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BioC 3.5: CHECK report for qpcrNorm on veracruz2

This page was generated on 2017-08-16 13:28:32 -0400 (Wed, 16 Aug 2017).

Package 1038/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpcrNorm 1.34.0
Jessica Mar
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/qpcrNorm
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: qpcrNorm
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qpcrNorm_1.34.0.tar.gz
StartedAt: 2017-08-16 06:54:14 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:54:59 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 45.2 seconds
RetCode: 0
Status:  OK 
CheckDir: qpcrNorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qpcrNorm_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/qpcrNorm.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpcrNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qpcrNorm’ version ‘1.34.0’
* 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 ‘qpcrNorm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
'library' or 'require' calls to packages already attached by Depends:
  ‘affy’ ‘limma’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘Biobase’
  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
calcCV : <anonymous>: no visible global function definition for ‘sd’
normQpcrRankInvariant: no visible global function definition for
  ‘median’
normQpcrRankInvariant: no visible binding for global variable ‘median’
plotVarMean: no visible binding for global variable ‘var’
plotVarMean: no visible global function definition for ‘plot’
plotVarMean: no visible global function definition for ‘abline’
plotVarMean: no visible global function definition for ‘lines’
plotVarMean: no visible global function definition for ‘lowess’
readQpcr: no visible global function definition for ‘read.table’
writeQpcr: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline lines lowess median plot read.table sd var write.table
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lowess", "median", "sd", "var")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.5-bioc/meat/qpcrNorm.Rcheck/00check.log’
for details.


qpcrNorm.Rcheck/00install.out:

* installing *source* package ‘qpcrNorm’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qpcrNorm)

qpcrNorm.Rcheck/qpcrNorm-Ex.timings:

nameusersystemelapsed
calcCV1.3010.0461.368
ctQc0.0000.0000.001
matrixByPlate0.1440.0030.154
normQpcrHouseKeepingGenes0.0060.0010.009
normQpcrQuantile0.1260.0030.130
normQpcrRankInvariant0.6140.0070.643
plotVarMean000
qpcrBatch-class0.0070.0010.008
qpcrBatch.object0.0050.0000.005
readQpcr0.0010.0000.000
readQpcrBatch000
writeQpcr000