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BioC 3.5: CHECK report for NormqPCR on malbec2

This page was generated on 2017-10-18 14:14:12 -0400 (Wed, 18 Oct 2017).

Package 903/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.22.0
James Perkins
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/NormqPCR
Branch: RELEASE_3_5
Last Commit: d827b79
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: NormqPCR
Version: 1.22.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.22.0.tar.gz
StartedAt: 2017-10-18 01:12:12 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:14:08 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: NormqPCR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NormqPCR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/NormqPCR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.22.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/home/biocbuild/bbs-3.5-bioc/meat/NormqPCR.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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 35.928  0.044  36.053
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.


NormqPCR.Rcheck/00install.out:

* installing *source* package ‘NormqPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (NormqPCR)

NormqPCR.Rcheck/NormqPCR-Ex.timings:

nameusersystemelapsed
Bladder0.0440.0080.052
BladderRepro0.0200.0000.019
Colon0.0040.0000.007
ComputeNRQs0.5200.0280.585
CqValues35.928 0.04436.053
NormqPCR-package000
combineTechReps0.1200.0000.124
combineTechRepsSD0.0720.0000.074
deltaCt0.0920.0000.094
deltaDeltaCt0.2240.0000.225
geNorm0.0040.0000.007
geomMean000
makeAllNAs0.1040.0000.105
makeAllNewVal0.0960.0000.092
replaceAboveCutOff0.0880.0000.087
replaceNAs0.0920.0000.092
selectHKs0.0480.0000.047
stabMeasureM0.1400.0000.142
stabMeasureRho0.0800.0000.077