Package: Gviz

Version: 1.3.10

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Gviz_1.3.10.tar.gz

StartedAt: 2013-01-16 03:26:06 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:31:58 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 352.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Gviz.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Gviz.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.3.10’
* 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 ... WARNING
Found the following significant warnings:
  Warning: subclass "refGeneratorSlot" of class "environment" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Gviz.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 for unstated 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 ... 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 ... NOTE
  No methods found in "IRanges" for requests: nlevels
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SequenceTrack-class   9.449  0.652  10.304
GeneRegionTrack-class 8.225  0.036   8.289
AnnotationTrack-class 6.621  0.068   6.690
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Gviz.Rcheck/00check.log’
for details.

* installing *source* package ‘Gviz’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: nlevels
Warning: subclass "refGeneratorSlot" of class "environment" is not local and cannot be updated for new inheritance information; consider setClassUnion()
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
   ‘Gviz.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
No methods found in "IRanges" for requests: nlevels

* DONE (Gviz)

name	user	system	elapsed
AlignedReadTrack-class	2.284	0.056	2.339
AnnotationTrack-class	6.621	0.068	6.690
BiomartGeneRegionTrack-class	3.928	0.008	3.983
DataTrack-class	1.108	0.020	1.132
DisplayPars-class	0.096	0.008	0.104
GeneRegionTrack-class	8.225	0.036	8.289
GenomeAxisTrack-class	4.272	0.004	4.275
IdeogramTrack-class	0.536	0.000	0.538
SequenceTrack-class	9.449	0.652	10.304
plotTracks	4.904	0.004	4.910