* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘cophescan’ ...
** package ‘cophescan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/RtmpIInI0N/R.INSTALL336e43152e2a61/cophescan/src'
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c hier_priors.cpp -o hier_priors.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o cophescan.so RcppExports.o hier_priors.o -fopenmp -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 '/tmp/RtmpIInI0N/R.INSTALL336e43152e2a61/cophescan/src'
make[1]: Entering directory '/tmp/RtmpIInI0N/R.INSTALL336e43152e2a61/cophescan/src'
make[1]: Leaving directory '/tmp/RtmpIInI0N/R.INSTALL336e43152e2a61/cophescan/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-cophescan/00new/cophescan/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘cophescan’
finding HTML links ... done
Hc.cutoff.fdr html
adjust_priors html
average_piks html
average_piks_list html
average_posterior_prob html
average_posterior_prob_list html
combine.bf html
cophe.bf_bf html
cophe.hyp.predict html
cophe.multitrait html
cophe.prepare.dat.single html
cophe.prepare.dat.susie html
finding level-2 HTML links ... done
cophe.single html
cophe.single.lbf html
cophe.susie html
cophe.susie.lbf html
cophe_heatmap html
cophe_multi_trait_data html
cophe_plot html
cophescan-package html
get_beta html
get_posterior_prob html
hypothesis.priors html
logd_alpha html
logd_beta html
logd_gamma html
loglik html
logpost html
logpriors html
logsum html
logsumexp html
metrop_run html
multitrait.simplify html
pars2pik html
pars_init html
per.snp.priors html
piks html
plot_trait_manhat html
posterior_prob html
prepare_plot_data html
propose html
run_metrop_priors html
sample_alpha html
sample_beta html
sample_gamma html
summary.cophe html
target 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
* creating tarball
packaged installation of ‘cophescan’ as ‘cophescan_1.4.0_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (cophescan)