* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘IOBR’ ...
** this is package ‘IOBR’ version ‘2.2.0’
** package ‘IOBR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘IOBR’
finding HTML links ... done
BinomialAUC html
BinomialModel html
CIBERSORT html
CalculatePref html
CalculateTimeROC html
Construct_con html
ConvertRownameToLoci html
CoreAlg html
DClsei html
DCrr html
DrawQQPlot html
EPIC html
Enet html
GetFractions.Abbas html
GetOutlierGenes html
IPS_calculation html
LR_cal html
MCPcounter.estimate html
ParseInputExpression html
PlotAUC html
PlotTimeROC html
ProcessingData html
PrognosticAUC html
PrognosticModel html
PrognosticResult html
RegressionResult html
RemoveBatchEffect html
SplitTrainTest html
Top_probe html
add_iobr_mirror html
add_riskscore html
anno_eset html
assimilate_data html
batch_cor html
batch_kruskal html
batch_pcc html
batch_sig_surv_plot html
batch_surv html
batch_wilcoxon html
best_cutoff html
best_cutoff2 html
calculate_break_month html
calculate_sig_score html
calculate_sig_score_integration html
calculate_sig_score_pca html
calculate_sig_score_ssgsea html
calculate_sig_score_zscore html
cell_bar_plot html
check_cancer_types html
check_eset html
clear_iobr_cache html
combine_pd_eset html
count2tpm html
creat_folder html
deconvo_cibersort html
deconvo_epic html
deconvo_estimate html
deconvo_ips html
deconvo_mcpcounter html
deconvo_quantiseq html
deconvo_ref html
deconvo_timer html
deconvo_tme html
deconvo_xcell html
deconvolute_quantiseq.default html
deconvolute_timer.default html
design_mytheme html
doPerm html
dot-appendSignatures html
dot-build_mut_matrices html
dot-create_mut_matrix html
download_iobr_data html
enrichment_barplot html
eset_distribution html
estimateScore html
exact_pvalue html
extract_sc_data html
feature_manipulation html
feature_select html
filterCommonGenes html
find_markers_in_bulk html
find_mutations html
find_outlier_samples html
find_variable_genes html
fixMixture html
format_msigdb html
format_signatures html
generateRef html
generateRef_DEseq2 html
generateRef_limma html
generateRef_rnaseq html
generateRef_seurat html
getHRandCIfromCoxph html
get_cols html
get_cor html
get_cor_matrix html
get_default_mirrors html
get_sig_sc html
gsva_use_new_api html
high_var_fea html
imvigor210_pdata html
iobr_cor_plot html
iobr_deconvo_pipeline html
iobr_deg html
iobr_pca html
ipsmap html
lasso_select html
limma.dif html
list_github_datasets html
list_iobr_mirrors html
load_data html
log2eset html
makeQN html
make_mut_matrix html
mapGenes html
mapbw html
mapcolors html
merge_duplicate html
merge_duplicates html
merge_eset html
microenvironmentScores html
mouse2human_eset html
null_models html
outputGCT html
output_sig html
palettes html
parallel_doperm html
patterns_to_na html
pdata_stad html
percent_bar_plot html
pie_chart html
plotPurity html
quanTIseq html
quantiseq_helper html
random_strata_cells html
rawEnrichmentAnalysis html
rbind_iobr html
remove_batcheffect html
remove_duplicate_genes html
remove_names html
reset_iobr_mirrors html
roc_time html
scaleCounts html
scale_matrix html
select_method html
sigScore html
sig_box html
sig_box_batch html
sig_forest html
sig_group html
sig_gsea html
sig_heatmap html
sig_pheatmap html
sig_roc html
sig_surv_plot html
signature_collection html
signature_score_calculation_methods html
spillOver html
stad_group html
subgroup_data html
subgroup_survival html
surv_group html
tcga_rna_preps html
tcga_stad_pdata html
test_for_infiltration html
timer_available_cancers html
timer_info html
tme_cluster html
tme_deconvolution_methods html
transformScores html
transform_data html
xCellAnalysis html
xCellSignifcanceBetaDist html
xCellSignifcanceRandomMatrix html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IOBR)