BioC 3.5: CHECK report for Gviz on toluca2

Package: Gviz

Version: 1.19.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.19.3.tar.gz

StartedAt: 2017-04-23 05:07:50 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:15:15 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 445.0 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_1.19.3.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 r72187)
* 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 ‘1.19.3’
* 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  6.0Mb
  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  13.098  0.965  14.224
AnnotationTrack-class   8.563  0.047   8.681
SequenceTrack-class     7.232  0.632   7.936
GeneRegionTrack-class   6.923  0.039   7.036
AlignedReadTrack-class  5.229  0.116   8.336
* 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	5.229	0.116	8.336
AlignmentsTrack-class	13.098	0.965	14.224
AnnotationTrack-class	8.563	0.047	8.681
BiomartGeneRegionTrack-class	3.952	0.025	4.051
DataTrack-class	0.931	0.014	0.951
DisplayPars-class	0.041	0.002	0.043
GeneRegionTrack-class	6.923	0.039	7.036
GenomeAxisTrack-class	3.436	0.009	3.484
IdeogramTrack-class	0.562	0.004	0.574
SequenceTrack-class	7.232	0.632	7.936
plotTracks	4.480	0.045	4.633