* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘myTAI’ ...
** this is package ‘myTAI’ version ‘2.3.4’
** package ‘myTAI’ 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/RtmpMzoG8A/R.INSTALL18b0c352adf958/myTAI/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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c null_txis.cpp -o null_txis.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sc_txi.cpp -o sc_txi.o
sc_txi.cpp: In function ‘Rcpp::NumericVector cpp_txi_sc(const arma::sp_mat&, const arma::vec&, int, int)’:
sc_txi.cpp:36:30: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
36 | if (strata_values.n_elem != n_genes) {
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o myTAI.so RcppExports.o null_txis.o sc_txi.o -latomic -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMzoG8A/R.INSTALL18b0c352adf958/myTAI/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMzoG8A/R.INSTALL18b0c352adf958/myTAI/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMzoG8A/R.INSTALL18b0c352adf958/myTAI/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-myTAI/00new/myTAI/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 ‘myTAI’
finding HTML links ... done
BulkPhyloExpressionSet html
BulkPhyloExpressionSet_from_df html
COUNT_TRANSFORMS html
ConservationTestResult html
Distribution html
PS_colours html
PhyloExpressionSetBase html
ScPhyloExpressionSet html
ScPhyloExpressionSet_from_matrix html
ScPhyloExpressionSet_from_seurat html
TAI html
TDI html
TEI html
TI_map html
TPI html
TXI html
TXI_conf_int html
TXI_std_dev html
TestResult html
age.apply html
as_BulkPhyloExpressionSet html
as_data_frame html
check_BulkPhyloExpressionSet html
check_PhyloExpressionSet html
check_ScPhyloExpressionSet html
collapse html
conf_int html
consensus html
convergence_plots html
cpp_txi_sc html
destroy_pattern html
diagnose_test_robustness html
distributions html
dot-TXI html
dot-TXI_sc html
dot-TXI_sc_adaptive html
dot-collapse_replicates html
dot-compute_reduction html
dot-fit_gamma html
dot-fit_normal html
dot-get_expression_from_seurat html
dot-get_p_value html
dot-memo_generate_conservation_txis html
dot-pTXI html
dot-plot_gene_heatmap_impl html
dot-prepare_sc_plot_data html
dot-pseudobulk_expression html
dot-to_std_expr html
downsample html
downsample_expression html
early_gene html
ec_score html
example_phyex_set html
example_phyex_set_old html
example_phyex_set_sc html
exp_p html
full_gatai_convergence_plot html
gatai_animate_destruction html
genes_filter_dynamic html
genes_lowly_expressed html
genes_top_expr html
genes_top_mean html
genes_top_variance html
geom_mean html
get_angles html
goodness_of_fit html
late_gene html
lc_score html
match_map html
match_map_sc_matrix html
match_map_sc_seurat html
mid_gene html
mod_pi html
new_options_property html
new_required_property html
normalise_stage_expression html
omit_matrix html
pTXI html
pair_score html
permute_PS html
petal_plot html
plot_contribution html
plot_cullen_frey html
plot_distribution_expression html
plot_distribution_pTAI html
plot_distribution_pTAI_qqplot html
plot_distribution_strata html
plot_gatai_results html
plot_gene_heatmap html
plot_gene_profiles html
plot_gene_space html
plot_mean_var html
plot_null_txi_sample html
plot_relative_expression_bar html
plot_relative_expression_line html
plot_sample_space html
plot_signature html
plot_signature_gene_quantiles html
plot_signature_multiple html
plot_signature_transformed html
plot_strata_expression html
print.TestResult html
quantile_rank html
reductive_hourglass_score html
rel_exp_matrix html
relative_expression html
remove_genes html
rename_phyex_set html
rev_mid_gene html
reverse_hourglass_score html
rowVars html
sTXI html
save_gatai_results_pdf html
select_genes html
set_expression html
stat_early_conservation_test html
stat_flatline_test html
stat_generate_conservation_txis html
stat_generic_conservation_test html
stat_late_conservation_test html
stat_pairwise_test html
stat_reductive_hourglass_test html
stat_reverse_hourglass_test html
strata_enrichment html
taxid html
tf html
tf_PS html
tf_stability html
threshold_comparison_plots html
transform_counts 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
* DONE (myTAI)