BioC 3.1: CHECK report for Rolexa on morelia

Package: Rolexa

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rolexa_1.24.0.tar.gz

StartedAt: 2015-10-09 05:51:11 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:53:37 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 146.6 seconds

RetCode: 0

Status:  OK

CheckDir: Rolexa.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rolexa_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Rolexa.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rolexa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rolexa’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘fork’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rolexa’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graphics’ ‘grDevices’ ‘methods’ ‘ShortRead’
A package should be listed in only one of these fields.
* 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
* 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
ChannelHistogram,SolexaIntensity : .local: warning in Mclust(data, G =
  G, model = "V"): partial argument match of 'model' to 'modelNames'
ChannelHistogram,SolexaIntensity : .local: warning in
  mclust1Dplot(data, parameters = hist$parameters, z = hist$z, what =
  "density", xlab = "Intensity", col = "red", new = TRUE): partial
  argument match of 'col' to 'colors'
ForkBatch: no visible binding for global variable ‘Rolexa.env’
ForkBatch: no visible global function definition for ‘fork’
ForkBatch: no visible global function definition for ‘wait’
QualityBoxPlots: no visible binding for global variable ‘Rolexa.env’
BatchAnalysis,RolexaRun : .local: no visible binding for global
  variable ‘Rolexa.env’
CombineFastQ,RolexaRun-SolexaPath : .local: no visible binding for
  global variable ‘Rolexa.env’
CombineReads,RolexaRun-SolexaPath : .local: no visible binding for
  global variable ‘Rolexa.env’
CombinedPlot,RolexaRun : .local: no visible binding for global variable
  ‘Rolexa.env’
FilterResults,RolexaRun : .local: no visible binding for global
  variable ‘Rolexa.env’
FilterResults,RolexaRun : .local: possible error in DNAStringSet(read2
  = apply(str[nrow + I, ], 1, paste, collapse = "")): unused argument
  (read2 = apply(str[nrow + I, ], 1, paste, collapse = ""))
OneBatch,RolexaRun : .local: no visible binding for global variable
  ‘Rolexa.env’
PlotCycles,RolexaRun : .local: no visible binding for global variable
  ‘Rolexa.env’
SaveResults,RolexaRun : .local: no visible binding for global variable
  ‘Rolexa.env’
SeqScore,RolexaRun : .local: no visible binding for global variable
  ‘Rolexa.env’
TileNormalize,RolexaRun : .local: no visible binding for global
  variable ‘Rolexa.env’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/Rolexa.Rcheck/00check.log’
for details.

* installing *source* package ‘Rolexa’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Rolexa)

name	user	system	elapsed
Batch	0.005	0.000	0.004
Model1	3.988	0.355	4.377
Model3	0.290	0.083	0.372
Plots1	0.959	0.082	1.043
Plots2	0.141	0.003	0.145
Plots3	0.115	0.024	0.269