BioC 3.2: CHECK report for EDASeq on moscato1

Package: EDASeq

Version: 2.4.1

Command: rm -rf EDASeq.buildbin-libdir EDASeq.Rcheck && mkdir EDASeq.buildbin-libdir EDASeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EDASeq.buildbin-libdir EDASeq_2.4.1.tar.gz >EDASeq.Rcheck\00install.out 2>&1 && cp EDASeq.Rcheck\00install.out EDASeq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=EDASeq.buildbin-libdir --install="check:EDASeq-install.out" --force-multiarch --no-vignettes --timings EDASeq_2.4.1.tar.gz

StartedAt: 2016-04-23 01:56:33 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:05:58 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 564.4 seconds

RetCode: 0

Status:  OK

CheckDir: EDASeq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf EDASeq.buildbin-libdir EDASeq.Rcheck && mkdir EDASeq.buildbin-libdir EDASeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EDASeq.buildbin-libdir EDASeq_2.4.1.tar.gz >EDASeq.Rcheck\00install.out 2>&1 && cp EDASeq.Rcheck\00install.out EDASeq-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=EDASeq.buildbin-libdir --install="check:EDASeq-install.out" --force-multiarch --no-vignettes --timings EDASeq_2.4.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/EDASeq.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '2.4.1'
* 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
.isAvailable: no visible global function definition for 'biocLite'
barplot,BamFileList : .local: no visible global function definition for
  'countBam'
plot,BamFileList-FastqFileList : .local: no visible global function
  definition for 'elementMetadata'
plot,BamFileList-FastqFileList : .local: no visible global function
  definition for 'countBam'
plotQuality,BamFile : .local: no visible global function definition for
  'path'
plotQuality,BamFile : .local: no visible global function definition for
  'narrow'
plotQuality,BamFileList : .local : <anonymous>: no visible global
  function definition for 'path'
plotQuality,BamFileList : .local : <anonymous>: no visible global
  function definition for 'narrow'
plotQuality,FastqFileList : .local : <anonymous>: no visible global
  function definition for 'quality'
plotQuality,FastqFileList : .local : <anonymous>: no visible global
  function definition for 'path'
plotQuality,FastqFileList : .local : <anonymous>: no visible global
  function definition for 'narrow'
* 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' ... [61s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getGeneLengthAndGCContent 11.55   0.05   41.82
** running examples for arch 'x64' ... [67s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getGeneLengthAndGCContent 6.71   0.08   45.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'plotPCA.R' [17s]
 [18s] OK
** running tests for arch 'x64' ...
  Running 'plotPCA.R' [16s]
 [16s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/EDASeq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'EDASeq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'barplot' from package 'graphics' in package 'EDASeq'
** 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_2.4.1.zip
* DONE (EDASeq)

name	user	system	elapsed
MDPlot-methods	0.85	0.01	1.21
SeqExpressionSet-class	0.10	0.00	0.11
betweenLaneNormalization-methods	0.24	0.00	0.27
biasBoxplot-methods	0.14	0.02	0.15
biasPlot-methods	0.33	0.00	0.33
getGeneLengthAndGCContent	11.55	0.05	41.82
newSeqExpressionSet	0.03	0.00	0.03
plotPCA-methods	0.76	0.01	1.50
plotRLE-methods	0.66	0.02	0.67
withinLaneNormalization-methods	0.74	0.01	0.74

name	user	system	elapsed
MDPlot-methods	0.37	0.02	0.39
SeqExpressionSet-class	0.09	0.00	0.09
betweenLaneNormalization-methods	0.58	0.01	0.60
biasBoxplot-methods	0.10	0.03	0.13
biasPlot-methods	0.31	0.02	0.32
getGeneLengthAndGCContent	6.71	0.08	45.28
newSeqExpressionSet	0.03	0.00	0.03
plotPCA-methods	1.25	0.03	1.28
plotRLE-methods	1.78	0.02	1.80
withinLaneNormalization-methods	0.31	0.01	0.32