BioC experimental data: CHECK report for encoDnaseI on perceval

Package: encoDnaseI

Version: 0.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings encoDnaseI_0.7.0.tar.gz

StartedAt: 2015-08-22 09:11:09 -0700 (Sat, 22 Aug 2015)

EndedAt: 2015-08-22 09:19:36 -0700 (Sat, 22 Aug 2015)

EllapsedTime: 507.7 seconds

RetCode: 0

Status:  OK

CheckDir: encoDnaseI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings encoDnaseI_0.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/encoDnaseI.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘encoDnaseI/DESCRIPTION’ ... OK
* this is package ‘encoDnaseI’ version ‘0.7.0’
* 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 ... [39s/45s] 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GGBase’ ‘GGtools’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeHg18track: warning in matrix(dataVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
WRC: warning in matrix(ans, nr = 2): partial argument match of 'nr' to
  'nrow'
[,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’
ALICOR: no visible global function definition for ‘p.value’
juxtaPlot: no visible global function definition for ‘p.value’
juxtaPlot: no visible global function definition for ‘xyplot’
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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/34s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
encoDnaseI 3.799  0.157   5.135
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/encoDnaseI.Rcheck/00check.log’
for details.

* installing *source* package ‘encoDnaseI’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘stats::IQR’ when loading ‘GGBase’
No methods found in "IRanges" for requests: aggregate
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘stats::IQR’ when loading ‘GGBase’
No methods found in "IRanges" for requests: aggregate
* DONE (encoDnaseI)

name	user	system	elapsed
encoDnaseI	3.799	0.157	5.135
hg18track-class	3.668	0.097	4.690
juxtaPlot	0.000	0.000	0.001