CHECK report for regionReport on veracruz1
This page was generated on 2018-04-11 14:57:15 -0400 (Wed, 11 Apr 2018).
regionReport 1.12.2
Leonardo Collado-Torres
| Snapshot Date: 2018-04-10 16:46:01 -0400 (Tue, 10 Apr 2018) |
| URL: https://git.bioconductor.org/packages/regionReport |
| Branch: RELEASE_3_6 |
| Last Commit: 67c95c2 |
| Last Changed Date: 2018-01-19 19:32:50 -0400 (Fri, 19 Jan 2018) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |
Summary
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regionReport_1.12.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/regionReport.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regionReport’ version ‘1.12.2’
* 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 ‘regionReport’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘DESeq2:::pvalueAdjustment’
See the note in ?`:::` about the use of this operator.
* 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 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 ... ERROR
Running examples in ‘regionReport-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: derfinderReport
> ### Title: Generate a HTML/PDF report exploring the basic results from
> ### derfinder
> ### Aliases: derfinderReport
>
> ### ** Examples
>
>
> ## Load derfinder
> library('derfinder')
>
> ## The output will be saved in the 'derfinderReport-example' directory
> dir.create('derfinderReport-example', showWarnings = FALSE, recursive = TRUE)
>
> ## For convenience, the derfinder output has been pre-computed
> file.copy(system.file(file.path('extdata', 'chr21'), package='derfinder',
+ mustWork=TRUE), 'derfinderReport-example', recursive = TRUE)
[1] TRUE
>
> ## Not run:
> ##D ## If you prefer, you can generate the output from derfinder
> ##D initialPath <- getwd()
> ##D setwd(file.path(initialPath, 'derfinderReport-example'))
> ##D
> ##D ## Collapse the coverage information
> ##D collapsedFull <- collapseFullCoverage(list(genomeData$coverage),
> ##D verbose=TRUE)
> ##D
> ##D ## Calculate library size adjustments
> ##D sampleDepths <- sampleDepth(collapsedFull, probs=c(0.5), nonzero=TRUE,
> ##D verbose=TRUE)
> ##D
> ##D ## Build the models
> ##D group <- genomeInfo$pop
> ##D adjustvars <- data.frame(genomeInfo$gender)
> ##D models <- makeModels(sampleDepths, testvars=group, adjustvars=adjustvars)
> ##D
> ##D ## Analyze chromosome 21
> ##D analyzeChr(chr='21', coverageInfo=genomeData, models=models,
> ##D cutoffFstat=1, cutoffType='manual', seeds=20140330, groupInfo=group,
> ##D mc.cores=1, writeOutput=TRUE, returnOutput=FALSE)
> ##D
> ##D ## Change the directory back to the original one
> ##D setwd(initialPath)
> ## End(Not run)
>
> ## Merge the results from the different chromosomes. In this case, there's
> ## only one: chr21
> mergeResults(chrs = '21', prefix = 'derfinderReport-example',
+ genomicState = genomicState$fullGenome)
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
2018-04-11 08:40:03 mergeResults: Saving options used
2018-04-11 08:40:03 Loading chromosome chr21
Neither 'cutoffFstatUsed' nor 'optionsStats' were supplied, so the FWER calculation step will be skipped.
2018-04-11 08:40:03 mergeResults: Saving fullNullSummary
2018-04-11 08:40:03 mergeResults: Re-calculating the p-values
2018-04-11 08:40:04 mergeResults: Saving fullRegions
2018-04-11 08:40:04 mergeResults: assigning genomic states
2018-04-11 08:40:04 annotateRegions: counting
2018-04-11 08:40:04 annotateRegions: annotating
2018-04-11 08:40:04 mergeResults: Saving fullAnnotatedRegions
2018-04-11 08:40:04 mergeResults: Saving fullFstats
2018-04-11 08:40:04 mergeResults: Saving fullTime
>
> ## Load the options used for calculating the statistics
> load(file.path('derfinderReport-example', 'chr21', 'optionsStats.Rdata'))
>
> ## Generate the HTML report
> report <- derfinderReport(prefix='derfinderReport-example', browse=FALSE,
+ nBestRegions=1, makeBestClusters=FALSE,
+ fullCov=list('21'=genomeDataRaw$coverage), optionsStats=optionsStats)
Writing 9 Bibtex entries ... OK
Results written to file 'derfinderReport-example/basicExploration/basicExploration.bib'
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
processing file: basicExploration.Rmd
inline R code fragments
label: docSetup (with options)
List of 3
$ bootstrap.show.code : logi FALSE
$ dev : symbol device
$ bootstrap.show.message: logi FALSE
ordinary text without R code
label: setup (with options)
List of 1
$ bootstrap.show.message: logi FALSE
ordinary text without R code
label: pvals (with options)
List of 4
$ fig.width : num 10
$ fig.height: num 10
$ eval : symbol nullExist
$ echo : symbol nullExist
sh: line 1: 52998 Abort trap: 6 'convert' 'basicExploration_files/figure-html/pvals-1.png' -trim 'basicExploration_files/figure-html/pvals-1.png' > /dev/null
ordinary text without R code
label: summPval (with options)
List of 2
$ eval: symbol nullExist
$ echo: symbol nullExist
inline R code fragments
label: summQval (with options)
List of 2
$ eval: symbol nullExist
$ echo: symbol nullExist
inline R code fragments
label: qsummary (with options)
List of 3
$ eval : symbol nullExist
$ echo : symbol nullExist
$ results: chr "asis"
inline R code fragments
label: summFwer (with options)
List of 2
$ eval: symbol fwerExist
$ echo: symbol fwerExist
inline R code fragments
label: FWERsummary (with options)
List of 3
$ eval : symbol fwerExist
$ echo : symbol fwerExist
$ results: chr "asis"
inline R code fragments
label: regLen (with options)
List of 4
$ fig.width : num 14
$ fig.height: num 14
$ eval : symbol hasSig
$ echo : symbol hasSig
sh: line 1: 53006 Abort trap: 6 'convert' 'basicExploration_files/figure-html/regLen-1.png' -trim 'basicExploration_files/figure-html/regLen-1.png' > /dev/null
ordinary text without R code
label: regLen2 (with options)
List of 4
$ fig.width : num 10
$ fig.height: num 10
$ eval : language !hasSig
$ echo : language !hasSig
inline R code fragments
label: regArea (with options)
List of 4
$ fig.width : num 14
$ fig.height: num 14
$ eval : symbol hasArea
$ echo : symbol hasArea
sh: line 1: 53016 Abort trap: 6 'convert' 'basicExploration_files/figure-html/regArea-1.png' -trim 'basicExploration_files/figure-html/regArea-1.png' > /dev/null
ordinary text without R code
label: regArea2 (with options)
List of 4
$ fig.width : num 10
$ fig.height: num 10
$ eval : language !hasArea
$ echo : language !hasArea
inline R code fragments
label: nullLengthArea (with options)
List of 4
$ fig.width : num 14
$ fig.height: num 14
$ eval : symbol nullExist
$ echo : symbol nullExist
sh: line 1: 53018 Abort trap: 6 'convert' 'basicExploration_files/figure-html/nullLengthArea-1.png' -trim 'basicExploration_files/figure-html/nullLengthArea-1.png' > /dev/null
inline R code fragments
label: meanCov (with options)
List of 4
$ fig.width : num 14
$ fig.height: num 14
$ eval : symbol hasSig
$ echo : symbol hasSig
sh: line 1: 53020 Abort trap: 6 'convert' 'basicExploration_files/figure-html/meanCov-1.png' -trim 'basicExploration_files/figure-html/meanCov-1.png' > /dev/null
ordinary text without R code
label: meanCov2 (with options)
List of 4
$ fig.width : num 10
$ fig.height: num 10
$ eval : language !hasSig
$ echo : language !hasSig
inline R code fragments
label: MAstyle (with options)
List of 2
$ fig.width : num 10
$ fig.height: num 10
sh: line 1: 53031 Abort trap: 6 'convert' 'basicExploration_files/figure-html/MAstyle-1.png' -trim 'basicExploration_files/figure-html/MAstyle-1.png' > /dev/null
inline R code fragments
label: genomeOverview1 (with options)
List of 6
$ message : logi FALSE
$ fig.width : num 7
$ fig.height: num 9
$ dpi : num 300
$ eval : symbol nullExist
$ echo : symbol nullExist
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
sh: line 1: 53036 Abort trap: 6 'convert' 'basicExploration_files/figure-html/genomeOverview1-1.png' -trim 'basicExploration_files/figure-html/genomeOverview1-1.png' > /dev/null
inline R code fragments
label: manhattanPlots (with options)
List of 2
$ echo : logi FALSE
$ results: chr "asis"
ordinary text without R code
label: genomeOverview2 (with options)
List of 4
$ message : logi FALSE
$ fig.width : num 7
$ fig.height: num 9
$ dpi : num 300
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
sh: line 1: 53073 Abort trap: 6 'convert' 'basicExploration_files/figure-html/genomeOverview2-1.png' -trim 'basicExploration_files/figure-html/genomeOverview2-1.png' > /dev/null
ordinary text without R code
label: annoReg (with options)
List of 1
$ results: chr "asis"
inline R code fragments
label: genomeOverview3 (with options)
List of 6
$ message : logi FALSE
$ fig.width : num 7
$ fig.height: num 9
$ dpi : num 300
$ eval : symbol hasSig
$ echo : symbol hasSig
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
sh: line 1: 53079 Abort trap: 6 'convert' 'basicExploration_files/figure-html/genomeOverview3-1.png' -trim 'basicExploration_files/figure-html/genomeOverview3-1.png' > /dev/null
inline R code fragments
label: plotRegions (with options)
List of 3
$ fig.width : num 10
$ fig.height : num 10
$ bootstrap.show.message: logi FALSE
sh: line 1: 53126 Abort trap: 6 'convert' 'basicExploration_files/figure-html/plotRegions-1.png' -trim 'basicExploration_files/figure-html/plotRegions-1.png' > /dev/null
sh: line 1: 53128 Abort trap: 6 'convert' 'basicExploration_files/figure-html/plotRegions-2.png' -trim 'basicExploration_files/figure-html/plotRegions-2.png' > /dev/null
ordinary text without R code
label: countTable (with options)
List of 1
$ results: chr "asis"
ordinary text without R code
label: vennDiagram (with options)
List of 2
$ fig.width : num 7
$ fig.height: num 7
sh: line 1: 53130 Abort trap: 6 'convert' 'basicExploration_files/figure-html/vennDiagram-1.png' -trim 'basicExploration_files/figure-html/vennDiagram-1.png' > /dev/null
inline R code fragments
label: vennDiagramSignificant (with options)
List of 4
$ eval : symbol hasSig
$ echo : symbol hasSig
$ fig.width : num 7
$ fig.height: num 7
sh: line 1: 53132 Abort trap: 6 'convert' 'basicExploration_files/figure-html/vennDiagramSignificant-1.png' -trim 'basicExploration_files/figure-html/vennDiagramSignificant-1.png' > /dev/null
inline R code fragments
label: bestAreaInfo (with options)
List of 1
$ results: chr "asis"
inline R code fragments
label: plotCluster (with options)
List of 4
$ message: logi FALSE
$ warning: logi FALSE
$ eval : symbol makeBestClusters
$ echo : symbol makeBestClusters
inline R code fragments
label: bestClusters (with options)
List of 6
$ message : logi FALSE
$ warning : logi FALSE
$ fig.width : num 20
$ fig.height: num 10
$ eval : symbol makeBestClusters
$ echo : symbol makeBestClusters
ordinary text without R code
label: permute2 (with options)
List of 2
$ eval: symbol usedPermutations
$ echo: symbol usedPermutations
inline R code fragments
label: permuteTable (with options)
List of 3
$ results: chr "asis"
$ eval : symbol usedPermutations
$ echo : symbol usedPermutations
ordinary text without R code
label: unnamed-chunk-1 (with options)
List of 2
$ child: symbol customCode
$ eval : symbol hasCustomCode
inline R code fragments
label: analysisCall (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: mergeCall (with options)
List of 1
$ echo: logi FALSE
inline R code fragments
label: thecall (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: reproducibility1 (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: reproducibility2 (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: reproducibility3 (with options)
List of 1
$ echo: logi FALSE
inline R code fragments
label: bibliography (with options)
List of 3
$ results: chr "asis"
$ echo : logi FALSE
$ warning: logi FALSE
Quitting from lines 698-700 (basicExploration.Rmd)
Error in if (resp$headers[["content-type"]] == "text/bibliography") content(resp) else print(bib) :
argument is of length zero
Calls: derfinderReport ... eval -> eval -> bibliography -> sapply -> lapply -> FUN
Execution halted
* 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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/regionReport.Rcheck/00check.log’
for details.
Installation output
regionReport.Rcheck/00install.out
Tests output
Example timings
regionReport.Rcheck/regionReport-Ex.timings