BioC experimental data: CHECK report for davidTiling on perceval

Package: davidTiling

Version: 1.2.19

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch davidTiling_1.2.19.tar.gz

StartedAt: 2014-04-04 10:25:48 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 10:32:15 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 386.9 seconds

RetCode: 0

Status:  OK

CheckDir: davidTiling.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/davidTiling.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘davidTiling/DESCRIPTION’ ... OK
* this is package ‘davidTiling’ version ‘1.2.19’
* 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 ‘davidTiling’ can be installed ... [19s/37s] OK
* checking installed package size ... NOTE
  installed size is 538.0Mb
  sub-directories of 1Mb or more:
    celfiles  305.9Mb
    data      229.5Mb
    website     2.3Mb
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘GO.db’ ‘tilingArray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... NOTE
GOHyperG: no visible global function definition for
  ‘replaceSystematicByCommonName’
scoreSegments: no visible binding for global variable ‘yeastFeatures’
scoreSegments: no visible binding for global variable ‘chrs’
* checking Rd files ... NOTE
prepare_Rd: GOHyperG.Rd:34-35: Dropping empty section \examples
prepare_Rd: getGO.Rd:32-33: Dropping empty section \examples
prepare_Rd: scatterWithHist.Rd:19-20: Dropping empty section \details
prepare_Rd: scoreSegments.Rd:103-104: Dropping empty section \examples
* 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 files in ‘vignettes’ ... OK
* checking examples ... [76s/77s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
davidTiling 59.641  1.451  61.235
probeAnno    6.855  0.828   7.688
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/davidTiling.Rcheck/00check.log’
for details.

* installing *source* package ‘davidTiling’ ...
** 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 (davidTiling)

name	user	system	elapsed
davidTiling	59.641	1.451	61.235
getAttributeField	0.004	0.007	0.012
gff	0.163	0.016	0.179
probeAnno	6.855	0.828	7.688
scatterWithHist	0.013	0.005	0.019
showDens	0.009	0.005	0.028
yeastFeatures	0.006	0.004	0.009