* 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)