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BioC 3.5: CHECK report for EDASeq on tokay2

This page was generated on 2017-10-18 14:21:28 -0400 (Wed, 18 Oct 2017).

Package 386/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDASeq 2.10.0
Davide Risso
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/EDASeq
Branch: RELEASE_3_5
Last Commit: 4d90eb7
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EDASeq
Version: 2.10.0
Command: rm -rf EDASeq.buildbin-libdir EDASeq.Rcheck && mkdir EDASeq.buildbin-libdir EDASeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EDASeq.buildbin-libdir EDASeq_2.10.0.tar.gz >EDASeq.Rcheck\00install.out 2>&1 && cp EDASeq.Rcheck\00install.out EDASeq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=EDASeq.buildbin-libdir --install="check:EDASeq-install.out" --force-multiarch --no-vignettes --timings EDASeq_2.10.0.tar.gz
StartedAt: 2017-10-17 23:30:51 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:37:46 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 414.4 seconds
RetCode: 0
Status:  OK  
CheckDir: EDASeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EDASeq.buildbin-libdir EDASeq.Rcheck && mkdir EDASeq.buildbin-libdir EDASeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EDASeq.buildbin-libdir EDASeq_2.10.0.tar.gz >EDASeq.Rcheck\00install.out 2>&1 && cp EDASeq.Rcheck\00install.out EDASeq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=EDASeq.buildbin-libdir --install="check:EDASeq-install.out" --force-multiarch --no-vignettes --timings EDASeq_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/EDASeq.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EDASeq/DESCRIPTION' ... OK
* this is package 'EDASeq' version '2.10.0'
* 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 'EDASeq' 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
* 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
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.availableOrgPkgs: no visible global function definition for
  'available.packages'
.gcLoess : ff: no visible global function definition for 'quantile'
.gcLoess : ff: no visible global function definition for 'loess'
.gcLoess : ff: no visible global function definition for 'predict'
.gcLoess : ff: no visible global function definition for 'median'
.gcQuant: no visible global function definition for 'quantile'
.gcQuant : f : <anonymous>: no visible global function definition for
  'median'
.gcQuant : f : <anonymous>: no visible global function definition for
  'quantile'
.isAvailable: no visible global function definition for 'biocLite'
newSeqExpressionSet: no visible global function definition for 'new'
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for 'smoothScatter'
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for 'lines'
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for 'lowess'
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for 'abline'
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for 'points'
MDPlot,matrix-numeric: no visible global function definition for
  'smoothScatter'
MDPlot,matrix-numeric: no visible global function definition for
  'lines'
MDPlot,matrix-numeric: no visible global function definition for
  'lowess'
MDPlot,matrix-numeric: no visible global function definition for
  'abline'
MDPlot,matrix-numeric: no visible global function definition for
  'points'
barplot,BamFileList: no visible global function definition for
  'countBam'
betweenLaneNormalization,matrix: no visible binding for global variable
  'quantile'
betweenLaneNormalization,matrix: no visible binding for global variable
  'median'
biasBoxplot,numeric-numeric: no visible global function definition for
  'quantile'
biasBoxplot,numeric-numeric: no visible global function definition for
  'abline'
biasPlot,matrix-numeric: no visible global function definition for
  'lowess'
biasPlot,matrix-numeric: no visible global function definition for
  'lines'
boxplot,FastqQuality: no visible global function definition for 'as'
counts<-,SeqExpressionSet-ANY: no visible global function definition
  for 'validObject'
exprs<-,SeqExpressionSet-ANY: no visible global function definition for
  'validObject'
initialize,SeqExpressionSet: no visible global function definition for
  'callNextMethod'
meanVarPlot,SeqExpressionSet: no visible global function definition for
  'quantile'
meanVarPlot,SeqExpressionSet: no visible global function definition for
  'smoothScatter'
meanVarPlot,SeqExpressionSet: no visible global function definition for
  'lines'
meanVarPlot,SeqExpressionSet: no visible global function definition for
  'abline'
meanVarPlot,SeqExpressionSet: no visible global function definition for
  'lowess'
normCounts<-,SeqExpressionSet: no visible global function definition
  for 'validObject'
offst<-,SeqExpressionSet: no visible global function definition for
  'validObject'
plot,BamFileList-FastqFileList: no visible global function definition
  for 'elementMetadata'
plot,BamFileList-FastqFileList: no visible global function definition
  for 'countBam'
plotNtFrequency,BamFile: no visible global function definition for
  'matplot'
plotNtFrequency,BamFile: no visible global function definition for
  'abline'
plotNtFrequency,BamFile: no visible global function definition for
  'legend'
plotNtFrequency,ShortRead: no visible global function definition for
  'matplot'
plotNtFrequency,ShortRead: no visible global function definition for
  'abline'
plotNtFrequency,ShortRead: no visible global function definition for
  'legend'
plotPCA,matrix: no visible global function definition for 'text'
plotPCA,matrix: no visible global function definition for 'pairs'
plotQuality,BamFile: no visible global function definition for
  'rainbow'
plotQuality,BamFile: no visible global function definition for 'path'
plotQuality,BamFile: no visible global function definition for 'narrow'
plotQuality,BamFile: no visible global function definition for 'as'
plotQuality,BamFileList: no visible global function definition for
  'rainbow'
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for 'path'
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for 'narrow'
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for 'as'
plotQuality,BamFileList: no visible global function definition for
  'lines'
plotQuality,FastqFileList: no visible global function definition for
  'rainbow'
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for 'quality'
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for 'path'
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for 'narrow'
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for 'as'
plotQuality,FastqFileList: no visible global function definition for
  'lines'
plotRLE,matrix: no visible global function definition for 'abline'
updateObject,SeqExpressionSet: no visible global function definition
  for 'callNextMethod'
Undefined global functions or variables:
  abline as available.packages biocLite callNextMethod countBam
  elementMetadata legend lines loess lowess matplot median narrow new
  pairs path points predict quality quantile rainbow smoothScatter text
  validObject
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "matplot", "pairs",
             "points", "smoothScatter", "text")
  importFrom("methods", "as", "callNextMethod", "new", "validObject")
  importFrom("stats", "loess", "lowess", "median", "predict", "quantile")
  importFrom("utils", "available.packages")
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
Examples with CPU or elapsed time > 5s
                          user system elapsed
getGeneLengthAndGCContent 9.85   0.26   14.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getGeneLengthAndGCContent 5.34   0.07    9.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'getLengthAndGC.R'
  Running 'plots.R'
 OK
** running tests for arch 'x64' ...
  Running 'getLengthAndGC.R'
  Running 'plots.R'
 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/EDASeq.Rcheck/00check.log'
for details.

EDASeq.Rcheck/00install.out:


install for i386

* installing *source* package 'EDASeq' ...
** 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 'EDASeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EDASeq' as EDASeq_2.10.0.zip
* DONE (EDASeq)

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

nameusersystemelapsed
MDPlot-methods0.410.030.53
SeqExpressionSet-class0.270.010.28
betweenLaneNormalization-methods0.140.030.17
biasBoxplot-methods0.200.020.22
biasPlot-methods0.310.030.35
getGeneLengthAndGCContent 9.85 0.2614.87
newSeqExpressionSet0.100.000.11
plotPCA-methods1.580.101.67
plotRLE-methods0.710.040.75
withinLaneNormalization-methods0.370.050.43

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

nameusersystemelapsed
MDPlot-methods0.300.000.29
SeqExpressionSet-class0.220.000.22
betweenLaneNormalization-methods0.100.020.11
biasBoxplot-methods0.110.000.11
biasPlot-methods0.170.010.18
getGeneLengthAndGCContent5.340.079.55
newSeqExpressionSet0.130.000.13
plotPCA-methods0.970.010.98
plotRLE-methods0.570.000.58
withinLaneNormalization-methods0.350.020.36