BioC 3.5: CHECK report for Gviz on oaxaca

Package: Gviz

Version: 1.19.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.19.2.tar.gz

StartedAt: 2017-03-04 04:14:17 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:21:08 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 410.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Gviz.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.19.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Gviz.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.19.2’
* 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 ‘Gviz’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.1Mb
* 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
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
  'cdsBy'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
  'fiveUTRsByTranscript'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
  'threeUTRsByTranscript'
Undefined global functions or variables:
  cdsBy fiveUTRsByTranscript threeUTRsByTranscript
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'GenomeAxisTrack,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
AlignmentsTrack-class 12.792  0.882  13.983
SequenceTrack-class    7.645  0.634   9.284
GeneRegionTrack-class  5.998  0.027   6.043
AnnotationTrack-class  5.143  0.036   5.227
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Gviz.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
AlignedReadTrack-class	4.034	0.087	4.123
AlignmentsTrack-class	12.792	0.882	13.983
AnnotationTrack-class	5.143	0.036	5.227
BiomartGeneRegionTrack-class	3.338	0.016	3.356
DataTrack-class	0.751	0.010	0.760
DisplayPars-class	0.040	0.002	0.041
GeneRegionTrack-class	5.998	0.027	6.043
GenomeAxisTrack-class	3.132	0.008	3.141
IdeogramTrack-class	0.491	0.005	0.497
SequenceTrack-class	7.645	0.634	9.284
plotTracks	4.428	0.068	4.501