Multiple platform build/check report for BioC 3.9 - CHECK report for methVisual on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methVisual.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methVisual_1.35.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/methVisual.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.35.0'
* 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 'methVisual' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'windows(n, lengthData, ': unused argument (rescale = "fixed") 
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/methVisual.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biostrings' 'grid'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  'gsubfn' 'plotrix' 'sqldf'
  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
Cooccurrence: no visible global function definition for 'windows'
makeDataMethGFF: no visible binding for global variable 'fn'
plotMatrixSNP: no visible global function definition for 'color.legend'
Undefined global functions or variables:
  color.legend fn windows
Consider adding
  importFrom("grDevices", "windows")
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
** running examples for arch 'x64' ... 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/methVisual.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/methVisual_1.35.0.tar.gz && rm -rf methVisual.buildbin-libdir && mkdir methVisual.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methVisual.buildbin-libdir methVisual_1.35.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL methVisual_1.35.0.zip && rm methVisual_1.35.0.tar.gz methVisual_1.35.0.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
 67 24270   67 16384    0     0  81257      0 --:--:-- --:--:-- --:--:-- 83591
100 24270  100 24270    0     0   117k      0 --:--:-- --:--:-- --:--:--  120k

install for i386

* installing *source* package 'methVisual' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'windows(n, lengthData, ': unused argument (rescale = "fixed") 
** help
*** installing help indices
  converting help for package 'methVisual'
    finding HTML links ... done
    Cooccurrence                            html  
    MethAlignNW                             html  
    MethDataInput                           html  
    MethLollipops                           html  
    MethylQC                                html  
    cgInAlign                               html  
    cgMethFinder                            html  
    coversionGenom                          html  
    findNonAligned                          html  
    heatMapMeth                             html  
    makeDataMethGFF                         html  
    makeLocalExpDir                         html  
    makeTabFilePath                         html  
    matrixSNP                               html  
    methCA                                  html  
    methData                                html  
    methFisherTest                          html  
    methWhitneyUTest                        html  
    plotAbsMethyl                           html  
    plotMatrixSNP                           html  
    readBisulfFASTA                         html  
    selectRefSeq                            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 'methVisual' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methVisual' as methVisual_1.35.0.zip
* DONE (methVisual)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'methVisual' successfully unpacked and MD5 sums checked

CHECK report for methVisual on tokay2

Summary

Command output

Installation output

Tests output

Example timings