* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘hahmmr’ ...
** package ‘hahmmr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTjhUJg/R.INSTALL2893ea711a7047/hahmmr/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'/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/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -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'/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/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bbinom.cpp -o bbinom.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'/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/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hmm.cpp -o hmm.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'/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/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c misc.cpp -o misc.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'/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/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mle.cpp -o mle.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'/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/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c poilog.cpp -o poilog.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o hahmmr.so RcppExports.o bbinom.o hmm.o misc.o mle.o poilog.o -lpthread -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTjhUJg/R.INSTALL2893ea711a7047/hahmmr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTjhUJg/R.INSTALL2893ea711a7047/hahmmr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTjhUJg/R.INSTALL2893ea711a7047/hahmmr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-hahmmr/00new/hahmmr/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘hahmmr’
    finding HTML links ... done
    acen_hg19                               html  
    acen_hg38                               html  
    analyze_allele                          html  
    analyze_joint                           html  
    annot_cm                                html  
    annot_segs                              html  
    approx_phi_post                         html  
    approx_theta_post_s2                    html  
    approx_theta_post_s3                    html  
    bulk_example                            html  
    calc_allele_LLR                         html  
    calc_allele_lik_s2                      html  
    calc_allele_lik_s3                      html  
    calc_exp_LLR                            html  
    calc_trans_mat_s15                      html  
    calc_trans_mat_s7                       html  
    check_cols                              html  
    check_matrix                            html  
    chrom_sizes_hg19                        html  
    chrom_sizes_hg38                        html  
    classify_alleles                        html  
    combine_bulk                            html  
    dbbinom                                 html  
    df_allele_example                       html  
    dpoilog                                 html  
    filter_genes                            html  
    fit_gamma                               html  
    fit_lnpois_cpp                          html  
    fit_ref_sse                             html  
    forward_back_allele                     html  
    gaps_hg19                               html  
    gaps_hg38                               html  
    gene_counts_example                     html  
    generate_postfix                        html  
    get_allele_bulk                         html  
    get_allele_hmm_s2                       html  
    get_allele_hmm_s3                       html  
    get_bulk                                html  
    get_exp_bulk                            html  
    get_trans_probs_s15                     html  
    get_trans_probs_s7                      html  
    gtf_hg19                                html  
    gtf_hg38                                html  
    gtf_mm10                                html  
    l_bbinom                                html  
    l_lnpois                                html  
    likelihood_allele                       html  
    logSumExp                               html  
    plot_bulks                              html  
    plot_psbulk                             html  
    pre_likelihood_hmm                      html  
    ref_hca                                 html  
    ref_hca_counts                          html  
    run_allele_hmm_s3                       html  
    run_allele_hmm_s5                       html  
    run_joint_hmm_s15                       html  
    run_joint_hmm_s7                        html  
    segs_example                            html  
    smooth_segs                             html  
    switch_prob_cm                          html  
    theta_hat_seg                           html  
    vcf_meta                                html  
    viterbi_allele                          html  
    viterbi_joint                           html  
    viterbi_joint_mat                       html  
** 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 (hahmmr)