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BioC 3.0: CHECK report for ReadqPCR on oaxaca

This page was generated on 2015-04-10 10:05:07 -0700 (Fri, 10 Apr 2015).

Package 733/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReadqPCR 1.12.0
James Perkins
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ReadqPCR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: ReadqPCR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ReadqPCR_1.12.0.tar.gz
StartedAt: 2015-04-10 02:41:37 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:42:25 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 48.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ReadqPCR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ReadqPCR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ReadqPCR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReadqPCR/DESCRIPTION’ ... OK
* this is package ‘ReadqPCR’ version ‘1.12.0’
* 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 ... [3s/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 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,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’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ReadqPCR.Rcheck/00check.log’
for details.

ReadqPCR.Rcheck/00install.out:

* 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
* DONE (ReadqPCR)

ReadqPCR.Rcheck/ReadqPCR-Ex.timings:

nameusersystemelapsed
ReadqPCR-package0.0010.0000.001
merge0.2620.0050.270
qpcR2CyclesSet3.1100.0893.356
read.qPCR0.1420.0070.150
read.taqman0.7010.0140.717
readLC4800.2740.0050.280
readLC480SampleInfo0.0120.0010.013