Package: ReadqPCR

Version: 1.24.0

Command: rm -rf ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && mkdir ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReadqPCR.buildbin-libdir ReadqPCR_1.24.0.tar.gz >ReadqPCR.Rcheck\00install.out 2>&1 && cp ReadqPCR.Rcheck\00install.out ReadqPCR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ReadqPCR.buildbin-libdir --install="check:ReadqPCR-install.out" --force-multiarch --no-vignettes --timings ReadqPCR_1.24.0.tar.gz

StartedAt: 2018-04-12 02:33:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:34:33 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 56.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ReadqPCR.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && mkdir ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReadqPCR.buildbin-libdir ReadqPCR_1.24.0.tar.gz >ReadqPCR.Rcheck\00install.out 2>&1 && cp ReadqPCR.Rcheck\00install.out ReadqPCR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ReadqPCR.buildbin-libdir --install="check:ReadqPCR-install.out" --force-multiarch --no-vignettes --timings ReadqPCR_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ReadqPCR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ReadqPCR/DESCRIPTION' ... OK
* this is package 'ReadqPCR' version '1.24.0'
* 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 'ReadqPCR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/qpcR2CyclesSet.Rd:30: missing file link 'reps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/read.qPCR.Rd:43: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/read.taqman.Rd:46: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/readLC480.Rd:61: missing file link 'eSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/readLC480SampleInfo.Rd:54: missing file link 'AnnotatedDataFrame-class'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ReadqPCR.Rcheck/00install.out' for details.
* 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 ... 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 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ReadqPCR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ReadqPCR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ReadqPCR'
    finding HTML links ... done
    CyclesSet-class                         html  
    ReadqPCR-package                        html  
    merge                                   html  
    qPCRBatch-class                         html  
    qpcR2CyclesSet                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/qpcR2CyclesSet.Rd:30: missing file link 'reps'
    read.qPCR                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/read.qPCR.Rd:43: missing file link 'ExpressionSet-class'
    read.taqman                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/read.taqman.Rd:46: missing file link 'ExpressionSet-class'
    readLC480                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/readLC480.Rd:61: missing file link 'eSet'
    readLC480SampleInfo                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpOsqvgk/R.INSTALL9bc60e06f88/ReadqPCR/man/readLC480SampleInfo.Rd:54: missing file link 'AnnotatedDataFrame-class'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ReadqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReadqPCR' as ReadqPCR_1.24.0.zip
* DONE (ReadqPCR)
In R CMD INSTALL
In R CMD INSTALL