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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PRONE.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PRONE_1.0.5.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/PRONE.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PRONE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PRONE' version '1.0.5'
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'PRONE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ':::' import not declared from: 'vegan'
Unexported objects imported by ':::' calls:
  'NormalyzerDE:::calculateAvgMadMem'
  'NormalyzerDE:::calculateAvgReplicateVariation'
  'NormalyzerDE:::calculatePercentageAvgDiffInMat'
  'NormalyzerDE:::calculateReplicateCV'
  'NormalyzerDE:::calculateSummarizedCorrelationVector'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'plot_intersection_enrichment.Rd':
plot_intersection_enrichment
  Code: function(se, de_res, comparison, ain = NULL, id_column =
                 "Gene.Names", organism = "hsapiens", source = "KEGG",
                 signif_thr = 0.05)
  Docs: function(se, de_res, ain = NULL, comparisons = NULL, id_column
                 = "Gene.Names", organism = "hsapiens", per_comparison
                 = TRUE, sources = c("GO:BP", "GO:MF", "GO:CC"), top =
                 10)
  Argument names in code not in docs:
    comparison source signif_thr
  Argument names in docs not in code:
    comparisons per_comparison sources top
  Mismatches in argument names (first 3):
    Position: 3 Code: comparison Docs: ain
    Position: 4 Code: ain Docs: comparisons
    Position: 7 Code: source Docs: per_comparison

* checking Rd \usage sections ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'PRONE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_intersection_enrichment
> ### Title: Intersect top N enrichment terms per normalization method
> ### Aliases: plot_intersection_enrichment
> 
> ### ** Examples
> 
> data(tuberculosis_TMT_se)
> data(tuberculosis_TMT_de_res)
> plot_intersection_enrichment(tuberculosis_TMT_se, tuberculosis_TMT_de_res,
+                 ain = c("IRS_on_RobNorm", "IRS_on_Median"),
+                 comparisons = NULL, id_column = "Gene.Names",
+                 organism = "hsapiens", per_comparison = TRUE,
+                 sources = c("GO:BP", "GO:MF", "GO:CC"), top = 10)
Error in plot_intersection_enrichment(tuberculosis_TMT_se, tuberculosis_TMT_de_res,  : 
  unused arguments (comparisons = NULL, per_comparison = TRUE, sources = c("GO:BP", "GO:MF", "GO:CC"), top = 10)
Execution halted
* 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: 1 ERROR, 2 WARNINGs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/PRONE.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL PRONE
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'PRONE' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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 (PRONE)