BioC 3.3: CHECK report for trackViewer on zin2

Package: trackViewer

Version: 1.8.4

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings trackViewer_1.8.4.tar.gz

StartedAt: 2016-10-13 07:31:47 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:36:21 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 274.2 seconds

RetCode: 0

Status:  OK

CheckDir: trackViewer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings trackViewer_1.8.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/trackViewer.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.4’
* 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
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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trackViewer-package 16.765  0.025  16.855
parseWIG             9.681  0.002   9.704
viewTracks           9.269  0.008   9.344
geneModelFromTxdb    7.857  0.233   8.194
* 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
  ‘/home/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	1.120	0.224	1.348
addArrowMark	0.012	0.000	0.012
addGuideLine	0.006	0.000	0.006
coverageGR	0.245	0.008	0.260
dandelion.plot	1.505	0.002	1.555
geneModelFromTxdb	7.857	0.233	8.194
getCurTrackViewport	0.005	0.000	0.004
importBam	0.278	0.000	0.279
importData	1.384	0.004	1.427
importScore	0.677	0.000	0.677
lolliplot	0.694	0.004	0.698
optimizeStyle	0.743	0.000	0.743
parse2GRanges	0.01	0.00	0.01
parseWIG	9.681	0.002	9.704
plotGRanges	0.888	0.004	0.894
track	0.048	0.000	0.048
trackViewer-package	16.765	0.025	16.855
trackViewerStyle	0.000	0.000	0.001
viewTracks	9.269	0.008	9.344