Package: biovizBase

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biovizBase_1.0.4.tar.gz

StartedAt: 2012-03-23 23:51:20 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:53:49 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 149.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: biovizBase.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/biovizBase.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'biovizBase/DESCRIPTION' ... OK
* this is package 'biovizBase' version '1.0.4'
* 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 whether package 'biovizBase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... WARNING
'library' or 'require' call not declared from: 'GenomicRanges'
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 sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* 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, see
  '/Users/biocbuild/bbs-2.9-bioc/meat/biovizBase.Rcheck/00check.log'
for details

* installing *source* package 'biovizBase' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'intro.Rnw' 
** testing if installed package can be loaded

* DONE (biovizBase)

name	user	system	elapsed
GCcontent	4.032	0.532	4.682
addSteppings-method	1.634	0.073	1.735
colorBlindSafePal	0	0	0
containLetters	0.001	0.001	0.001
darned_hg19_subset500	0.078	0.003	0.082
genesymbol	0.289	0.018	0.315
getBioColor	0.001	0.000	0.001
getIdeogram	0.000	0.000	0.001
hg19Ideogram	0.079	0.001	0.083
hg19IdeogramCyto	0.046	0.001	0.048
isIdeogram	0.007	0.002	0.008
isMatchedWithModel	2.634	0.084	2.733
isSimpleIdeogram	0.303	0.002	0.307
maxGap-method	0.632	0.014	0.666
pileupAsGRanges	0.000	0.000	0.001
pileupGRangesAsVariantTable	0	0	0
plotColorLegend	0.005	0.000	0.005
showColor	0	0	0
shrinkageFun-method	0.277	0.007	0.293
transformGRangesForEvenSpace	0.398	0.006	0.406
transformGRangesToDfWithTicks	0.273	0.007	0.281