BioC 3.5: CHECK report for Gviz on veracruz2

Package: Gviz

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.20.0.tar.gz

StartedAt: 2017-10-18 04:42:20 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:48:52 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 392.8 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_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Gviz.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.20.0’
* 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 12.045  0.893  13.329
SequenceTrack-class    7.341  0.658  10.433
GeneRegionTrack-class  7.148  0.067  11.780
GenomeAxisTrack-class  3.631  0.025   6.130
* 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	3.952	0.115	4.189
AlignmentsTrack-class	12.045	0.893	13.329
AnnotationTrack-class	4.421	0.049	4.697
BiomartGeneRegionTrack-class	3.703	0.037	3.868
DataTrack-class	0.853	0.018	0.902
DisplayPars-class	0.041	0.002	0.044
GeneRegionTrack-class	7.148	0.067	11.780
GenomeAxisTrack-class	3.631	0.025	6.130
IdeogramTrack-class	0.546	0.006	0.907
SequenceTrack-class	7.341	0.658	10.433
plotTracks	4.054	0.057	4.279