BioC 3.3: CHECK report for trackViewer on moscato2

Package: trackViewer

Version: 1.8.4

Command: rm -rf trackViewer.buildbin-libdir trackViewer.Rcheck && mkdir trackViewer.buildbin-libdir trackViewer.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trackViewer.buildbin-libdir trackViewer_1.8.4.tar.gz >trackViewer.Rcheck\00install.out 2>&1 && cp trackViewer.Rcheck\00install.out trackViewer-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=trackViewer.buildbin-libdir --install="check:trackViewer-install.out" --force-multiarch --no-vignettes --timings trackViewer_1.8.4.tar.gz

StartedAt: 2016-10-13 09:40:17 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 09:51:10 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 653.0 seconds

RetCode: 0

Status:  OK

CheckDir: trackViewer.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf trackViewer.buildbin-libdir trackViewer.Rcheck && mkdir trackViewer.buildbin-libdir trackViewer.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trackViewer.buildbin-libdir trackViewer_1.8.4.tar.gz >trackViewer.Rcheck\00install.out 2>&1 && cp trackViewer.Rcheck\00install.out trackViewer-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=trackViewer.buildbin-libdir --install="check:trackViewer-install.out" --force-multiarch --no-vignettes --timings trackViewer_1.8.4.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/trackViewer.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
trackViewer-package 21.38   0.07   21.46
viewTracks          12.10   0.02   12.12
parseWIG            11.64   0.02   11.65
geneModelFromTxdb   10.31   0.48   10.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
trackViewer-package 34.01   0.17   34.21
viewTracks          19.25   0.02   19.28
parseWIG            16.17   0.00   16.16
geneModelFromTxdb   11.23   0.58   11.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/trackViewer.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'trackViewer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trackViewer' as trackViewer_1.8.4.zip
* DONE (trackViewer)

name	user	system	elapsed
GRoperator	1.26	0.02	1.28
addArrowMark	0.02	0.00	0.01
addGuideLine	0	0	0
coverageGR	0.24	0.00	0.23
dandelion.plot	1.64	0.00	1.64
geneModelFromTxdb	10.31	0.48	10.91
getCurTrackViewport	0	0	0
importBam	0.41	0.00	0.41
importData	1.57	0.02	1.78
importScore	1.02	0.03	1.04
lolliplot	0.86	0.03	0.89
optimizeStyle	0.79	0.01	0.81
parse2GRanges	0.02	0.00	0.02
parseWIG	11.64	0.02	11.65
plotGRanges	0.87	0.00	0.87
track	0.05	0.00	0.05
trackViewer-package	21.38	0.07	21.46
trackViewerStyle	0	0	0
viewTracks	12.10	0.02	12.12

name	user	system	elapsed
GRoperator	1.66	0.01	1.67
addArrowMark	0.01	0.00	0.01
addGuideLine	0.02	0.00	0.02
coverageGR	0.39	0.02	0.41
dandelion.plot	2.12	0.00	2.12
geneModelFromTxdb	11.23	0.58	11.91
getCurTrackViewport	0	0	0
importBam	0.38	0.00	0.37
importData	1.96	0.03	2.00
importScore	0.88	0.02	0.89
lolliplot	1.17	0.01	1.18
optimizeStyle	1.09	0.00	1.09
parse2GRanges	0.01	0.00	0.02
parseWIG	16.17	0.00	16.16
plotGRanges	2.01	0.00	2.01
track	0.11	0.00	0.11
trackViewer-package	34.01	0.17	34.21
trackViewerStyle	0	0	0
viewTracks	19.25	0.02	19.28