* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pmartR’ ...
** package ‘pmartR’ 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/RtmpJJzBTg/R.INSTALL3c23ce137a3b3d/pmartR/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/BH/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/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/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calculate_cv.cpp -o calculate_cv.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/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_missing_cpp.cpp -o count_missing_cpp.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/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c imd_anova.cpp -o imd_anova.o
imd_anova.cpp: In function ‘arma::mat fold_change_diff_na_okay(arma::mat, arma::mat)’:
imd_anova.cpp:154:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
154 | for(int k=0;k<of_int.size();k++){
| ~^~~~~~~~~~~~~~
imd_anova.cpp: In function ‘Rcpp::List anova_cpp(arma::mat, Rcpp::NumericVector, int, arma::mat, arma::mat, arma::mat, arma::uvec, arma::uvec)’:
imd_anova.cpp:218:16: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
218 | if (X.n_cols > m) {
| ~~~~~~~~~^~~
imd_anova.cpp:249:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
249 | for (int k = 0; k < continuous_covar_inds.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
imd_anova.cpp:259:31: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
259 | if (group_ids_pred.n_elem > m) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~
imd_anova.cpp: In function ‘Rcpp::List two_factor_anova_cpp(arma::mat, arma::mat, arma::mat, arma::colvec, arma::mat, arma::mat, arma::uvec, arma::uvec)’:
imd_anova.cpp:508:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
508 | for (int k = 0; k < continuous_covar_inds.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
imd_anova.cpp:521:31: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
521 | if (group_ids_pred.n_elem > n_groups) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
imd_anova.cpp:481:18: warning: ‘sigma2_full’ may be used uninitialized [-Wmaybe-uninitialized]
481 | sig_est(i) = sigma2_full;
| ~~~~~~~~~~~^~~~~~~~~~~~~
imd_anova.cpp:406:22: note: ‘sigma2_full’ was declared here
406 | double sigma2_red, sigma2_full;
| ^~~~~~~~~~~
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/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kw_rcpp.cpp -o kw_rcpp.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/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nonmissing_per_grp.cpp -o nonmissing_per_grp.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o pmartR.so RcppExports.o calculate_cv.o count_missing_cpp.o imd_anova.o kw_rcpp.o nonmissing_per_grp.o -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/RtmpJJzBTg/R.INSTALL3c23ce137a3b3d/pmartR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJJzBTg/R.INSTALL3c23ce137a3b3d/pmartR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJJzBTg/R.INSTALL3c23ce137a3b3d/pmartR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pmartR/00new/pmartR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘pmartR’
finding HTML links ... done
DESeq2_wrapper html
RNA_filter html
all_subset html
anova_filter html
anova_test html
applyFilt html
as.isobaricpepData html
as.lipidData html
as.metabData html
as.multiData html
as.nmrData html
as.pepData html
as.proData html
as.seqData html
as.trelliData html
as.trelliData.edata html
bpquant html
bpquant_mod html
column_matches_exact html
combine_lipidData html
combine_techreps html
complete_mols html
cor_result html
create_comparisonDF html
custom_filter html
custom_sampnames html
cv_filter html
diffexp_seq html
dim_reduction html
dispersion_est html
dot-is_edata html
edata_replace html
edata_summary html
edata_transform html
edgeR_wrapper html
find_fmeta_cnames html
fit_surv html
fmeta_matches html
get_check_names html
get_comparisons html
get_data_class html
get_data_info html
get_data_norm html
get_data_scale html
get_data_scale_orig html
get_edata_cname html
get_emeta_cname html
get_fdata_cname html
get_filter_type html
get_filters html
get_group_DF html
get_group_formula html
get_group_table html
get_isobaric_info html
get_isobaric_norm html
get_lsmeans html
get_meta_info html
get_nmr_info html
get_nmr_norm html
get_pred_grid html
get_spans_params html
group_comparison_anova html
group_comparison_imd html
group_designation html
gtest_filter html
gtest_heatmap html
imd_anova html
imd_test html
imdanova_filter html
los html
mad_transform html
make_volcano_plot_df html
mean_center html
median_center html
missingval_result html
molecule_filter html
nonmissing_per_group html
normRes_tests html
normalize_global html
normalize_global_basic html
normalize_isobaric html
normalize_loess html
normalize_nmr html
normalize_quantile html
normalize_zero_one_scaling html
p_adjustment_anova html
plot-RNAFilt html
plot-SPANSRes html
plot-corRes html
plot-customFilt html
plot-cvFilt html
plot-dataRes html
plot-dimRes html
plot-imdanovaFilt html
plot-isobaricnormRes html
plot-isobaricpepData html
plot-lipidData html
plot-metabData html
plot-moleculeFilt html
plot-naRes html
plot-nmrData html
plot-nmrnormRes html
plot-normRes html
plot-pepData html
plot-proData html
plot-proteomicsFilt html
plot-rmdFilt html
plot-seqData html
plot-totalCountFilt html
plot.statRes html
plot_km html
pmartR html
pmartR_filter_worker html
ppp html
ppp_rip html
pquant html
pre_imdanova_melt html
prep_flags html
print-RNAFilt html
print-customFilt html
print-cvFilt html
print-dataRes html
print-imdanovaFilt html
print-lipidData html
print-metabData html
print-moleculeFilt html
print-normRes html
print-pepData html
print-proData html
print-proteomicsFilt html
print-rmdFilt html
print-seqData html
print-totalCountFilt html
print.RNAFiltSummary html
print.customFilterSummary html
print.cvFilterSummary html
print.imdanovaFilterSummary html
print.moleculeFilterSummary html
print.proteomicsFilterSummary html
print.rmdFilterSummary html
print.totalCountFiltSummary html
protein_quant html
proteomics_filter html
qrollup html
reexports html
replace_nas html
replace_zeros html
report_dataRes html
rip html
rmd_conversion html
rmd_filter html
rrollup html
run_group_meancor html
run_kurtosis html
run_mad html
run_prop_missing html
run_skewness html
set_check_names html
set_data_info html
set_filter html
set_isobaric_info html
set_meta_info html
set_nmr_info html
spans_make_distribution html
spans_procedure html
statRes-class html
statRes_output html
statres_barplot html
statres_volcano_plot html
summary-isobaricnormRes html
summary-nmrnormRes html
summary-omicsData html
summary-pmartR-results html
summary-trelliData html
summary.RNAFilt html
summary.customFilt html
summary.cvFilt html
summary.imdanovaFilt html
summary.moleculeFilt html
summary.proteomicsFilt html
summary.rmdFilt html
summary.totalCountFilt html
summary_km html
surv_designation html
take_diff html
total_count_filter html
trelli_abundance_boxplot html
trelli_abundance_heatmap html
trelli_abundance_histogram html
trelli_foldchange_bar html
trelli_foldchange_boxplot html
trelli_foldchange_heatmap html
trelli_foldchange_volcano html
trelli_missingness_bar html
trelli_panel_by html
trelli_precheck html
trelli_pvalue_filter html
trelli_rnaseq_boxplot html
trelli_rnaseq_heatmap html
trelli_rnaseq_histogram html
trelli_rnaseq_nonzero_bar html
vector_replace html
voom_wrapper html
zero_one_scale html
zrollup html
zscore_transform 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 (pmartR)