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BioC 3.6: CHECK report for affycomp on tokay1

This page was generated on 2017-08-16 13:26:12 -0400 (Wed, 16 Aug 2017).

Package 17/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycomp 1.53.0
Rafael A. Irizarry
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affycomp
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affycomp
Version: 1.53.0
Command: rm -rf affycomp.buildbin-libdir affycomp.Rcheck && mkdir affycomp.buildbin-libdir affycomp.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycomp.buildbin-libdir affycomp_1.53.0.tar.gz >affycomp.Rcheck\00install.out 2>&1 && cp affycomp.Rcheck\00install.out affycomp-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affycomp.buildbin-libdir --install="check:affycomp-install.out" --force-multiarch --no-vignettes --timings affycomp_1.53.0.tar.gz
StartedAt: 2017-08-15 21:36:42 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:38:50 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 128.1 seconds
RetCode: 0
Status:  OK  
CheckDir: affycomp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affycomp.buildbin-libdir affycomp.Rcheck && mkdir affycomp.buildbin-libdir affycomp.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycomp.buildbin-libdir affycomp_1.53.0.tar.gz >affycomp.Rcheck\00install.out 2>&1 && cp affycomp.Rcheck\00install.out affycomp-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affycomp.buildbin-libdir --install="check:affycomp-install.out" --force-multiarch --no-vignettes --timings affycomp_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affycomp.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 'affycomp/DESCRIPTION' ... OK
* this is package 'affycomp' version '1.53.0'
* 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 'affycomp' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'splines' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name =
  l$method.name, add.legend = FALSE, main = main): partial argument
  match of 'method.name' to 'method.names'
affycompPlot: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableAll: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableOverallSNR: warning in vector(mode = "character", len = N):
  partial argument match of 'len' to 'length'
tableRanks: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
affycomp.compfig2: no visible global function definition for 'plot'
affycomp.compfig2: no visible global function definition for 'lines'
affycomp.compfig2: no visible global function definition for 'legend'
affycomp.compfig2b: no visible global function definition for 'plot'
affycomp.compfig2b: no visible global function definition for 'lines'
affycomp.compfig2b: no visible global function definition for 'legend'
affycomp.compfig3: no visible global function definition for 'boxplot'
affycomp.compfig4a: no visible global function definition for 'plot'
affycomp.compfig4a: no visible global function definition for 'lines'
affycomp.compfig4a: no visible global function definition for 'legend'
affycomp.compfig4b: no visible global function definition for 'plot'
affycomp.compfig4b: no visible global function definition for 'lines'
affycomp.compfig4b: no visible global function definition for 'legend'
affycomp.compfig4b: no visible global function definition for 'abline'
affycomp.compfig4c: no visible global function definition for 'plot'
affycomp.compfig4c: no visible global function definition for 'lines'
affycomp.compfig4c: no visible global function definition for 'legend'
affycomp.compfig4c: no visible global function definition for 'abline'
affycomp.compfig5a: no visible global function definition for 'plot'
affycomp.compfig5a: no visible global function definition for 'lines'
affycomp.compfig5a: no visible global function definition for 'legend'
affycomp.compfig5b: no visible global function definition for 'plot'
affycomp.compfig5b: no visible global function definition for 'lines'
affycomp.compfig5b: no visible global function definition for 'legend'
affycomp.compfig5cde: no visible global function definition for 'plot'
affycomp.compfig5cde: no visible global function definition for 'lines'
affycomp.compfig5cde: no visible global function definition for
  'legend'
affycomp.compfig7: no visible global function definition for 'boxplot'
affycomp.compfigs: no visible global function definition for 'par'
affycomp.compfigs: no visible global function definition for
  'dev.interactive'
affycomp.figure1: no visible global function definition for
  'topo.colors'
affycomp.figure1: no visible global function definition for
  'heat.colors'
affycomp.figure1: no visible global function definition for 'plot'
affycomp.figure1: no visible global function definition for 'points'
affycomp.figure1: no visible global function definition for 'text'
affycomp.figure1b: no visible global function definition for
  'topo.colors'
affycomp.figure1b: no visible global function definition for
  'heat.colors'
affycomp.figure1b: no visible global function definition for 'plot'
affycomp.figure1b: no visible global function definition for 'points'
affycomp.figure1b: no visible global function definition for 'text'
affycomp.figure2: no visible global function definition for 'plot'
affycomp.figure3: no visible global function definition for 'plot'
affycomp.figure3: no visible global function definition for 'abline'
affycomp.figure3: no visible global function definition for 'points'
affycomp.figure4a: no visible global function definition for 'plot'
affycomp.figure4a: no visible global function definition for 'lines'
affycomp.figure4b: no visible global function definition for 'plot'
affycomp.figure4b: no visible global function definition for 'abline'
affycomp.figure5a: no visible global function definition for 'plot'
affycomp.figure6a: no visible global function definition for 'matplot'
affycomp.figure6a: no visible global function definition for 'lines'
affycomp.figure6a: no visible global function definition for 'abline'
affycomp.figure6b: no visible global function definition for 'plot'
affycomp.figure6b: no visible global function definition for 'lines'
affycomp.figure6b: no visible global function definition for 'abline'
affycomp.figure7: no visible global function definition for 'lm'
affycomp.figure7: no visible global function definition for 'plot'
affycomp.figure7: no visible global function definition for 'lines'
affycomp.figure7: no visible global function definition for 'abline'
affycomp.figures: no visible global function definition for 'par'
affycomp.figures: no visible global function definition for
  'dev.interactive'
assessDilution: no visible global function definition for 'exprs'
assessDilution: no visible global function definition for 'pData'
assessDilution : <anonymous>: no visible global function definition for
  'cor'
assessDilution : <anonymous>: no visible binding for global variable
  'sd'
assessDilution: no visible global function definition for 'lm'
assessDilution: no visible global function definition for 'median'
assessDilution: no visible global function definition for 'cor'
assessFC: no visible global function definition for 'exprs'
assessFC: no visible global function definition for 'pData'
assessFC: no visible global function definition for 'quantile'
assessFC: no visible global function definition for 'lm'
assessFC2: no visible global function definition for 'exprs'
assessFC2: no visible global function definition for 'pData'
assessLS: no visible global function definition for 'exprs'
assessLS: no visible global function definition for 'pData'
assessLS: no visible global function definition for 'featureNames'
assessLS: no visible global function definition for 'lm'
assessLS: no visible global function definition for 'cor'
assessMA: no visible global function definition for 'exprs'
assessMA: no visible global function definition for 'pData'
assessMA2: no visible global function definition for 'exprs'
assessMA2: no visible global function definition for 'pData'
assessMA2: no visible global function definition for 'featureNames'
assessMA2: no visible binding for global variable 'median'
assessSD: no visible global function definition for 'exprs'
assessSD: no visible global function definition for 'assayDataElement'
assessSD: no visible global function definition for 'pData'
assessSD : <anonymous>: no visible binding for global variable 'sd'
assessSD: no visible global function definition for 'cor'
assessSignal: no visible global function definition for 'exprs'
assessSignal: no visible global function definition for 'pData'
assessSignal: no visible global function definition for 'featureNames'
assessSignal: no visible global function definition for 'lm'
assessSpikeIn2: no visible global function definition for 'exprs'
assessSpikeInSD: no visible global function definition for 'pData'
assessSpikeInSD: no visible global function definition for
  'featureNames'
assessSpikeInSD: no visible global function definition for 'esApply'
assessSpikeInSD: no visible binding for global variable 'sd'
assessSpikeInSD: no visible global function definition for 'loess'
exprset.log: no visible global function definition for 'exprs'
exprset.log: no visible global function definition for 'exprs<-'
getData: no visible global function definition for 'data'
read.dilution: no visible global function definition for 'read.csv'
read.dilution: no visible global function definition for 'sampleNames'
read.dilution: no visible global function definition for 'new'
read.spikein: no visible global function definition for 'read.csv'
read.spikein: no visible global function definition for 'sampleNames'
read.spikein: no visible global function definition for 'new'
remove.hgu133a.xhyb: no visible global function definition for
  'featureNames'
tableMA2 : myauc: no visible global function definition for 'approx'
tableMA2: no visible global function definition for 'IQR'
tableMA2: no visible global function definition for 'quantile'
tableOverallSNR: no visible global function definition for 'median'
tableOverallSNR: no visible global function definition for 'IQR'
tableOverallSNR: no visible global function definition for 'quantile'
tableSD: no visible global function definition for 'IQR'
tableSpikeInSD: no visible global function definition for 'quantile'
Undefined global functions or variables:
  IQR abline addVigs2WinMenu approx assayDataElement boxplot cor data
  dev.interactive esApply exprs exprs<- featureNames heat.colors legend
  lines lm loess matplot median new pData par plot points quantile
  read.csv sampleNames sd text topo.colors
Consider adding
  importFrom("grDevices", "dev.interactive", "heat.colors",
             "topo.colors")
  importFrom("graphics", "abline", "boxplot", "legend", "lines",
             "matplot", "par", "plot", "points", "text")
  importFrom("methods", "new")
  importFrom("stats", "IQR", "approx", "cor", "lm", "loess", "median",
             "quantile", "sd")
  importFrom("utils", "data", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
** running examples for arch 'x64' ... OK
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/affycomp.Rcheck/00check.log'
for details.


affycomp.Rcheck/00install.out:


install for i386

* installing *source* package 'affycomp' ...
** R
** data
** 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 'affycomp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affycomp' as affycomp_1.53.0.zip
* DONE (affycomp)

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

nameusersystemelapsed
SD0.660.030.90
affycomp.compfigs.auxiliary0.490.031.79
affycomp.figures.auxiliary0.560.030.60
affycomp.table0.440.000.44
affycompPlot1.060.061.12

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

nameusersystemelapsed
SD0.900.060.95
affycomp.compfigs.auxiliary0.700.030.74
affycomp.figures.auxiliary0.630.050.68
affycomp.table0.370.010.39
affycompPlot1.380.051.42