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BioC 3.4: CHECK report for NormqPCR on tokay1

This page was generated on 2017-04-15 16:16:47 -0400 (Sat, 15 Apr 2017).

Package 847/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormqPCR 1.20.0
James Perkins
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/NormqPCR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: NormqPCR
Version: 1.20.0
Command: rm -rf NormqPCR.buildbin-libdir NormqPCR.Rcheck && mkdir NormqPCR.buildbin-libdir NormqPCR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NormqPCR.buildbin-libdir NormqPCR_1.20.0.tar.gz >NormqPCR.Rcheck\00install.out 2>&1 && cp NormqPCR.Rcheck\00install.out NormqPCR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=NormqPCR.buildbin-libdir --install="check:NormqPCR-install.out" --force-multiarch --no-vignettes --timings NormqPCR_1.20.0.tar.gz
StartedAt: 2017-04-14 23:50:34 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:53:52 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 197.6 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NormqPCR.buildbin-libdir NormqPCR_1.20.0.tar.gz >NormqPCR.Rcheck\00install.out 2>&1 && cp NormqPCR.Rcheck\00install.out NormqPCR-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=NormqPCR.buildbin-libdir --install="check:NormqPCR-install.out" --force-multiarch --no-vignettes --timings NormqPCR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/NormqPCR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.20.0'
* 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 40.43    0.1   41.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
CqValues 53.39   0.04   53.55
* 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-3.4-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_1.20.0.zip
* DONE (NormqPCR)

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

nameusersystemelapsed
Bladder0.020.000.01
BladderRepro0.000.020.02
Colon0.000.010.01
ComputeNRQs0.250.000.36
CqValues40.43 0.1041.49
NormqPCR-package000
combineTechReps0.050.000.04
combineTechRepsSD0.050.000.05
deltaCt0.070.000.08
deltaDeltaCt0.130.000.12
geNorm0.000.010.02
geomMean000
makeAllNAs0.080.000.08
makeAllNewVal0.090.000.09
replaceAboveCutOff0.100.000.09
replaceNAs0.070.000.08
selectHKs0.030.000.03
stabMeasureM0.040.000.04
stabMeasureRho0.030.000.03

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

nameusersystemelapsed
Bladder0.010.000.02
BladderRepro0.020.000.01
Colon0.000.020.02
ComputeNRQs0.450.000.45
CqValues53.39 0.0453.55
NormqPCR-package000
combineTechReps0.060.000.06
combineTechRepsSD0.070.000.06
deltaCt0.090.000.10
deltaDeltaCt0.130.000.12
geNorm0.010.000.02
geomMean000
makeAllNAs0.110.000.11
makeAllNewVal0.170.000.17
replaceAboveCutOff0.140.000.14
replaceNAs0.150.000.15
selectHKs0.040.000.03
stabMeasureM0.040.000.05
stabMeasureRho0.000.030.03