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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings iPAC_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/iPAC.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 'iPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPAC' version '1.32.0'
* 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 'iPAC' 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
Package in Depends field not imported from: 'gdata'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Plot.Protein.Linear: no visible global function definition for
  'heat.colors'
Plot.Protein.Linear: no visible global function definition for 'gray'
Plot.Protein.Linear: no visible global function definition for
  'topo.colors'
Plot.Protein.Linear: no visible global function definition for
  'cm.colors'
Plot.Protein.Linear: no visible global function definition for 'par'
Plot.Protein.Linear: no visible global function definition for 'rect'
Plot.Protein.Linear: no visible global function definition for 'text'
SetTextContrastColor: no visible global function definition for
  'col2rgb'
calcorder: no visible global function definition for 'dist'
calcorder: no visible global function definition for 'cmdscale'
difforder0: no visible global function definition for 'pbinom'
difforder0: no visible global function definition for 'dmultinom'
difforder1: no visible global function definition for 'dmultinom'
nmc: no visible global function definition for 'pbeta'
plotLinear: no visible global function definition for 'pdf'
plotLinear: no visible global function definition for 'dev.off'
plotLinear: no visible global function definition for 'dev.copy2pdf'
plotMDS: no visible global function definition for 'pdf'
plotMDS: no visible global function definition for 'dev.off'
plotMDS: no visible global function definition for 'dev.copy2pdf'
Undefined global functions or variables:
  cm.colors cmdscale col2rgb dev.copy2pdf dev.off dist dmultinom gray
  heat.colors par pbeta pbinom pdf rect text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "col2rgb", "dev.copy2pdf",
             "dev.off", "gray", "heat.colors", "pdf", "topo.colors")
  importFrom("graphics", "par", "rect", "text")
  importFrom("stats", "cmdscale", "dist", "dmultinom", "pbeta", "pbinom")
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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ClusterFind         68.95   0.47   77.52
nmc                 18.11   0.01   18.13
get.Positions       12.88   1.25   14.92
Plot.Protein.Linear  3.04   0.34   24.34
get.Remapped.Order   2.98   0.10    9.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ClusterFind         72.92   0.67   76.14
get.Positions       28.71   8.00   37.45
nmc                 21.40   0.05   21.43
Plot.Protein.Linear  3.97   0.91    5.10
* 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/iPAC.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/iPAC_1.32.0.tar.gz && rm -rf iPAC.buildbin-libdir && mkdir iPAC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iPAC.buildbin-libdir iPAC_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL iPAC_1.32.0.zip && rm iPAC_1.32.0.tar.gz iPAC_1.32.0.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  163k  100  163k    0     0  2627k      0 --:--:-- --:--:-- --:--:-- 2966k

install for i386

* installing *source* package 'iPAC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iPAC'
    finding HTML links ... done
    ClusterFind                             html  
    KRAS.Mutations                          html  
    PIK3CA.Mutations                        html  
    Plot.Protein.Linear                     html  
    get.AASeq                               html  
    get.AlignedPositions                    html  
    get.Positions                           html  
    get.Remapped.Order                      html  
    get.SingleLetterCode                    html  
    iPAC-package                            html  
    nmc                                     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 'iPAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iPAC' as iPAC_1.32.0.zip
* DONE (iPAC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'iPAC' successfully unpacked and MD5 sums checked