BioC 3.4: CHECK report for trackViewer on morelia

Package: trackViewer

Version: 1.9.14

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trackViewer_1.9.14.tar.gz

StartedAt: 2016-09-20 14:00:14 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 14:04:58 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 283.9 seconds

RetCode: 0

Status:  OK

CheckDir: trackViewer.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 trackViewer_1.9.14.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/trackViewer.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.9.14’
* 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 ‘trackViewer’ 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 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
geneModelFromTxdb: no visible global function definition for 'columns'
lolliplot: no visible binding for global variable 'stack.factors'
Undefined global functions or variables:
  columns stack.factors
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trackViewer-package 15.060  0.199  15.265
parseWIG             9.021  0.050   9.077
viewTracks           8.489  0.041   8.536
geneModelFromTxdb    7.266  0.376  18.253
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/trackViewer.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GRoperator	0.516	0.011	0.527
addArrowMark	0.008	0.000	0.009
addGuideLine	0.004	0.000	0.005
coverageGR	0.289	0.002	0.291
dandelion.plot	1.319	0.006	1.326
geneModelFromTxdb	7.266	0.376	18.253
getCurTrackViewport	0.003	0.000	0.003
importBam	0.218	0.008	0.241
importData	1.259	0.015	1.322
importScore	0.627	0.021	0.648
lolliplot	0.552	0.006	0.559
optimizeStyle	0.889	0.016	0.906
parse2GRanges	0.007	0.000	0.008
parseWIG	9.021	0.050	9.077
plotGRanges	0.794	0.010	0.805
track	0.037	0.001	0.038
trackViewer-package	15.060	0.199	15.265
trackViewerStyle	0	0	0
viewTracks	8.489	0.041	8.536