BioC 3.0: CHECK report for Gviz on perceval

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: 2015-04-10 02:35:11 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:44:57 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 585.9 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-darwin10.8.0 (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 ... [49s/64s] 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 ... [86s/88s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
AlignmentsTrack              14.953  1.944  17.308
SequenceTrack-class           7.570  1.391   9.826
GeneRegionTrack-class         8.253  0.069   8.461
plotTracks                    7.380  0.115   7.542
AnnotationTrack-class         7.189  0.076   7.455
GenomeAxisTrack-class         5.558  0.027   5.739
BiomartGeneRegionTrack-class  5.034  0.037   5.136
* 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	3.080	0.087	3.191
AlignmentsTrack	14.953	1.944	17.308
AnnotationTrack-class	7.189	0.076	7.455
BiomartGeneRegionTrack-class	5.034	0.037	5.136
DataTrack-class	0.927	0.020	0.965
DisplayPars-class	0.049	0.002	0.052
GeneRegionTrack-class	8.253	0.069	8.461
GenomeAxisTrack-class	5.558	0.027	5.739
IdeogramTrack-class	0.480	0.006	0.502
SequenceTrack-class	7.570	1.391	9.826
plotTracks	7.380	0.115	7.542