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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLP_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MLP.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLP’ version ‘1.54.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MLP’ 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 ... OK
* 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 ... NOTE
checkRd: (-1) getGeneSets.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGeneSets.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
addGeneSetDescription 65.618  8.717  74.794
getGeneSets           61.842  2.051  98.880
MLP                   23.325  1.644  25.050
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.KEGG.R’
 ERROR
Running the tests in ‘tests/test.KEGG.R’ failed.
Last 13 lines of output:
  + 	species = "Mouse", 
  + 	geneSetSource = "KEGG", 
  + 	entrezIdentifiers = names(pvalues)
  + ))
     user  system elapsed 
   33.823   0.213  67.567 
  > 
  > set.seed(111)
  > mlpOut <- MLP(
  + 	geneSet = geneSet, 
  + 	geneStatistic = pvalues
  + ) 	
  Error in x[n - 0:19] : only 0's may be mixed with negative subscripts
  Calls: MLP ... quantileCurves -> vv -> smdecreasing1 -> lsfit -> as.matrix
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MLP.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MLP
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MLP’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (MLP)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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(MLP)
> 
> pathPValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
> load(pathPValues)
> 
> pvalues <- examplePValues[seq.int(1000)]
> 
> system.time(geneSet <- getGeneSets(
+ 	species = "Mouse", 
+ 	geneSetSource = "KEGG", 
+ 	entrezIdentifiers = names(pvalues)
+ ))
   user  system elapsed 
 33.823   0.213  67.567 
> 
> set.seed(111)
> mlpOut <- MLP(
+ 	geneSet = geneSet, 
+ 	geneStatistic = pvalues
+ ) 	
Error in x[n - 0:19] : only 0's may be mixed with negative subscripts
Calls: MLP ... quantileCurves -> vv -> smdecreasing1 -> lsfit -> as.matrix
Execution halted