BioC 3.3: CHECK report for trackViewer on morelia

Package: trackViewer

Version: 1.7.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trackViewer_1.7.10.tar.gz

StartedAt: 2016-04-21 08:13:56 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 08:19:42 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 345.7 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_1.7.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/trackViewer.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.7.10’
* 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 ... [25s/25s] 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
GRbin: no visible global function definition for 'queryHits'
GRbin: no visible global function definition for 'subjectHits'
coverageGR: no visible global function definition for 'subjectHits'
coverageGR: no visible global function definition for 'queryHits'
dandelion.plot: no visible global function definition for 'queryHits'
disjoinGRs: no visible global function definition for 'subjectHits'
disjoinGRs: no visible global function definition for 'queryHits'
geneModelFromTxdb: no visible global function definition for
  'subjectHits'
geneModelFromTxdb: no visible global function definition for 'columns'
grid.dandelion: no visible global function definition for 'col2rgb'
grid.lollipop: no visible global function definition for 'col2rgb'
importScore : filterByRange: no visible global function definition for
  'queryHits'
lolliplot: no visible global function definition for 'queryHits'
optimizeStyle: no visible global function definition for 'palette'
Undefined global functions or variables:
  col2rgb columns palette queryHits subjectHits
Consider adding
  importFrom("grDevices", "col2rgb", "palette")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [79s/79s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trackViewer-package 21.401  0.303  21.790
parseWIG            12.768  0.049  12.860
viewTracks          12.112  0.053  12.201
geneModelFromTxdb    8.924  0.487   9.437
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/13s]
 [13s/13s] 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-3.3-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	0.885	0.041	0.929
addArrowMark	0.012	0.001	0.012
addGuideLine	0.006	0.000	0.007
coverageGR	0.341	0.005	0.351
dandelion.plot	1.967	0.013	1.988
geneModelFromTxdb	8.924	0.487	9.437
getCurTrackViewport	0.005	0.000	0.005
importBam	0.326	0.003	0.329
importData	1.609	0.031	1.659
importScore	0.864	0.036	0.903
lolliplot	0.946	0.005	0.960
optimizeStyle	0.846	0.010	0.857
parse2GRanges	0.012	0.000	0.011
parseWIG	12.768	0.049	12.860
plotGRanges	1.173	0.003	1.184
track	0.065	0.001	0.066
trackViewer-package	21.401	0.303	21.790
trackViewerStyle	0.001	0.000	0.001
viewTracks	12.112	0.053	12.201