BioC 3.4: CHECK report for OperaMate on morelia

Package: OperaMate

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OperaMate_1.6.0.tar.gz

StartedAt: 2017-04-15 05:51:42 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 05:54:06 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 143.4 seconds

RetCode: 0

Status:  OK

CheckDir: OperaMate.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OperaMate_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/OperaMate.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OperaMate/DESCRIPTION’ ... OK
* this is package ‘OperaMate’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OperaMate’ 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
* 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
cellData: no visible global function definition for ‘combn’
cellSigAnalysis: no visible global function definition for
  ‘write.table’
cellSigPlot: no visible binding for global variable ‘strwidth’
cellSigPlot: no visible binding for global variable ‘strheight’
fitStable: no visible global function definition for ‘abline’
generateReport: no visible global function definition for ‘write.table’
operaMate : configParser: no visible global function definition for
  ‘read.csv’
parseFullTab: no visible global function definition for ‘read.delim’
parseMatrix: no visible global function definition for ‘read.delim’
parseTab: no visible global function definition for ‘read.delim’
wellQC : <anonymous>: no visible global function definition for
  ‘boxplot’
wellQC: no visible global function definition for ‘boxplot’
cellNorm,cellData: no visible global function definition for
  ‘capture.output’
show,cellData: no visible global function definition for ‘str’
show,expData: no visible global function definition for ‘str’
Undefined global functions or variables:
  abline boxplot capture.output combn read.csv read.delim str strheight
  strwidth write.table
Consider adding
  importFrom("graphics", "abline", "boxplot", "strheight", "strwidth")
  importFrom("utils", "capture.output", "combn", "read.csv",
             "read.delim", "str", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
operaMate 55.844  1.343  67.645
cellViz   14.908  0.399  15.729
* 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/OperaMate.Rcheck/00check.log’
for details.

* installing *source* package ‘OperaMate’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OperaMate)

name	user	system	elapsed
cellData-class	0.003	0.000	0.002
cellLoad	0.567	0.009	0.579
cellMean	0.013	0.001	0.015
cellNorm	0.048	0.001	0.050
cellNumLoad	0.007	0.001	0.008
cellQC	0.260	0.014	0.277
cellSig	0.699	0.016	0.718
cellSigAnalysis	0.935	0.007	3.126
cellSigAnalysisPlot	0.303	0.011	2.441
cellSigPlot	0.338	0.010	0.359
cellViz	14.908	0.399	15.729
data	0.013	0.002	0.016
expData-class	0.007	0.000	0.008
generateReport	0.028	0.002	0.030
loadAll	0.520	0.003	0.523
operaMate	55.844	1.343	67.645
parseTemplete	0.050	0.001	0.053