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BioC experimental data: CHECK report for ccTutorial on zin2

This page was generated on 2016-10-08 19:29:06 -0700 (Sat, 08 Oct 2016).

Package 34/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ccTutorial 1.10.0
Joern Toedling
Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/ccTutorial
Last Changed Rev: 3760 / Revision: 3935
Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 

Summary

Package: ccTutorial
Version: 1.10.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ccTutorial_1.10.0.tar.gz
StartedAt: 2016-10-08 09:10:28 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 09:14:13 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 224.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ccTutorial.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ccTutorial_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/ccTutorial.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 ‘ccTutorial’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 790.3Mb
  sub-directories of 1Mb or more:
    PairData       448.5Mb
    data            77.8Mb
    doc              5.3Mb
    exonerateData  202.3Mb
    expression      49.9Mb
    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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Ringo’ ‘affy’ ‘topGO’
  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 ... 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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 ... OK
Examples with CPU or elapsed time > 5s
   user system elapsed
X 13.43  0.128  13.571
* 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
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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
X13.430 0.12813.571
arrayGenesToProbeSets0.0480.0000.048
barreraExpressionX0.2070.0000.207
chersX1.1100.0041.115
mm9g2p0.8070.0040.811
mm9gene2GO0.0390.0000.039
mm9genes0.0870.0000.087
probeAnno0.0010.0000.000