* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pureseqtmr’ ...
** this is package ‘pureseqtmr’ version ‘1.4’
** package ‘pureseqtmr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpve5HKk/R.INSTALL3f455353ad4dc/pureseqtmr/src'
g++-14 -std=gnu++17 -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/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  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c calc_distance_to_tmh_center_from_topology_str_cpp_stl.cpp -o calc_distance_to_tmh_center_from_topology_str_cpp_stl.o
g++-14 -std=gnu++17 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c load_fasta_file_as_tibble_cpp_raw.cpp -o load_fasta_file_as_tibble_cpp_raw.o
g++-14 -std=gnu++17 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c load_fasta_file_as_tibble_cpp_stl.cpp -o load_fasta_file_as_tibble_cpp_stl.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o pureseqtmr.so RcppExports.o calc_distance_to_tmh_center_from_topology_str_cpp_stl.o load_fasta_file_as_tibble_cpp_raw.o load_fasta_file_as_tibble_cpp_stl.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpve5HKk/R.INSTALL3f455353ad4dc/pureseqtmr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpve5HKk/R.INSTALL3f455353ad4dc/pureseqtmr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpve5HKk/R.INSTALL3f455353ad4dc/pureseqtmr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pureseqtmr/00new/pureseqtmr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘pureseqtmr’
    finding HTML links ... done
    are_tmhs                                html  
    are_valid_protein_sequences             html  
    calc_distance_to_tmh_center_from_topology
                                            html  
    calc_distance_to_tmh_center_from_topology_str
                                            html  
    calc_distance_to_tmh_center_from_topology_str_cpp_stl
                                            html  
    check_protein_sequence                  html  
    check_protein_sequences                 html  
    check_pureseqtm_installation            html  
    check_topology                          html  
    check_topology_str                      html  
    convert_tmhmm_to_pureseqtm_topology     html  
    count_n_tmhs                            html  
    create_pureseqtm_files                  html  
    create_pureseqtm_proteome_file          html  
    default_params_doc                      html  
    get_default_pureseqtm_folder            html  
    get_example_filename                    html  
    get_example_filenames                   html  
    get_pureseqtm_url                       html  
    get_pureseqtm_version                   html  
    install_pureseqtm                       html  
    is_on_appveyor                          html  
    is_on_ci                                html  
    is_on_github_actions                    html  
    is_on_travis                            html  
    is_protein_name_line                    html  
    is_pureseqtm_installed                  html  
    is_tmh                                  html  
    is_topology_line                        html  
    is_valid_protein_sequence               html  
    load_fasta_file_as_tibble               html  
    load_fasta_file_as_tibble_cpp           html  
    load_fasta_file_as_tibble_cpp_raw       html  
    load_fasta_file_as_tibble_r             html  
    load_topology_file_as_tibble            html  
    mock_predict_topologies_from_sequences
                                            html  
    mock_predict_topology                   html  
    parse_pureseqtm_proteome_text           html  
    plot_topology                           html  
    predict_topologies_from_sequences       html  
    predict_topology                        html  
    predict_topology_from_sequence          html  
    pureseqtmr                              html  
    pureseqtmr_report                       html  
    run_pureseqtm_proteome                  html  
    save_tibble_as_fasta_file               html  
    tally_tmhs                              html  
    uninstall_pureseqtm                     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 (pureseqtmr)