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BioC 3.0: CHECK report for compEpiTools on moscato1

This page was generated on 2015-04-10 09:50:56 -0700 (Fri, 10 Apr 2015).

Package 191/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.0.4
Kamal Kishore
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/compEpiTools
Last Changed Rev: 101596 / Revision: 102249
Last Changed Date: 2015-03-30 07:52:59 -0700 (Mon, 30 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  ERROR 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ ERROR ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: compEpiTools
Version: 1.0.4
Command: rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.0.4.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.0.4.tar.gz
StartedAt: 2015-04-10 00:03:48 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:17:25 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 817.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: compEpiTools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf compEpiTools.buildbin-libdir compEpiTools.Rcheck && mkdir compEpiTools.buildbin-libdir compEpiTools.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compEpiTools.buildbin-libdir compEpiTools_1.0.4.tar.gz >compEpiTools.Rcheck\00install.out 2>&1 && cp compEpiTools.Rcheck\00install.out compEpiTools-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=compEpiTools.buildbin-libdir --install="check:compEpiTools-install.out" --force-multiarch --no-vignettes --timings compEpiTools_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/compEpiTools.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 'compEpiTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compEpiTools' version '1.0.4'
* 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 'compEpiTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'compEpiTools-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotStallingIndex
> ### Title: Stalling Index plots
> ### Aliases: plotStallingIndex
> 
> ### ** Examples
> 
>   require(TxDb.Mmusculus.UCSC.mm9.knownGene)
Loading required package: TxDb.Mmusculus.UCSC.mm9.knownGene
Loading required package: GenomicFeatures

Attaching package: 'GenomicFeatures'

The following object is masked from 'package:topGO':

    genes

>   require(org.Mm.eg.db)
Loading required package: org.Mm.eg.db
>   txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
>   isActiveSeq(txdb) <- c(rep(FALSE,18), TRUE, rep(FALSE, length(isActiveSeq(txdb))-19))
>   # pointing to Pol2 BAM file
>   # BAM file from the GEO GSM1234478 sample, limited to chr19:3200000-4000000
>   Pol2bam <- system.file("extdata", "Pol2.bam", package="compEpiTools")
>   # loading Pol2 peaks as a GRanges object
>   # built based on the BED file from the GEO GSM1234478 sample
>   # limited to chr19:3200000-4000000
>   Pol2GR <- system.file("extdata", "Pol2GR.Rda", package="compEpiTools")
>   load(Pol2GR)
>   egs <- distanceFromTSS(Pol2GR, txdb=txdb)
>   egs <- unique(egs$nearest_gene_id)
>   SI_matrix <- stallingIndex(BAMlist=list(Pol2bam), peakGRlist=list(Pol2GR), 
+     genesList=list(egs), transcriptDB=txdb, countMode='gene')
Error in stallingIndex(BAMlist = list(Pol2bam), peakGRlist = list(Pol2GR),  : 
  genesList has to contain characters ...
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'compEpiTools-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotStallingIndex
> ### Title: Stalling Index plots
> ### Aliases: plotStallingIndex
> 
> ### ** Examples
> 
>   require(TxDb.Mmusculus.UCSC.mm9.knownGene)
Loading required package: TxDb.Mmusculus.UCSC.mm9.knownGene
Loading required package: GenomicFeatures

Attaching package: 'GenomicFeatures'

The following object is masked from 'package:topGO':

    genes

>   require(org.Mm.eg.db)
Loading required package: org.Mm.eg.db
>   txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
>   isActiveSeq(txdb) <- c(rep(FALSE,18), TRUE, rep(FALSE, length(isActiveSeq(txdb))-19))
>   # pointing to Pol2 BAM file
>   # BAM file from the GEO GSM1234478 sample, limited to chr19:3200000-4000000
>   Pol2bam <- system.file("extdata", "Pol2.bam", package="compEpiTools")
>   # loading Pol2 peaks as a GRanges object
>   # built based on the BED file from the GEO GSM1234478 sample
>   # limited to chr19:3200000-4000000
>   Pol2GR <- system.file("extdata", "Pol2GR.Rda", package="compEpiTools")
>   load(Pol2GR)
>   egs <- distanceFromTSS(Pol2GR, txdb=txdb)
>   egs <- unique(egs$nearest_gene_id)
>   SI_matrix <- stallingIndex(BAMlist=list(Pol2bam), peakGRlist=list(Pol2GR), 
+     genesList=list(egs), transcriptDB=txdb, countMode='gene')
Error in stallingIndex(BAMlist = list(Pol2bam), peakGRlist = list(Pol2GR),  : 
  genesList has to contain characters ...
Execution halted

compEpiTools.Rcheck/00install.out:


install for i386

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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.0.4.zip
* DONE (compEpiTools)

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

nameusersystemelapsed
GR2fasta-methods1.030.002.89
GRanges2ucsc-methods000
GRangesInPromoters-methods4.590.114.69
GRannotate-methods5.040.115.15
GRannotateSimple1.670.021.69
GRbaseCoverage-methods0.140.000.15
GRcoverage-methods0.20.00.2
GRcoverageSummit-methods0.110.000.11
GRenrichment-methods0.120.000.12
GRmidpoint-methods0.020.000.02
GRsetwidth0.040.000.03
TSS2.630.112.75
countOverlapsInBins-methods0.270.000.27
distanceFromTSS-methods3.230.113.33
enhancers0.780.030.81
findLncRNA1.390.011.41
getPromoterClass-methods 0.74 0.0520.67
heatmapData1.900.061.97
heatmapPlot4.110.034.13
makeGtfFromDb 2.64 0.5054.52
matchEnhancers5.080.085.24
overlapOfGRanges-methods0.110.000.11
palette2d0.090.000.09

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

nameusersystemelapsed
GR2fasta-methods1.700.041.75
GRanges2ucsc-methods000
GRangesInPromoters-methods6.400.166.56
GRannotate-methods5.680.125.80
GRannotateSimple2.500.132.63
GRbaseCoverage-methods0.160.000.15
GRcoverage-methods0.250.000.25
GRcoverageSummit-methods0.150.020.17
GRenrichment-methods0.200.000.21
GRmidpoint-methods0.050.000.04
GRsetwidth0.060.000.06
TSS3.480.073.56
countOverlapsInBins-methods0.330.000.32
distanceFromTSS-methods3.880.053.94
enhancers0.970.030.99
findLncRNA1.570.051.63
getPromoterClass-methods 0.81 0.0125.52
heatmapData1.970.021.99
heatmapPlot4.820.034.86
makeGtfFromDb2.380.522.92
matchEnhancers5.340.065.40
overlapOfGRanges-methods0.140.000.14
palette2d0.10.00.1