Package: encoDnaseI

Version: 0.1.9

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch encoDnaseI_0.1.9.tar.gz

StartedAt: 2012-03-07 13:52:55 -0800 (Wed, 07 Mar 2012)

EndedAt: 2012-03-07 14:02:29 -0800 (Wed, 07 Mar 2012)

EllapsedTime: 573.6 seconds

RetCode: 0

Status:  OK

CheckDir: encoDnaseI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-data-experiment/meat/encoDnaseI.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 'encoDnaseI/DESCRIPTION' ... OK
* this is package 'encoDnaseI' version '0.1.9'
* 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 'encoDnaseI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data  10.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ALICOR: no visible binding for global variable 'rawCD4'
WRC: no visible binding for global variable 'd19'
* 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
  Error in .requirePackage(package) : 
    unable to find required package 'snpMatrix'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  c19g.rda             141Kb     54Kb       xz
  demoPGM1ssr.rda      526Kb    445Kb       xz
  demoTrk19.rda        141Kb     52Kb       xz
  rawCD4.rda           3.6Mb    1.4Mb       xz
  rawCd4DnaseI.rda     3.6Mb    1.4Mb       xz
  rawHelaDnaseI.rda    2.5Mb    1.3Mb       xz
  sOSR2.rda             21Kb     18Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'SNPlocs.Hsapiens.dbSNP.20090506'
* 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

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

* DONE (encoDnaseI)

name	user	system	elapsed
encoDnaseI	4.754	0.168	4.968
hg18track-class	7.574	0.293	8.324
juxtaPlot	0	0	0