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CHECK report for NormqPCR on malbec2

This page was generated on 2018-10-17 08:23:45 -0400 (Wed, 17 Oct 2018).

Package 1000/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.26.0
James Perkins
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/NormqPCR
Branch: RELEASE_3_7
Last Commit: 43ca4a8
Last Changed Date: 2018-04-30 10:35:20 -0400 (Mon, 30 Apr 2018)
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  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: NormqPCR
Version: 1.26.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NormqPCR_1.26.0.tar.gz
StartedAt: 2018-10-16 02:23:26 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:25:06 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 100.2 seconds
RetCode: 0
Status:  OK 
CheckDir: NormqPCR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NormqPCR_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/NormqPCR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormqPCR/DESCRIPTION’ ... OK
* this is package ‘NormqPCR’ version ‘1.26.0’
* 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 ‘NormqPCR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
stabMeasureM: no visible global function definition for ‘sd’
ComputeNRQs,qPCRBatch: no visible global function definition for ‘effs’
ComputeNRQs,qPCRBatch: no visible global function definition for
  ‘se.effs’
CqValues,CyclesSet: no visible binding for global variable ‘l5’
CqValues,CyclesSet: no visible global function definition for ‘effs<-’
CqValues,CyclesSet: no visible global function definition for
  ‘se.effs<-’
combineTechReps,qPCRBatch: no visible binding for global variable
  ‘median’
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  ‘sd’
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  ‘median’
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  ‘mad’
deltaDeltaCt,qPCRBatch: no visible global function definition for ‘sd’
selectHKs,matrix: no visible global function definition for ‘sd’
stabMeasureRho,matrix: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate effs effs<- l5 mad median sd se.effs se.effs<-
Consider adding
  importFrom("stats", "aggregate", "mad", "median", "sd")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
CqValues 34.54  0.076  34.707
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.



Installation output

NormqPCR.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL NormqPCR
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘NormqPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘NormqPCR.Rnw’ 
** testing if installed package can be loaded
* DONE (NormqPCR)

Tests output


Example timings

NormqPCR.Rcheck/NormqPCR-Ex.timings

nameusersystemelapsed
Bladder0.0160.0000.015
BladderRepro0.0040.0000.006
Colon0.0080.0000.007
ComputeNRQs0.4880.0040.620
CqValues34.540 0.07634.707
NormqPCR-package000
combineTechReps0.0400.0000.049
combineTechRepsSD0.0720.0000.070
deltaCt0.0800.0000.089
deltaDeltaCt0.1040.0000.104
geNorm0.0040.0000.007
geomMean000
makeAllNAs0.0920.0000.091
makeAllNewVal0.0840.0000.085
replaceAboveCutOff0.0800.0000.077
replaceNAs0.0760.0000.077
selectHKs0.0280.0000.026
stabMeasureM0.1080.0000.110
stabMeasureRho0.0720.0040.076