BioC 2.14: CHECK report for inSilicoMerging on petty

Package: inSilicoMerging

Version: 1.8.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch inSilicoMerging_1.8.7.tar.gz

StartedAt: 2014-10-07 22:36:41 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:40:40 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 238.8 seconds

RetCode: 0

Status:  OK

CheckDir: inSilicoMerging.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 --no-multiarch inSilicoMerging_1.8.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/inSilicoMerging.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘inSilicoMerging/DESCRIPTION’ ... OK
* this is package ‘inSilicoMerging’ version ‘1.8.7’
* 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 ‘inSilicoMerging’ can be installed ... [14s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘DWD’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [52s/78s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotMDS             13.173  0.523  17.366
merge               11.815  0.928  28.162
plotRLE              9.752  0.603  13.708
plotGeneWiseBoxPlot  8.028  0.477  11.964
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘inSilicoMerging_unit_tests.R’ [13s/28s]
 [13s/28s] OK
* checking for unstated dependencies in vignettes ... OK
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/inSilicoMerging.Rcheck/00check.log’
for details.

* installing *source* package ‘inSilicoMerging’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (inSilicoMerging)

name	user	system	elapsed
merge	11.815	0.928	28.162
plotGeneWiseBoxPlot	8.028	0.477	11.964
plotMDS	13.173	0.523	17.366
plotRLE	9.752	0.603	13.708