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BioC experimental data: CHECK report for encoDnaseI on petty

This page was generated on 2013-10-08 16:07:32 -0700 (Tue, 08 Oct 2013).

Package 46/156HostnameOS / ArchBUILDCHECKBUILD BIN
encoDnaseI 0.1.16
VJ Carey
Snapshot Date: 2013-10-08 10:15:19 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/encoDnaseI
Last Changed Rev: 2317 / Revision: 2510
Last Changed Date: 2013-04-03 15:11:40 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: encoDnaseI
Version: 0.1.16
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch encoDnaseI_0.1.16.tar.gz
StartedAt: 2013-10-08 13:53:34 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 13:59:35 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 361.3 seconds
RetCode: 0
Status:  OK 
CheckDir: encoDnaseI.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-data-experiment/meat/encoDnaseI.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [32s/33s] OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  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 sizes of PDF files under 'inst/doc' ... 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 ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
hg18track-class 5.973  0.167   6.202
* 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
  '/Users/biocbuild/bbs-2.12-data-experiment/meat/encoDnaseI.Rcheck/00check.log'
for details.

encoDnaseI.Rcheck/00install.out:

* 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)

encoDnaseI.Rcheck/encoDnaseI-Ex.timings:

nameusersystemelapsed
encoDnaseI4.5210.1214.645
hg18track-class5.9730.1676.202
juxtaPlot0.0170.0100.026