* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘hahmmr’ ...
** this is package ‘hahmmr’ version ‘1.0.0’
** package ‘hahmmr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTqtlu2/R.INSTALL1ef80942d8595f/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
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
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
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTqtlu2/R.INSTALL1ef80942d8595f/hahmmr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTqtlu2/R.INSTALL1ef80942d8595f/hahmmr/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTqtlu2/R.INSTALL1ef80942d8595f/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)