Package: MiChip

Version: 1.40.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MiChip.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MiChip_1.40.0.tar.gz

StartedAt: 2020-04-15 04:45:23 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:46:04 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 40.5 seconds

RetCode: 0

Status:  OK

CheckDir: MiChip.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MiChip.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MiChip_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MiChip.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MiChip/DESCRIPTION' ... OK
* this is package 'MiChip' version '1.40.0'
* 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 'MiChip' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
boxplotData: no visible global function definition for 'jpeg'
boxplotData: no visible global function definition for 'boxplot'
boxplotData: no visible global function definition for 'rainbow'
boxplotData: no visible global function definition for 'dev.off'
boxplotDataNoFile: no visible global function definition for 'boxplot'
boxplotDataNoFile: no visible global function definition for 'rainbow'
correctForFlags: no visible global function definition for 'new'
myForgivingMedian: no visible global function definition for 'na.omit'
myForgivingMedian: no visible global function definition for 'median'
myForgivingMedian: no visible global function definition for 'sd'
naOmitMedian: no visible global function definition for 'na.omit'
naOmitMedian: no visible global function definition for 'mad'
naOmitMedian: no visible global function definition for 'median'
normalizePerChipMedian: no visible global function definition for
  'na.omit'
normalizePerChipMedian: no visible global function definition for
  'median'
normalizePerChipMedian: no visible global function definition for 'new'
outputAnnotatedDataMatrix: no visible global function definition for
  'write.table'
panelCor: no visible global function definition for 'cor.test'
panelCor: no visible binding for global variable 'na.omit'
panelCor: no visible global function definition for 'strwidth'
panelCor: no visible global function definition for 'text'
parseRawData: no visible global function definition for 'read.table'
parseRawData: no visible global function definition for 'new'
plotIntensitiesScatter: no visible global function definition for
  'jpeg'
plotIntensitiesScatter: no visible global function definition for
  'pairs'
plotIntensitiesScatter : <anonymous>: no visible global function
  definition for 'points'
plotIntensitiesScatter : <anonymous>: no visible global function
  definition for 'abline'
plotIntensitiesScatter: no visible global function definition for
  'dev.off'
removeUnwantedRows: no visible global function definition for 'new'
summarizeIntensitiesAsMedian: no visible binding for global variable
  'median'
summarizeIntensitiesAsMedian: no visible global function definition for
  'new'
Undefined global functions or variables:
  abline boxplot cor.test dev.off jpeg mad median na.omit new pairs
  points rainbow read.table sd strwidth text write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "rainbow")
  importFrom("graphics", "abline", "boxplot", "pairs", "points",
             "strwidth", "text")
  importFrom("methods", "new")
  importFrom("stats", "cor.test", "mad", "median", "na.omit", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
** 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/MiChip.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MiChip_1.40.0.tar.gz && rm -rf MiChip.buildbin-libdir && mkdir MiChip.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MiChip.buildbin-libdir MiChip_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MiChip_1.40.0.zip && rm MiChip_1.40.0.tar.gz MiChip_1.40.0.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  421k  100  421k    0     0  8420k      0 --:--:-- --:--:-- --:--:-- 8960k

install for i386

* installing *source* package 'MiChip' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MiChip'
    finding HTML links ... done
    MiChip                                  html  
    boxplotData                             html  
    boxplotDataNoFile                       html  
    correctForFlags                         html  
    myForgivingMedian                       html  
    naOmitMedian                            html  
    normalizePerChipMedian                  html  
    outputAnnotatedDataMatrix               html  
    panelCor                                html  
    parseRawData                            html  
    plotIntensitiesScatter                  html  
    removeUnwantedRows                      html  
    returnAnnotatedDataMatrix               html  
    setIntensityCutoff                      html  
    standardRemoveRows                      html  
    summarizeIntensitiesAsMedian            html  
    workedExampleMedianNormalize            html  
    workedExampleNotNormalizedData          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 'MiChip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MiChip' as MiChip_1.40.0.zip
* DONE (MiChip)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MiChip' successfully unpacked and MD5 sums checked