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BioC 3.4: CHECK report for MiChip on tokay1

This page was generated on 2017-04-15 16:16:00 -0400 (Sat, 15 Apr 2017).

Package 767/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MiChip 1.28.0
Jonathon Blake
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/MiChip
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MiChip
Version: 1.28.0
Command: rm -rf MiChip.buildbin-libdir MiChip.Rcheck && mkdir MiChip.buildbin-libdir MiChip.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MiChip.buildbin-libdir MiChip_1.28.0.tar.gz >MiChip.Rcheck\00install.out 2>&1 && cp MiChip.Rcheck\00install.out MiChip-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MiChip.buildbin-libdir --install="check:MiChip-install.out" --force-multiarch --no-vignettes --timings MiChip_1.28.0.tar.gz
StartedAt: 2017-04-14 23:32:18 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:32:56 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 37.8 seconds
RetCode: 0
Status:  OK  
CheckDir: MiChip.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MiChip.buildbin-libdir MiChip.Rcheck && mkdir MiChip.buildbin-libdir MiChip.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MiChip.buildbin-libdir MiChip_1.28.0.tar.gz >MiChip.Rcheck\00install.out 2>&1 && cp MiChip.Rcheck\00install.out MiChip-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MiChip.buildbin-libdir --install="check:MiChip-install.out" --force-multiarch --no-vignettes --timings MiChip_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/MiChip.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.28.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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-3.4-bioc/meat/MiChip.Rcheck/00check.log'
for details.


MiChip.Rcheck/00install.out:


install for i386

* installing *source* package 'MiChip' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MiChip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MiChip' as MiChip_1.28.0.zip
* DONE (MiChip)

MiChip.Rcheck/examples_i386/MiChip-Ex.timings:

nameusersystemelapsed
boxplotData000
boxplotDataNoFile000
correctForFlags000
myForgivingMedian000
naOmitMedian000
normalizePerChipMedian000
outputAnnotatedDataMatrix000
panelCor000
parseRawData000
plotIntensitiesScatter000
removeUnwantedRows000
returnAnnotatedDataMatrix000
setIntensityCutoff000
standardRemoveRows000
summarizeIntensitiesAsMedian000
workedExampleMedianNormalize2.000.142.14
workedExampleNotNormalizedData000

MiChip.Rcheck/examples_x64/MiChip-Ex.timings:

nameusersystemelapsed
boxplotData000
boxplotDataNoFile000
correctForFlags000
myForgivingMedian000
naOmitMedian000
normalizePerChipMedian000
outputAnnotatedDataMatrix000
panelCor000
parseRawData000
plotIntensitiesScatter000
removeUnwantedRows000
returnAnnotatedDataMatrix000
setIntensityCutoff000
standardRemoveRows000
summarizeIntensitiesAsMedian000
workedExampleMedianNormalize1.400.061.52
workedExampleNotNormalizedData000