BioC experimental data: CHECK report for ccTutorial on petty

Package: ccTutorial

Version: 1.0.23

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ccTutorial_1.0.23.tar.gz

StartedAt: 2013-10-08 13:08:38 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 13:16:16 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 457.9 seconds

RetCode: 0

Status:  OK

CheckDir: ccTutorial.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-data-experiment/meat/ccTutorial.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 'ccTutorial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ccTutorial' version '1.0.23'
* 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 'ccTutorial' can be installed ... [30s/52s] OK
* checking installed package size ... NOTE
  installed size is 790.4Mb
  sub-directories of 1Mb or more:
    PairData       448.5Mb
    data            77.8Mb
    doc              5.4Mb
    exonerateData  202.3Mb
    expression      49.9Mb
    vignettes        6.3Mb
* 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'ccTutorial.pdf' from 600Kb to 192Kb
     compacted 'ccTutorialSupplement.pdf' from 4.6Mb to 3.3Mb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile', 'ccTutorial.tex', 'ccTutorialSupplement.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [42s/43s] OK
Examples with CPU or elapsed time > 5s
    user system elapsed
X 24.947   0.43  25.419
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-data-experiment/meat/ccTutorial.Rcheck/00check.log'
for details.

* installing *source* package 'ccTutorial' ...
** R
** data
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (ccTutorial)

name	user	system	elapsed
X	24.947	0.430	25.419
arrayGenesToProbeSets	0.181	0.006	0.272
barreraExpressionX	0.131	0.011	0.384
chersX	0.809	0.039	0.869
mm9g2p	1.025	0.059	1.111
mm9gene2GO	0.172	0.021	0.197
mm9genes	0.119	0.006	0.126
probeAnno	0.003	0.005	0.008