BioC 3.1: CHECK report for MiChip on petty

Package: MiChip

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MiChip_1.22.0.tar.gz

StartedAt: 2015-10-09 00:17:12 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:18:05 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 52.7 seconds

RetCode: 0

Status:  OK

CheckDir: MiChip.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MiChip_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/MiChip.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MiChip/DESCRIPTION’ ... OK
* this is package ‘MiChip’ version ‘1.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MiChip’ can be installed ... [4s/4s] 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
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/6s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/MiChip.Rcheck/00check.log’
for details.

* 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
* DONE (MiChip)

name	user	system	elapsed
boxplotData	0.001	0.000	0.001
boxplotDataNoFile	0.001	0.000	0.001
correctForFlags	0.001	0.000	0.010
myForgivingMedian	0.001	0.000	0.002
naOmitMedian	0.001	0.000	0.001
normalizePerChipMedian	0.001	0.000	0.002
outputAnnotatedDataMatrix	0.001	0.000	0.002
panelCor	0.002	0.000	0.001
parseRawData	0.001	0.000	0.002
plotIntensitiesScatter	0.001	0.001	0.001
removeUnwantedRows	0.001	0.000	0.002
returnAnnotatedDataMatrix	0.001	0.001	0.002
setIntensityCutoff	0.001	0.000	0.002
standardRemoveRows	0.001	0.001	0.001
summarizeIntensitiesAsMedian	0.001	0.000	0.001
workedExampleMedianNormalize	2.657	0.108	3.550
workedExampleNotNormalizedData	0.001	0.000	0.001