BioC 3.0: CHECK report for Gviz on oaxaca

Package: Gviz

Version: 1.10.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Gviz_1.10.11.tar.gz

StartedAt: 2015-04-09 01:11:05 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 01:18:31 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 446.2 seconds

RetCode: 0

Status:  OK

CheckDir: Gviz.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Gviz_1.10.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Gviz.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.10.11’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘grid’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’
  ‘GenomicRanges’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [37s/38s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    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
.findMismatches: no visible global function definition for
  ‘consensusString’
.moreInd: no visible global function definition for ‘grid.polyline’
subseq,SequenceTrack: no visible global function definition for
  ‘unmasked’
subseq,SequenceTrack: no visible global function definition for
  ‘complement’
* 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 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 ... [69s/72s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
AlignmentsTrack       11.392  0.982  12.621
SequenceTrack-class    8.794  0.681  11.612
GeneRegionTrack-class  7.058  0.040   7.171
AnnotationTrack-class  6.032  0.042   6.113
plotTracks             5.957  0.016   6.051
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	2.106	0.048	2.157
AlignmentsTrack	11.392	0.982	12.621
AnnotationTrack-class	6.032	0.042	6.113
BiomartGeneRegionTrack-class	4.376	0.029	4.426
DataTrack-class	0.795	0.013	0.816
DisplayPars-class	0.042	0.001	0.043
GeneRegionTrack-class	7.058	0.040	7.171
GenomeAxisTrack-class	4.258	0.014	4.783
IdeogramTrack-class	0.319	0.003	0.451
SequenceTrack-class	8.794	0.681	11.612
plotTracks	5.957	0.016	6.051