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BioC 3.2: CHECK report for ReadqPCR on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:33 -0400 (Tue, 27 Oct 2015).

Package 862/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReadqPCR 1.16.0
James Perkins
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ReadqPCR
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ReadqPCR
Version: 1.16.0
Command: rm -rf ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && mkdir ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReadqPCR.buildbin-libdir ReadqPCR_1.16.0.tar.gz >ReadqPCR.Rcheck\00install.out 2>&1 && cp ReadqPCR.Rcheck\00install.out ReadqPCR-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ReadqPCR.buildbin-libdir --install="check:ReadqPCR-install.out" --force-multiarch --no-vignettes --timings ReadqPCR_1.16.0.tar.gz
StartedAt: 2015-10-27 04:57:20 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:58:00 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 40.0 seconds
RetCode: 0
Status:  OK  
CheckDir: ReadqPCR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && mkdir ReadqPCR.buildbin-libdir ReadqPCR.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReadqPCR.buildbin-libdir ReadqPCR_1.16.0.tar.gz >ReadqPCR.Rcheck\00install.out 2>&1 && cp ReadqPCR.Rcheck\00install.out ReadqPCR-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ReadqPCR.buildbin-libdir --install="check:ReadqPCR-install.out" --force-multiarch --no-vignettes --timings ReadqPCR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/ReadqPCR.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.16.0'
* 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 ... 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
* 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
.readLC480txt: no visible global function definition for
  'AnnotatedDataFrame'
read.LC480SampleInfo: no visible global function definition for
  'AnnotatedDataFrame'
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 '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 : .local: 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 : .local: no visible global function
  definition for 'pData'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'pData'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'varMetadata'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'phenoData'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'pData<-'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'varMetadata<-'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'phenoData<-'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'featureData'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'fData<-'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'featureData<-'
merge,eSet-AnnotatedDataFrame : .local: no visible global function
  definition for 'protocolData'
merge,eSet-AnnotatedDataFrame : .local: 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'
* 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' ... [3s] OK
** running examples for arch 'x64' ... [4s] 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
  'C:/biocbld/bbs-3.2-bioc/meat/ReadqPCR.Rcheck/00check.log'
for details.


ReadqPCR.Rcheck/00install.out:


install for i386

* installing *source* package 'ReadqPCR' ...
** 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 'ReadqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReadqPCR' as ReadqPCR_1.16.0.zip
* DONE (ReadqPCR)

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

nameusersystemelapsed
ReadqPCR-package000
merge0.120.000.12
qpcR2CyclesSet1.310.051.36
read.qPCR0.060.000.06
read.taqman0.340.000.35
readLC4800.130.000.12
readLC480SampleInfo000

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

nameusersystemelapsed
ReadqPCR-package000
merge0.250.000.25
qpcR2CyclesSet1.620.061.69
read.qPCR0.080.000.08
read.taqman0.410.000.40
readLC4800.120.000.13
readLC480SampleInfo0.020.000.01