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BioC experimental data: CHECK report for ccTutorial on moscato1

This page was generated on 2015-04-08 17:40:59 -0700 (Wed, 08 Apr 2015).

Package 30/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ccTutorial 1.3.1
Joern Toedling
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/ccTutorial
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ccTutorial
Version: 1.3.1
Command: rm -rf ccTutorial.buildbin-libdir ccTutorial.Rcheck && mkdir ccTutorial.buildbin-libdir ccTutorial.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ccTutorial.buildbin-libdir ccTutorial_1.3.1.tar.gz >ccTutorial.Rcheck\00install.out 2>&1 && cp ccTutorial.Rcheck\00install.out ccTutorial-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ccTutorial.buildbin-libdir --install="check:ccTutorial-install.out" --force-multiarch --no-vignettes --timings ccTutorial_1.3.1.tar.gz
StartedAt: 2015-04-08 09:15:18 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 09:37:09 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 1310.9 seconds
RetCode: 0
Status:  OK  
CheckDir: ccTutorial.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ccTutorial.buildbin-libdir ccTutorial.Rcheck && mkdir ccTutorial.buildbin-libdir ccTutorial.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ccTutorial.buildbin-libdir ccTutorial_1.3.1.tar.gz >ccTutorial.Rcheck\00install.out 2>&1 && cp ccTutorial.Rcheck\00install.out ccTutorial-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ccTutorial.buildbin-libdir --install="check:ccTutorial-install.out" --force-multiarch --no-vignettes --timings ccTutorial_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-data-experiment/meat/ccTutorial.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ccTutorial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ccTutorial' version '1.3.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [35s] OK
Examples with CPU or elapsed time > 5s
   user system elapsed
X 20.68    0.1   20.78
** running examples for arch 'x64' ... [39s] OK
Examples with CPU or elapsed time > 5s
   user system elapsed
X 21.41   0.16   21.56
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-data-experiment/meat/ccTutorial.Rcheck/00check.log'
for details.

ccTutorial.Rcheck/00install.out:


install for i386

* 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.

install for x64

* installing *source* package 'ccTutorial' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'ccTutorial' as ccTutorial_1.3.1.zip
* DONE (ccTutorial)

ccTutorial.Rcheck/examples_i386/ccTutorial-Ex.timings:

nameusersystemelapsed
X20.68 0.1020.78
arrayGenesToProbeSets0.070.000.61
barreraExpressionX0.110.010.12
chersX1.460.021.49
mm9g2p0.970.000.97
mm9gene2GO0.050.000.05
mm9genes0.090.000.11
probeAnno000

ccTutorial.Rcheck/examples_x64/ccTutorial-Ex.timings:

nameusersystemelapsed
X21.41 0.1621.56
arrayGenesToProbeSets0.040.010.06
barreraExpressionX0.130.000.13
chersX1.860.021.87
mm9g2p0.90.01.4
mm9gene2GO0.050.000.05
mm9genes0.10.00.1
probeAnno000