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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PanomiR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PanomiR_0.99.8.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PanomiR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PanomiR/DESCRIPTION' ... OK
* this is package 'PanomiR' version '0.99.8'
* 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 'PanomiR' 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 R 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 ... OK
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
pathwayGeneTab  6.5   0.61    7.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PanomiR
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'PanomiR' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PanomiR'
    finding HTML links ... done
    aggInvCoverFn                           html  
    aggInvFn                                html  
    aggLogCoverFn                           html  
    aggLogFn                                html  
    alignToUniverse                         html  
    clusterPlot                             html  
    differentialPathwayAnalysis             html  
    enrichAllPairs                          html  
    getDesignMatrix                         html  
    getDiffExpTable                         html  
    getResidual                             html  
    gscExample                              html  
    jackKnifeBase                           html  
    linColumnFinder                         html  
    mappingPathwaysClusters                 html  
    methodProbBase                          html  
    miRNAPathwayEnrichment                  html  
    miniTestsPanomiR                        html  
    msigdb_c2                               html  
    pCutCoverFn                             html  
    pCutFn                                  html  
    path_gene_table                         html  
    pathwayGeneTab                          html  
    pathwaySummary                          html  
    pcxnToNet                               html  
    prioritizeMicroRNA                      html  
    reportEnrichment                        html  
    samplingDataBase                        html  
    sumlogCoverFn                           html  
    sumlogFn                                html  
    sumzCoverFn                             html  
    sumzFn                                  html  
    tableFromGSC                            html  
    targetScan_03                           html  
** 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 (PanomiR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'DMCHMM' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(PanomiR)
> 
> test_check("PanomiR")


'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 6 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
   5.53    0.50    6.03