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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_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SPONGE.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPONGE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPONGE’ version ‘1.29.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* 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-3.21-bioc/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 ... INFO
  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
checkLambda: no visible binding for global variable ‘i’
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’
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’
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 AJCC_PATHOLOGIC_TUMOR_STAGE Accuracy Analysed
  CLAUDIN_SUBTYPE Class Entrez_Gene_Id J MeanDecreaseGini Model Module
  PATIENT_ID Patient Run SUBTYPE Score Value attach.big.matrix chunk
  cor_cut cov.matrices.k cov.matrices.m cov.matrix df_cut dt.m
  each.miRNA elastic.net fn_convert_gene_names g_expr g_expr_batch gene
  geneA geneA_idx geneB geneB_idx gene_combis ginv head i is k m mir
  mirna mscor mwhich na.omit p.adj p.val precomputed_cov_matrices
  quantile read.delim sampleID solution sub.n trained.model
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 17.043  0.589  17.707
sponge_build_null_model              11.161  0.079  11.283
sponge_run_benchmark                  9.528  0.197   9.749
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/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/4.5-x86_64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 
 49.333   1.682  67.457