Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

CHECK report for NormqPCR on merida1

This page was generated on 2019-04-16 11:55:38 -0400 (Tue, 16 Apr 2019).

Package 1062/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.28.0
James Perkins
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/NormqPCR
Branch: RELEASE_3_8
Last Commit: 562ece9
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: NormqPCR
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NormqPCR_1.28.0.tar.gz
StartedAt: 2019-04-16 01:36:23 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:38:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 137.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: NormqPCR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NormqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NormqPCR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/NormqPCR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormqPCR/DESCRIPTION’ ... OK
* this is package ‘NormqPCR’ version ‘1.28.0’
* 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 ‘/Users/biocbuild/bbs-3.8-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 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
CqValues,CyclesSet: no visible binding for global variable ‘l5’
Undefined global functions or variables:
  l5
* 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
Examples with CPU or elapsed time > 5s
           user system elapsed
CqValues 61.007  0.782  64.174
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/NormqPCR.Rcheck/00check.log’
for details.



Installation output

NormqPCR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NormqPCR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘NormqPCR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘NormqPCR.Rnw’ 
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (NormqPCR)

Tests output


Example timings

NormqPCR.Rcheck/NormqPCR-Ex.timings

nameusersystemelapsed
Bladder0.0200.0040.024
BladderRepro0.0090.0030.014
Colon0.0100.0020.013
ComputeNRQs0.3070.0050.317
CqValues61.007 0.78264.174
NormqPCR-package0.0010.0000.000
combineTechReps0.0660.0000.066
combineTechRepsSD0.1280.0010.131
deltaCt0.1440.0020.149
deltaDeltaCt0.1900.0010.194
geNorm0.0100.0020.013
geomMean000
makeAllNAs0.1500.0020.155
makeAllNewVal0.1790.0020.182
replaceAboveCutOff0.1500.0010.151
replaceNAs0.1550.0020.157
selectHKs0.0420.0030.045
stabMeasureM0.1940.0030.201
stabMeasureRho0.1300.0040.138