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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcot2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pcot2_1.56.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcot2.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pcot2/DESCRIPTION' ... OK
* this is package 'pcot2' version '1.56.0'
* 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 whether package 'pcot2' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
'library' or 'require' call to 'amap' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Cor: no visible global function definition for 'var'
Cor: no visible global function definition for 'cov2cor'
aveProbe: no visible binding for global variable 'median'
corplot: no visible global function definition for 'hclust'
corplot2: no visible global function definition for 'cor'
corplot2: no visible global function definition for 'layout'
corplot2: no visible global function definition for 'par'
corplot2: no visible global function definition for 'hclust'
corplot2: no visible global function definition for 'image'
corplot2: no visible global function definition for 'title'
corplot2: no visible global function definition for 'box'
corplot2: no visible global function definition for 'axis'
corplot2: no visible global function definition for 'plot.new'
geneLocator: no visible global function definition for 'plot.new'
geneLocator: no visible global function definition for 'par'
geneLocator: no visible global function definition for 'image'
geneLocator: no visible global function definition for 'title'
geneLocator: no visible global function definition for 'axis'
geneLocator: no visible global function definition for 'locator'
pco: no visible global function definition for 'cmdscale'
pcot2: no visible global function definition for 'p.adjust'
plotCor: no visible global function definition for 'par'
plotCor: no visible global function definition for 'layout'
plotCor: no visible global function definition for 'image'
plotCor: no visible global function definition for 'title'
plotCor: no visible global function definition for 'box'
plotCor: no visible global function definition for 'axis'
rb: no visible global function definition for 'rgb'
rg: no visible global function definition for 'rgb'
rg: no visible global function definition for 'dnorm'
t2: no visible global function definition for 'var'
t2: no visible global function definition for 'pf'
t2.unequ: no visible global function definition for 'var'
wb: no visible global function definition for 'rgb'
wb: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  axis box cmdscale cor cov2cor dnorm hclust image layout locator
  median p.adjust par pf plot.new rgb title var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "box", "image", "layout", "locator",
             "par", "plot.new", "title")
  importFrom("stats", "cmdscale", "cor", "cov2cor", "dnorm", "hclust",
             "median", "p.adjust", "pf", "var")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
pcot2    12.98    0.0   14.95
aveProbe  8.84    0.7    9.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
aveProbe 10.61   0.49   14.97
pcot2     9.47   0.00    9.55
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcot2.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pcot2_1.56.0.tar.gz && rm -rf pcot2.buildbin-libdir && mkdir pcot2.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcot2.buildbin-libdir pcot2_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pcot2_1.56.0.zip && rm pcot2_1.56.0.tar.gz pcot2_1.56.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  201k  100  201k    0     0  3236k      0 --:--:-- --:--:-- --:--:-- 3662k

install for i386

* installing *source* package 'pcot2' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pcot2'
    finding HTML links ... done
    aveProbe                                html  
    corplot                                 html  
    corplot2                                html  
    getImat                                 html  
    pcot2-internal                          html  
    pcot2                                   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

install for x64

* installing *source* package 'pcot2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcot2' as pcot2_1.56.0.zip
* DONE (pcot2)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pcot2' successfully unpacked and MD5 sums checked