Package: GSEABenchmarkeR

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GSEABenchmarkeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GSEABenchmarkeR_1.3.2.tar.gz

StartedAt: 2019-04-09 01:24:15 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:28:21 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 246.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: GSEABenchmarkeR.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GSEABenchmarkeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GSEABenchmarkeR_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GSEABenchmarkeR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEABenchmarkeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABenchmarkeR’ version ‘1.3.2’
* package encoding: UTF-8
* 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 ‘GSEABenchmarkeR’ 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
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 86355 Illegal instruction: 4  LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --encoding=UTF-8 > 'GSEABenchmarkeR-Ex.Rout' 2>&1 < GSEABenchmarkeR-Ex.R
 ERROR
Running examples in ‘GSEABenchmarkeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runEA
> ### Title: Application of enrichment methods to multiple datasets
> ### Aliases: runEA
> 
> ### ** Examples
> 
> 
>     # loading three datasets from the GEO2KEGG compendium
>     geo2kegg <- loadEData("geo2kegg", nr.datasets=3)
Loading GEO2KEGG data compendium ...
> 
>     # only considering the first 1000 probes for demonstration
>     geo2kegg <- lapply(geo2kegg, function(d) d[1:1000,]) 
> 
>     # preprocessing and DE analysis for two of the datasets
>     geo2kegg <- maPreproc(geo2kegg[2:3])
Summarizing probe level expression ...
>     geo2kegg <- runDE(geo2kegg)
> 
>     # getting a subset of human KEGG gene sets
>     gs.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
>     kegg.gs <- EnrichmentBrowser::getGenesets(gs.file)
> 
>     # applying two methods to two datasets 
>     res <- runEA(geo2kegg, methods=c("ora", "camera"), gs=kegg.gs, perm=0)
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GSEABenchmarkeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GSEABenchmarkeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GSEABenchmarkeR’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSEABenchmarkeR)

name	user	system	elapsed
bpPlot	0.016	0.001	0.017
cacheResource	2.231	0.151	2.399
evalNrSigSets	1.767	0.035	1.812
evalRelevance	0.446	0.014	0.462
evalTypeIError	14.067	7.040	17.239
loadEData	34.108	7.688	51.622
maPreproc	1.836	0.186	2.753
readDataId2diseaseCodeMap	0.004	0.014	0.019
readResults	1.221	0.743	0.429
runDE	1.526	0.584	1.670