BioC experimental data: CHECK report for encoDnaseI on george2

Package: encoDnaseI

Version: 0.1.16

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings encoDnaseI_0.1.16.tar.gz

StartedAt: 2013-10-08 12:42:14 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 12:51:10 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 535.3 seconds

RetCode: 0

Status:  OK

CheckDir: encoDnaseI.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-data-experiment/meat/encoDnaseI.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘encoDnaseI/DESCRIPTION’ ... OK
* this is package ‘encoDnaseI’ version ‘0.1.16’
* 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 ‘encoDnaseI’ can be installed ... [47s/49s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
* 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 ... NOTE
WRC: warning in matrix(ans, nr = 2): partial argument match of 'nr' to
  'nrow'
makeHg18track: warning in matrix(dataVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
[,hg18track-ANY-ANY-ANY: warning in matrix(dataVals(x)[kpinds], nc =
  1): partial argument match of 'nc' to 'ncol'
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 ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Makefile.sw’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [49s/54s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
encoDnaseI      9.805  0.124  11.389
hg18track-class 9.396  0.124   9.582
* 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

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.12-data-experiment/meat/encoDnaseI.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
encoDnaseI	9.805	0.124	11.389
hg18track-class	9.396	0.124	9.582
juxtaPlot	0.036	0.004	0.041