Package: qpcrNorm

Version: 1.41.0

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_1.41.0.tar.gz

StartedAt: 2019-04-09 03:05:32 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:06:15 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 43.0 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_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qpcrNorm.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.41.0’
* 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 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’ ...
** 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
* DONE (qpcrNorm)

name	user	system	elapsed
calcCV	1.300	0.181	1.484
ctQc	0	0	0
matrixByPlate	0.168	0.011	0.179
normQpcrHouseKeepingGenes	0.006	0.001	0.007
normQpcrQuantile	0.180	0.009	0.190
normQpcrRankInvariant	0.481	0.121	0.605
plotVarMean	0	0	0
qpcrBatch-class	0.005	0.001	0.006
qpcrBatch.object	0.007	0.002	0.009
readQpcr	0	0	0
readQpcrBatch	0	0	0
writeQpcr	0.000	0.001	0.000