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BioC 2.12: CHECK report for IdMappingAnalysis on moscato2

This page was generated on 2013-10-09 09:39:06 -0700 (Wed, 09 Oct 2013).

Package 334/671HostnameOS / ArchBUILDCHECKBUILD BIN
IdMappingAnalysis 1.4.0
Alex Lisovich , Roger Day
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/IdMappingAnalysis
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ ERROR ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  ERROR  OK 

Summary

Package: IdMappingAnalysis
Version: 1.4.0
Command: rm -rf IdMappingAnalysis.buildbin-libdir && mkdir IdMappingAnalysis.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IdMappingAnalysis.buildbin-libdir IdMappingAnalysis_1.4.0.tar.gz >IdMappingAnalysis-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=IdMappingAnalysis.buildbin-libdir --install="check:IdMappingAnalysis-install.out" --force-multiarch --no-vignettes --timings IdMappingAnalysis_1.4.0.tar.gz && mv IdMappingAnalysis.buildbin-libdir/* IdMappingAnalysis.Rcheck/ && rmdir IdMappingAnalysis.buildbin-libdir
StartedAt: 2013-10-09 02:41:02 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:43:45 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 163.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: IdMappingAnalysis.Rcheck
Warnings: NA

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/IdMappingAnalysis.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IdMappingAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdMappingAnalysis' version '1.4.0'
* 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 whether package 'IdMappingAnalysis' can be installed ... OK
* checking installed package size ... OK
* 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
* 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
* 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 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 ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... WARNING
checkRd: (3) CsvList.merge.Misc.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) as.list.IdMap.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) boxplotdataJitter.JointUniquePairs.Rd:23: \synopsis will be removed in R 3.1.0
checkRd: (3) byColNames.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) byColumn.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) byRow.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) byRowNames.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) copy.Display.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) create.Display.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) create.UniquePairs.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) do.apply.DataFilter.Rd:27: \synopsis will be removed in R 3.1.0
checkRd: (3) fisherTransform.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) fisherTransformInverse.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) fisherTransformJacobean.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) interleave.Misc.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) line.loess.Display.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) line.unsorted.Display.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) log10.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) minAvgCountConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) minCountConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) minCountGroupConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) pack.experiments.CorrData.Rd:21: \synopsis will be removed in R 3.1.0
checkRd: (3) progressMsg.Display.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) removeNASeries.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) swapKeys.IdMap.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) swapKeys.UniquePairs.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) textBoundingBox.Display.Rd:28: \synopsis will be removed in R 3.1.0
checkRd: (3) to.base.Misc.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) to.binary.logical.Misc.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) to.index.expr.Misc.Rd:25: \synopsis will be removed in R 3.1.0
checkRd: (3) words.Misc.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) zoom.pars.Display.Rd:20: \synopsis will be removed in R 3.1.0
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'IdMappingAnalysis-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: log10.DataFilter
> ### Title: Compute log10 of a numerical vector combined with thresholding
> ###   on minimum value
> ### Aliases: log10.DataFilter DataFilter.log10 log10.DataFilter
> ###   log10,DataFilter-method
> ### Keywords: internal methods
> 
> ### ** Examples
> 
>  #compute log10 transform of mrna experiment data replacing (clipping)
>  #the output values with log10(0.5)for input values < 0.5
>  fltExperimentSet<-DataFilter$do.apply(examples$mrnaExperimentSet,
+          byRows=TRUE,filterFun=DataFilter$log10,filtParams=c(0.5,log10(0.5)),verbose=TRUE);
filtering experiment set...
Error in log10(static, ...) : 
  3 arguments passed to 'log10' which requires 1
Calls: <Anonymous> -> do.apply -> do.apply.DataFilter -> filterFun
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'IdMappingAnalysis-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: log10.DataFilter
> ### Title: Compute log10 of a numerical vector combined with thresholding
> ###   on minimum value
> ### Aliases: log10.DataFilter DataFilter.log10 log10.DataFilter
> ###   log10,DataFilter-method
> ### Keywords: internal methods
> 
> ### ** Examples
> 
>  #compute log10 transform of mrna experiment data replacing (clipping)
>  #the output values with log10(0.5)for input values < 0.5
>  fltExperimentSet<-DataFilter$do.apply(examples$mrnaExperimentSet,
+          byRows=TRUE,filterFun=DataFilter$log10,filtParams=c(0.5,log10(0.5)),verbose=TRUE);
filtering experiment set...
Error in log10(static, ...) : 
  3 arguments passed to 'log10' which requires 1
Calls: <Anonymous> -> do.apply -> do.apply.DataFilter -> filterFun
Execution halted

IdMappingAnalysis.Rcheck/00install.out:


install for i386

* installing *source* package 'IdMappingAnalysis' ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'IdMappingAnalysis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IdMappingAnalysis' as IdMappingAnalysis_1.4.0.zip
* DONE (IdMappingAnalysis)