BioC 3.0: CHECK report for GenoView on oaxaca

Package: GenoView

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenoView_1.0.0.tar.gz

StartedAt: 2015-04-10 00:00:49 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:07:25 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 396.5 seconds

RetCode: 0

Status:  OK

CheckDir: GenoView.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 --no-multiarch GenoView_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenoView.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenoView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenoView’ version ‘1.0.0’
* 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 ‘GenoView’ can be installed ... [34s/35s] 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
intSel: no visible global function definition for ‘IRanges’
makeGR: no visible global function definition for ‘IRanges’
makeGR: no visible global function definition for ‘seqlevels<-’
makeGR: no visible global function definition for ‘keepSeqlevels’
makeGR: no visible global function definition for ‘seqlengths<-’
mepGUI: no visible global function definition for ‘metadata’
mepHuman: no visible global function definition for ‘seqlengths’
mepHuman: no visible binding for global variable ‘pfam.df’
mepHuman: no visible global function definition for ‘IRanges’
mepTxtInt: no visible global function definition for ‘metadata’
mutExonPlot: no visible global function definition for ‘%over%’
updatePFAM: no visible global function definition for ‘IRanges’
* 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 ... [20s/22s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenoView.Rcheck/00check.log’
for details.

* installing *source* package ‘GenoView’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenoView)

name	user	system	elapsed
GenoView-package	0.002	0.000	0.003
PFAMIDE	0.000	0.000	0.001
colSel	0.001	0.000	0.001
intSel	0.074	0.000	0.074
makeGR	0.172	0.003	0.204
makePFAMObjs	1.631	0.314	2.384
mep-Interfaces	0.002	0.000	0.002
mepHuman	0.003	0.000	0.003
mutExonPlot	0.001	0.001	0.002
notebookVis	0.001	0.000	0.002
pfam.df	0.002	0.000	0.003
plotExonRect	0.441	0.011	0.514
printOption	0.001	0.001	0.002
sample.mut.df	0	0	0
updatePFAM	0.001	0.000	0.002