##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bigPint.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings bigPint_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/bigPint.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 'bigPint/DESCRIPTION' ... OK
* this is package 'bigPint' version '1.11.0'
* 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 'bigPint' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 22.6Mb
  sub-directories of 1Mb or more:
    data              11.0Mb
    help               3.2Mb
    shiny-dashboards   5.0Mb
    shiny-examples     3.1Mb
* 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 LazyData ... WARNING
  LazyData DB of 11.0 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* 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
plotSM       40.21   0.66   40.86
plotClusters 14.47   1.19   15.89
plotLitre     4.36   1.53    5.96
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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: 1 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/bigPint.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL bigPint
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'bigPint' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bigPint'
    finding HTML links ... done
    bigPint                                 html  
    convertSEPair                           html  
    convertSESubsetGenes                    html  
    plotClusters                            html  
    plotLitre                               html  
    plotLitreApp                            html  
    plotPCP                                 html  
    plotPCPApp                              html  
    plotSM                                  html  
    plotSMApp                               html  
    plotVolcano                             html  
    plotVolcanoApp                          html  
    se_soybean_cn_sub                       html  
    se_soybean_ir_sub                       html  
    soybean_cn                              html  
    soybean_cn_metrics                      html  
    soybean_cn_sub                          html  
    soybean_cn_sub_metrics                  html  
    soybean_ir                              html  
    soybean_ir_metrics                      html  
    soybean_ir_sub                          html  
    soybean_ir_sub_metrics                  html  
*** 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 (bigPint)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'receptLoss' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ttgsea' 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.

> BiocGenerics:::testPackage("bigPint")


RUNIT TEST PROTOCOL -- Thu Mar 17 18:35:13 2022 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bigPint RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
3: In xtfrm.data.frame(x) : cannot xtfrm data frames
4: In xtfrm.data.frame(x) : cannot xtfrm data frames
5: In xtfrm.data.frame(x) : cannot xtfrm data frames
6: In xtfrm.data.frame(x) : cannot xtfrm data frames
7: In xtfrm.data.frame(x) : cannot xtfrm data frames
8: In xtfrm.data.frame(x) : cannot xtfrm data frames
> 
> proc.time()
   user  system elapsed 
   5.89    0.57    6.43