* 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/RtmpAQBA6a/R.INSTALL2ea2f35be9b5fd/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/RtmpAQBA6a/R.INSTALL2ea2f35be9b5fd/hahmmr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpAQBA6a/R.INSTALL2ea2f35be9b5fd/hahmmr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpAQBA6a/R.INSTALL2ea2f35be9b5fd/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)