Package: qpcrNorm

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qpcrNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qpcrNorm_1.42.0.tar.gz

StartedAt: 2019-10-16 05:52:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:53:50 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 60.6 seconds

RetCode: 0

Status:  OK

CheckDir: qpcrNorm.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qpcrNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qpcrNorm_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qpcrNorm.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.42.0’
* 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 : : 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 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-3.9-bioc/meat/qpcrNorm.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qpcrNorm
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘qpcrNorm’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qpcrNorm)

name	user	system	elapsed
calcCV	1.520	0.421	1.944
ctQc	0.000	0.000	0.001
matrixByPlate	0.185	0.027	0.213
normQpcrHouseKeepingGenes	0.011	0.005	0.015
normQpcrQuantile	0.201	0.042	0.244
normQpcrRankInvariant	0.796	0.286	1.085
plotVarMean	0.000	0.001	0.001
qpcrBatch-class	0.008	0.004	0.012
qpcrBatch.object	0.008	0.003	0.012
readQpcr	0.001	0.000	0.000
readQpcrBatch	0.000	0.001	0.000
writeQpcr	0.001	0.000	0.000