BioC 2.13: CHECK report for Gviz on zin1

Package: Gviz

Version: 1.6.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Gviz_1.6.0.tar.gz

StartedAt: 2014-04-05 01:46:08 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:50:29 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 261.4 seconds

RetCode: 0

Status:  OK

CheckDir: Gviz.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Gviz.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.6.0’
* 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 ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicFeatures’ ‘biomaRt’ ‘rtracklayer’
A package should be listed in only one of these fields.
* 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 ... NOTE
‘:::’ call which should be ‘::’: ‘IRanges:::isSingleString’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘lattice:::chooseFace’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.DEFAULT_FILL_COL’ ‘.DEFAULT_SHADED_COL’ ‘.PLOT_TYPES’
  ‘.parMappings’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Gviz.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SequenceTrack-class   6.921  0.236   7.167
GeneRegionTrack-class 6.520  0.044   6.584
AnnotationTrack-class 4.920  0.040   5.003
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/Gviz.Rcheck/00check.log’
for details.

* installing *source* package ‘Gviz’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘subset’ from package ‘base’ in package ‘Gviz’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘Gviz’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Gviz)

name	user	system	elapsed
AlignedReadTrack-class	1.968	0.032	2.116
AnnotationTrack-class	4.920	0.040	5.003
BiomartGeneRegionTrack-class	3.289	0.016	3.309
DataTrack-class	1.144	0.020	1.165
DisplayPars-class	0.044	0.004	0.048
GeneRegionTrack-class	6.520	0.044	6.584
GenomeAxisTrack-class	3.740	0.004	3.750
IdeogramTrack-class	0.352	0.008	0.359
SequenceTrack-class	6.921	0.236	7.167
plotTracks	4.600	0.008	4.617