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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPONGE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPONGE_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/SPONGE.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPONGE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPONGE’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .idea
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  spongEffects_logo/Endprodukt_Schrift rechts.png
  spongEffects_logo/Endprodukt_Schrift unten.png
  spongEffects_logo/SpongEffekt_Endprodukt_Logo alleinstehend.png
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SPONGE’ can be installed ... WARNING
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
  Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
  Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
  Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
  Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
  Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
  Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
  Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/SPONGE.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with no role:
  Fabio Boniolo
  Azim Dehghani Amirabad
  Dennis Kostka
  Marcel H. Schulz
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘httr’ ‘tibble’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check_and_convert_expression_data: no visible global function
  definition for ‘is’
check_and_convert_expression_data: no visible global function
  definition for ‘attach.big.matrix’
check_and_convert_expression_data: no visible global function
  definition for ‘mwhich’
checkLambda: no visible binding for global variable ‘i’
compute_p_values: no visible binding for global variable ‘cor_cut’
compute_p_values: no visible binding for global variable ‘df_cut’
compute_p_values: no visible global function definition for ‘J’
compute_p_values: no visible binding for global variable ‘.I’
compute_p_values: no visible binding for global variable ‘.EACHI’
compute_p_values: no visible binding for global variable ‘p.val’
compute_p_values: no visible binding for global variable ‘p.adj’
define_modules: no visible binding for global variable ‘geneA’
define_modules: no visible binding for global variable ‘geneB’
determine_cutoffs_for_null_model_partitioning: no visible binding for
  global variable ‘cor_cut’
determine_cutoffs_for_null_model_partitioning: no visible binding for
  global variable ‘df_cut’
enrichment_modules: no visible binding for global variable ‘Module’
filter_ceRNA_network: no visible binding for global variable ‘gene’
fn_discretize_spongeffects: no visible global function definition for
  ‘quantile’
fn_filter_network: no visible binding for global variable ‘mscor’
fn_filter_network: no visible binding for global variable ‘p.adj’
fn_gene_miRNA_F_test: no visible binding for global variable ‘mirna’
fn_get_model_coef: no visible binding for global variable ‘gene’
get_central_modules: no visible binding for global variable ‘gene’
isplitDT2 : nextEl: no visible global function definition for ‘.’
plot_accuracy_sensitivity_specificity: no visible binding for global
  variable ‘Accuracy’
plot_accuracy_sensitivity_specificity: no visible binding for global
  variable ‘Model’
plot_accuracy_sensitivity_specificity: no visible binding for global
  variable ‘Run’
plot_accuracy_sensitivity_specificity: no visible binding for global
  variable ‘Class’
plot_accuracy_sensitivity_specificity: no visible binding for global
  variable ‘Value’
plot_confusion_matrices: no visible global function definition for
  ‘na.omit’
plot_density_scores: no visible binding for global variable
  ‘MeanDecreaseGini’
plot_density_scores: no visible binding for global variable ‘Patient’
plot_density_scores: no visible binding for global variable ‘Score’
plot_density_scores: no visible binding for global variable ‘Class’
plot_heatmaps: no visible binding for global variable
  ‘MeanDecreaseGini’
plot_involved_miRNAs_to_modules: no visible binding for global variable
  ‘MeanDecreaseGini’
plot_top_modules: no visible binding for global variable
  ‘trained.model’
plot_top_modules: no visible binding for global variable
  ‘MeanDecreaseGini’
plot_top_modules: no visible binding for global variable ‘Module’
plot_top_modules: no visible binding for global variable ‘Analysed’
prepare_metabric_for_spongEffects: no visible global function
  definition for ‘read.delim’
prepare_metabric_for_spongEffects: no visible binding for global
  variable ‘Entrez_Gene_Id’
prepare_metabric_for_spongEffects: no visible global function
  definition for ‘fn_convert_gene_names’
prepare_metabric_for_spongEffects: no visible binding for global
  variable ‘CLAUDIN_SUBTYPE’
prepare_metabric_for_spongEffects: no visible binding for global
  variable ‘PATIENT_ID’
prepare_tcga_for_spongEffects: no visible binding for global variable
  ‘sampleID’
prepare_tcga_for_spongEffects: no visible binding for global variable
  ‘SUBTYPE’
prepare_tcga_for_spongEffects: no visible binding for global variable
  ‘PATIENT_ID’
prepare_tcga_for_spongEffects: no visible binding for global variable
  ‘AJCC_PATHOLOGIC_TUMOR_STAGE’
processChunk: no visible binding for global variable ‘geneA_idx’
processChunk: no visible binding for global variable ‘geneB_idx’
processChunk: no visible binding for global variable ‘geneA’
processChunk: no visible binding for global variable ‘geneB’
processChunk: no visible binding for global variable ‘mirna’
Random_spongEffects: no visible binding for global variable
  ‘Sponge.modules’
sample_zero_mscor_cov: no visible binding for global variable
  ‘solution’
sample_zero_mscor_cov: no visible global function definition for ‘ginv’
sample_zero_mscor_cov: no visible binding for global variable ‘i’
sample_zero_mscor_data: no visible binding for global variable
  ‘cov.matrix’
sponge: no visible global function definition for ‘is’
sponge: no visible binding for global variable ‘i’
sponge: no visible global function definition for ‘attach.big.matrix’
sponge: no visible binding for global variable ‘gene_combis’
sponge_build_null_model: no visible binding for global variable
  ‘precomputed_cov_matrices’
sponge_build_null_model: no visible binding for global variable
  ‘cov.matrices.m’
sponge_build_null_model: no visible binding for global variable
  ‘cov.matrices.k’
sponge_build_null_model: no visible binding for global variable ‘m’
sponge_build_null_model: no visible binding for global variable ‘k’
sponge_compute_p_values: no visible binding for global variable ‘dt.m’
sponge_compute_p_values: no visible binding for global variable
  ‘cor_cut’
sponge_compute_p_values: no visible binding for global variable
  ‘df_cut’
sponge_gene_miRNA_interaction_filter: no visible global function
  definition for ‘is’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘chunk’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘g_expr_batch’
sponge_gene_miRNA_interaction_filter : <anonymous>: no visible binding
  for global variable ‘g_expr_batch’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘gene’
sponge_gene_miRNA_interaction_filter: no visible binding for global
  variable ‘g_expr’
sponge_network: no visible binding for global variable ‘gene’
sponge_network: no visible binding for global variable ‘mir’
sponge_plot_network_centralities: no visible global function definition
  for ‘head’
sponge_plot_simulation_results: no visible binding for global variable
  ‘mscor’
sponge_run_benchmark: no visible binding for global variable
  ‘precomputed_cov_matrices’
sponge_run_benchmark: no visible binding for global variable
  ‘elastic.net’
sponge_run_benchmark: no visible binding for global variable
  ‘each.miRNA’
sponge_subsampling: no visible binding for global variable ‘sub.n’
sponge_subsampling: no visible binding for global variable ‘geneA’
sponge_subsampling: no visible binding for global variable ‘geneB’
Undefined global functions or variables:
  . .EACHI .I Accuracy AJCC_PATHOLOGIC_TUMOR_STAGE Analysed
  attach.big.matrix chunk Class CLAUDIN_SUBTYPE cor_cut cov.matrices.k
  cov.matrices.m cov.matrix df_cut dt.m each.miRNA elastic.net
  Entrez_Gene_Id fn_convert_gene_names g_expr g_expr_batch gene
  gene_combis geneA geneA_idx geneB geneB_idx ginv head i is J k m
  MeanDecreaseGini mir mirna Model Module mscor mwhich na.omit p.adj
  p.val Patient PATIENT_ID precomputed_cov_matrices quantile read.delim
  Run sampleID Score solution Sponge.modules sub.n SUBTYPE
  trained.model Value
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "quantile")
  importFrom("utils", "head", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: fn_RF_classifier.Rd:30-32: Dropping empty section \value
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘train_genes_miRNA_candidates’
Undocumented data sets:
  ‘train_genes_miRNA_candidates’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'Random_spongEffects.Rd'
  ‘min.expression’
Documented arguments not in \usage in Rd file 'Random_spongEffects.Rd':
  ‘train_gene_expr’ ‘test_gene_expr’ ‘train_meta_data’ ‘test_meta_data’
  ‘train_meta_data_type’ ‘test_meta_data_type’ ‘metric’ ‘tunegrid_c’
  ‘n.folds’ ‘repetitions’ ‘min.expr’

Documented arguments not in \usage in Rd file 'calibrate_model.Rd':
  ‘modules’

Undocumented arguments in Rd file 'plot_confusion_matrices.Rd'
  ‘subtypes.testing.factors’
Documented arguments not in \usage in Rd file 'plot_confusion_matrices.Rd':
  ‘subtypes_testing_factors’

Documented arguments not in \usage in Rd file 'plot_density_scores.Rd':
  ‘meta_data_type’

Documented arguments not in \usage in Rd file 'plot_top_modules.Rd':
  ‘bioMart_gene_symbol_columns’ ‘bioMart_gene_ensembl’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
sponge_gene_miRNA_interaction_filter 6.483  0.303   6.786
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/SPONGE.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPONGE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘SPONGE’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
Note: next used in wrong context: no loop is visible 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** testing if installed package keeps a record of temporary installation path
* DONE (SPONGE)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SPONGE)
Warning messages:
1: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' 
2: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' 
3: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' 
4: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' 
5: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' 
6: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' 
7: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' 
> 
> test_check("SPONGE")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 163 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 163 ]
> 
> proc.time()
   user  system elapsed 
 19.867   0.722  27.662