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BioC 3.5: CHECK report for NormqPCR on tokay2

This page was generated on 2017-08-16 13:21:10 -0400 (Wed, 16 Aug 2017).

Package 903/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.22.0
James Perkins
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/NormqPCR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK 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: rm -rf NormqPCR.buildbin-libdir NormqPCR.Rcheck && mkdir NormqPCR.buildbin-libdir NormqPCR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NormqPCR.buildbin-libdir NormqPCR_1.22.0.tar.gz >NormqPCR.Rcheck\00install.out 2>&1 && cp NormqPCR.Rcheck\00install.out NormqPCR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=NormqPCR.buildbin-libdir --install="check:NormqPCR-install.out" --force-multiarch --no-vignettes --timings NormqPCR_1.22.0.tar.gz
StartedAt: 2017-08-16 01:38:10 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:41:45 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 215.7 seconds
RetCode: 0
Status:  OK  
CheckDir: NormqPCR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf NormqPCR.buildbin-libdir NormqPCR.Rcheck && mkdir NormqPCR.buildbin-libdir NormqPCR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NormqPCR.buildbin-libdir NormqPCR_1.22.0.tar.gz >NormqPCR.Rcheck\00install.out 2>&1 && cp NormqPCR.Rcheck\00install.out NormqPCR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=NormqPCR.buildbin-libdir --install="check:NormqPCR-install.out" --force-multiarch --no-vignettes --timings NormqPCR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/NormqPCR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
CqValues 41.13   0.07   42.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
CqValues 47.5   0.05   47.59
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/NormqPCR.Rcheck/00check.log'
for details.


NormqPCR.Rcheck/00install.out:


install for i386

* installing *source* package 'NormqPCR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'NormqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormqPCR' as NormqPCR_1.22.0.zip
* DONE (NormqPCR)

NormqPCR.Rcheck/examples_i386/NormqPCR-Ex.timings:

nameusersystemelapsed
Bladder0.060.010.08
BladderRepro0.010.000.02
Colon0.010.000.02
ComputeNRQs0.500.000.59
CqValues41.13 0.0742.02
NormqPCR-package000
combineTechReps0.110.000.11
combineTechRepsSD0.080.000.08
deltaCt0.080.000.07
deltaDeltaCt0.260.000.27
geNorm0.020.000.02
geomMean000
makeAllNAs0.120.000.12
makeAllNewVal0.100.000.09
replaceAboveCutOff0.100.000.11
replaceNAs0.080.000.08
selectHKs0.050.010.06
stabMeasureM0.120.020.14
stabMeasureRho0.110.010.13

NormqPCR.Rcheck/examples_x64/NormqPCR-Ex.timings:

nameusersystemelapsed
Bladder0.070.020.09
BladderRepro0.050.010.06
Colon0.010.000.01
ComputeNRQs0.550.000.55
CqValues47.50 0.0547.59
NormqPCR-package000
combineTechReps0.120.000.13
combineTechRepsSD0.100.000.09
deltaCt0.090.000.10
deltaDeltaCt0.250.000.25
geNorm0.000.010.01
geomMean000
makeAllNAs0.100.020.11
makeAllNewVal0.090.000.10
replaceAboveCutOff0.090.000.09
replaceNAs0.100.000.09
selectHKs0.060.000.07
stabMeasureM0.160.000.15
stabMeasureRho0.090.020.11