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BioC experimental data: CHECK report for ccTutorial on perceval

This page was generated on 2014-04-04 17:29:13 -0700 (Fri, 04 Apr 2014).

Package 23/181HostnameOS / ArchBUILDCHECKBUILD BIN
ccTutorial 1.0.26
Joern Toedling
Snapshot Date: 2014-04-04 06:15:32 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/ccTutorial
Last Changed Rev: 2748 / Revision: 2768
Last Changed Date: 2014-03-25 11:32:07 -0700 (Tue, 25 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: ccTutorial
Version: 1.0.26
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ccTutorial_1.0.26.tar.gz
StartedAt: 2014-04-04 10:17:00 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 10:26:56 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 595.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ccTutorial.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/ccTutorial.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ccTutorial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ccTutorial’ version ‘1.0.26’
* 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 ... [39s/57s] OK
* checking installed package size ... NOTE
  installed size is 790.3Mb
  sub-directories of 1Mb or more:
    data            77.8Mb
    doc              5.3Mb
    exonerateData  202.3Mb
    expression      49.9Mb
    PairData       448.5Mb
    vignettes        6.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘affy’ ‘Ringo’ ‘topGO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [52s/53s] OK
Examples with CPU or elapsed time > 5s
   user system elapsed
X 32.31  0.558  32.992
* 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 were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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

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)

ccTutorial.Rcheck/ccTutorial-Ex.timings:

nameusersystemelapsed
X32.310 0.55832.992
arrayGenesToProbeSets0.2990.0090.345
barreraExpressionX0.1300.0230.239
chersX0.7670.0500.818
mm9g2p0.9040.0561.057
mm9gene2GO0.2090.0230.266
mm9genes0.1060.0060.112
probeAnno0.0020.0040.006