Package: ReadqPCR

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ReadqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ReadqPCR_1.26.0.tar.gz

StartedAt: 2018-10-16 23:35:12 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:36:01 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 49.5 seconds

RetCode: 0

Status:  OK

CheckDir: ReadqPCR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ReadqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ReadqPCR_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ReadqPCR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReadqPCR/DESCRIPTION’ ... OK
* this is package ‘ReadqPCR’ version ‘1.26.0’
* 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 ‘ReadqPCR’ 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
* 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:
  ‘affy’ ‘methods’
  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
.read.TaqBatch: no visible global function definition for ‘read.delim’
.read.qPCR: no visible global function definition for ‘read.table’
.readLC480txt: no visible global function definition for ‘read.table’
.readLC480txt: no visible global function definition for
  ‘AnnotatedDataFrame’
.readLC480txt: no visible global function definition for ‘new’
qpcR2CyclesSet: no visible global function definition for ‘new’
read.LC480SampleInfo: no visible global function definition for
  ‘read.table’
read.LC480SampleInfo: no visible global function definition for
  ‘AnnotatedDataFrame’
read.qPCR: no visible global function definition for ‘new’
read.qPCR: no visible global function definition for ‘pData’
read.qPCR: no visible global function definition for ‘assayDataNew’
read.taqman: no visible global function definition for ‘new’
read.taqman: no visible global function definition for ‘pData’
read.taqman: no visible global function definition for ‘assayDataNew’
effs,qPCRBatch: no visible global function definition for ‘fData’
effs<-,qPCRBatch: no visible global function definition for ‘fData’
effs<-,qPCRBatch: no visible global function definition for ‘fData<-’
exprs.well.order,qPCRBatch: no visible global function definition for
  ‘assayDataElement’
exprs.well.order<-,qPCRBatch: no visible global function definition for
  ‘assayDataElementReplace’
exprs,CyclesSet: no visible global function definition for
  ‘assayDataElement’
exprs,qPCRBatch: no visible global function definition for
  ‘assayDataElement’
exprs<-,CyclesSet-ANY: no visible global function definition for
  ‘assayDataElementReplace’
exprs<-,qPCRBatch-ANY: no visible global function definition for
  ‘assayDataElementReplace’
merge,AnnotatedDataFrame-eSet: no visible global function definition
  for ‘pData’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘pData’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘varMetadata’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘phenoData’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘pData<-’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘varMetadata<-’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘phenoData<-’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘featureData’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘fData<-’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘featureData<-’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘protocolData’
merge,eSet-AnnotatedDataFrame: no visible global function definition
  for ‘protocolData<-’
se.effs,qPCRBatch: no visible global function definition for ‘fData’
se.effs<-,qPCRBatch: no visible global function definition for ‘fData’
se.effs<-,qPCRBatch: no visible global function definition for
  ‘fData<-’
se.exprs,qPCRBatch: no visible global function definition for
  ‘assayDataElement’
se.exprs<-,qPCRBatch: no visible global function definition for
  ‘assayDataElementReplace’
Undefined global functions or variables:
  AnnotatedDataFrame assayDataElement assayDataElementReplace
  assayDataNew fData fData<- featureData featureData<- new pData
  pData<- phenoData phenoData<- protocolData protocolData<- read.delim
  read.table varMetadata varMetadata<-
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "read.delim", "read.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ReadqPCR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ReadqPCR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ReadqPCR’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ReadqPCR.Rnw’ 
** testing if installed package can be loaded
* DONE (ReadqPCR)

name	user	system	elapsed
ReadqPCR-package	0.002	0.000	0.002
merge	0.170	0.004	0.177
qpcR2CyclesSet	1.763	0.120	1.907
read.qPCR	0.173	0.002	0.177
read.taqman	0.559	0.007	0.573
readLC480	0.143	0.013	0.157
readLC480SampleInfo	0.011	0.001	0.012