ReadqPCR 1.18.0
James Perkins
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ReadqPCR | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ReadqPCR_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ReadqPCR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReadqPCR/DESCRIPTION’ ... OK
* this is package ‘ReadqPCR’ version ‘1.18.0’
* 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
‘assayDataElement’
effs<-,qPCRBatch: no visible global function definition for
‘assayDataElementReplace’
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
‘assayDataElement’
se.effs<-,qPCRBatch: no visible global function definition for
‘assayDataElementReplace’
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<- 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
‘/home/biocbuild/bbs-3.3-bioc/meat/ReadqPCR.Rcheck/00check.log’
for details.