothur_list html
read_mothur_oligos html
read_mothur_rabund html
read_mothur_shared html
read_mothur_taxonomy html
read_phyloseq html
read_qiime2 html
read_qiime2_feature_table html
read_qiime2_metadata html
read_qiime2_taxonomy html
remove_file html
report html
save_dataset html
sort_dataframe html
strollur-package html
strollur html
strollur_example html
summary html
unpack_qiime2_artifact html
write_fasta html
write_mothur html
write_mothur_cons_taxonomy html
write_mothur_count html
write_mothur_design html
write_mothur_list html
write_mothur_rabund html
write_mothur_shared html
write_phyloseq html
write_taxonomy html
xdev_abundance html
xdev_add_references html
xdev_add_report html
xdev_add_sequences html
xdev_assign_bin_representative_sequences
html
xdev_assign_bin_taxonomy html
xdev_assign_bins html
xdev_assign_sequence_abundance html
xdev_assign_sequence_taxonomy html
xdev_assign_sequence_taxonomy_tidy html
xdev_assign_treatments html
xdev_count html
xdev_get_abundances_by_sample html
xdev_get_by_sample html
xdev_get_list_vector html
xdev_get_sequences html
xdev_has_sequence_taxonomy html
xdev_merge_bins html
xdev_merge_sequences html
xdev_names html
xdev_remove_bins html
xdev_remove_lineages html
xdev_remove_samples html
xdev_remove_sequences html
xdev_report html
xdev_set_abundance html
xdev_set_abundances html
xdev_set_dataset_name html
xdev_set_sequences 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 (strollur)