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ccTutorial 1.0.17
Joern Toedling
Snapshot Date: 2011-07-02 23:15:14 -0700 (Sat, 02 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ccTutorial
Last Changed Rev: 1044 / Revision: 1676
Last Changed Date: 2009-10-13 18:55:23 -0700 (Tue, 13 Oct 2009)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.7) / i386  OK [ WARNINGS ] OK 

Summary

Package: ccTutorial
Version: 1.0.17
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ccTutorial_1.0.17.tar.gz
StartedAt: 2011-07-03 00:37:48 -0700 (Sun, 03 Jul 2011)
EndedAt: 2011-07-03 00:43:14 -0700 (Sun, 03 Jul 2011)
EllapsedTime: 326.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ccTutorial.Rcheck
Warnings: 2

Command output

* using log directory '/Users/biocbuild/bbs-2.8-data-experiment/meat/ccTutorial.Rcheck'
* using R version 2.13.0 (2011-04-13)
* using platform: x86_64-apple-darwin9.8.0 (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 '1.0.17'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ccTutorial' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 790.4Mb
  sub-directories of 1Mb or more:
    data            77.8Mb
    doc              5.4Mb
    exonerateData  202.3Mb
    expression      49.9Mb
    PairData       448.5Mb
    vignettes        6.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'ccTutorial.pdf' from 600Kb to 227Kb
     compacted 'ccTutorialSupplement.pdf' from 4.6Mb to 3.4Mb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
  Unused files in inst/doc which are pointless or misleading
  as they will be re-created from the vignettes:
   ccTutorial.R
   ccTutorialSupplement.R

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.8-data-experiment/meat/ccTutorial.Rcheck/00check.log'
for details

ccTutorial.Rcheck/00install.out:

* installing *source* package 'ccTutorial' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: limma
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loading required package: grid

Attaching package: 'affy'

The following object(s) are masked from 'package:Ringo':

    probes

Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI

Loading required package: SparseM
Package SparseM (0.89) loaded.
	   To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

    backsolve


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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (ccTutorial)

ccTutorial.Rcheck/ccTutorial-Ex.timings:

nameusersystemelapsed
X25.812 0.41026.223
arrayGenesToProbeSets0.0590.0050.064
barreraExpressionX0.1950.0040.202
chersX1.9280.0852.013
mm9g2p1.1570.0411.198
mm9gene2GO0.0510.0030.054
mm9genes0.1270.0070.133
probeAnno000