BioC 3.6: CHECK report for regionReport on tokay1

Package: regionReport

Version: 1.11.3

Command: rm -rf regionReport.buildbin-libdir regionReport.Rcheck && mkdir regionReport.buildbin-libdir regionReport.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=regionReport.buildbin-libdir regionReport_1.11.3.tar.gz >regionReport.Rcheck\00install.out 2>&1 && cp regionReport.Rcheck\00install.out regionReport-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=regionReport.buildbin-libdir --install="check:regionReport-install.out" --force-multiarch --no-vignettes --timings regionReport_1.11.3.tar.gz

StartedAt: 2017-08-16 01:56:34 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:07:09 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 634.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: regionReport.Rcheck

Warnings: NA

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###
### Running command:
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###   rm -rf regionReport.buildbin-libdir regionReport.Rcheck && mkdir regionReport.buildbin-libdir regionReport.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=regionReport.buildbin-libdir regionReport_1.11.3.tar.gz >regionReport.Rcheck\00install.out 2>&1 && cp regionReport.Rcheck\00install.out regionReport-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=regionReport.buildbin-libdir --install="check:regionReport-install.out" --force-multiarch --no-vignettes --timings regionReport_1.11.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/regionReport.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'regionReport/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'regionReport' version '1.11.3'
* 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 '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
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
renderReport    88.87   4.13   94.72
derfinderReport 31.89   4.25   38.06
DESeq2Report    33.91   1.75   42.28
edgeReport      16.33   1.34   18.97
** running examples for arch 'x64' ... ERROR
Running examples in 'regionReport-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: edgeReport
> ### Title: Generate a HTML/PDF report exploring edgeR results
> ### Aliases: edgeReport
> 
> ### ** Examples
> 
> 
> ## Create example data using DEFormats
> library('DEFormats')
> set.seed(20160407)
> counts <- simulateRnaSeqData()
> group <- rep(c("A", "B"), each = 3)
> 
> ## Create DGEList object
> library('edgeR')
Loading required package: limma

Attaching package: 'edgeR'

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

    DGEList

> dge <- DGEList(counts, group = group)
> 
> ## Perform DE analysis with edgeR
> design <- model.matrix( ˜ group)
> dge <- estimateDisp(dge, design)
> fit <- glmFit(dge, design)
> lrt <- glmLRT(fit, coef = 2)
> 
> ## The output will be saved in the 'edgeReport-example' directory
> dir.create('edgeReport-example', showWarnings = FALSE, recursive = TRUE)
> 
> ## Generate the HTML report
> report <- edgeReport(dge, lrt, project = 'edgeR-example', intgroup = 'group',
+     outdir = 'edgeReport-example')
Warning in `[.bibentry`(citation("edgeR"), 5) : subscript out of bounds
Warning in c.bibentry(knitcitations = citation("knitcitations"), regionReport = citation("regionReport")[1],  :
  method is only applicable to 'bibentry' objects
Writing 12 Bibtex entries ... OK
Results written to file 'edgeReport-example/edgeRexploration.bib'


processing file: edgeRexploration.Rmd
   inline R code fragments

Warning in `[[.bibentry`(bib, c("edgeR1", "edgeR2", "edgeR5", "edgeR6")) :
  subscript out of bounds
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: PCA
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/PCA-1.png" -trim "edgeRexploration_files/figure-html/PCA-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/PCA-1.png" -trim "edgeRexploration_files/figure-html/PCA-1.png"' execution failed with error code 4
   inline R code fragments

label: sampleDist
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/sampleDist-1.png" -trim "edgeRexploration_files/figure-html/sampleDist-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/sampleDist-1.png" -trim "edgeRexploration_files/figure-html/sampleDist-1.png"' execution failed with error code 4
  ordinary text without R code

label: MAplotalpha
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/MAplotalpha-1.png" -trim "edgeRexploration_files/figure-html/MAplotalpha-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/MAplotalpha-1.png" -trim "edgeRexploration_files/figure-html/MAplotalpha-1.png"' execution failed with error code 4
   inline R code fragments

label: MAplotalphaHalf
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/MAplotalphaHalf-1.png" -trim "edgeRexploration_files/figure-html/MAplotalphaHalf-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/MAplotalphaHalf-1.png" -trim "edgeRexploration_files/figure-html/MAplotalphaHalf-1.png"' execution failed with error code 4
   inline R code fragments

label: MAplotalpha-nBest
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/MAplotalpha-nBest-1.png" -trim "edgeRexploration_files/figure-html/MAplotalpha-nBest-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/MAplotalpha-nBest-1.png" -trim "edgeRexploration_files/figure-html/MAplotalpha-nBest-1.png"' execution failed with error code 4
   inline R code fragments

label: pvalueHistogram
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/pvalueHistogram-1.png" -trim "edgeRexploration_files/figure-html/pvalueHistogram-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/pvalueHistogram-1.png" -trim "edgeRexploration_files/figure-html/pvalueHistogram-1.png"' execution failed with error code 4
  ordinary text without R code

label: pvalueSumm
  ordinary text without R code

label: pvalueTable (with options) 
List of 1
 $ results: chr "asis"

  ordinary text without R code

label: padjHistogram
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/padjHistogram-1.png" -trim "edgeRexploration_files/figure-html/padjHistogram-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/padjHistogram-1.png" -trim "edgeRexploration_files/figure-html/padjHistogram-1.png"' execution failed with error code 4
   inline R code fragments

label: padjSumm
   inline R code fragments

label: padjTable (with options) 
List of 1
 $ results: chr "asis"

   inline R code fragments

label: topFeatures (with options) 
List of 1
 $ results: chr "asis"

   inline R code fragments

label: plotCounts
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-1.png" -trim "edgeRexploration_files/figure-html/plotCounts-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-1.png" -trim "edgeRexploration_files/figure-html/plotCounts-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-2.png" -trim "edgeRexploration_files/figure-html/plotCounts-2.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-2.png" -trim "edgeRexploration_files/figure-html/plotCounts-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-3.png" -trim "edgeRexploration_files/figure-html/plotCounts-3.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-3.png" -trim "edgeRexploration_files/figure-html/plotCounts-3.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-4.png" -trim "edgeRexploration_files/figure-html/plotCounts-4.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-4.png" -trim "edgeRexploration_files/figure-html/plotCounts-4.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-5.png" -trim "edgeRexploration_files/figure-html/plotCounts-5.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-5.png" -trim "edgeRexploration_files/figure-html/plotCounts-5.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-6.png" -trim "edgeRexploration_files/figure-html/plotCounts-6.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-6.png" -trim "edgeRexploration_files/figure-html/plotCounts-6.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-7.png" -trim "edgeRexploration_files/figure-html/plotCounts-7.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-7.png" -trim "edgeRexploration_files/figure-html/plotCounts-7.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-8.png" -trim "edgeRexploration_files/figure-html/plotCounts-8.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-8.png" -trim "edgeRexploration_files/figure-html/plotCounts-8.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-9.png" -trim "edgeRexploration_files/figure-html/plotCounts-9.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-9.png" -trim "edgeRexploration_files/figure-html/plotCounts-9.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-10.png" -trim "edgeRexploration_files/figure-html/plotCounts-10.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-10.png" -trim "edgeRexploration_files/figure-html/plotCounts-10.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-11.png" -trim "edgeRexploration_files/figure-html/plotCounts-11.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-11.png" -trim "edgeRexploration_files/figure-html/plotCounts-11.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-12.png" -trim "edgeRexploration_files/figure-html/plotCounts-12.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-12.png" -trim "edgeRexploration_files/figure-html/plotCounts-12.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-13.png" -trim "edgeRexploration_files/figure-html/plotCounts-13.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-13.png" -trim "edgeRexploration_files/figure-html/plotCounts-13.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-14.png" -trim "edgeRexploration_files/figure-html/plotCounts-14.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-14.png" -trim "edgeRexploration_files/figure-html/plotCounts-14.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-15.png" -trim "edgeRexploration_files/figure-html/plotCounts-15.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-15.png" -trim "edgeRexploration_files/figure-html/plotCounts-15.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-16.png" -trim "edgeRexploration_files/figure-html/plotCounts-16.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-16.png" -trim "edgeRexploration_files/figure-html/plotCounts-16.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-17.png" -trim "edgeRexploration_files/figure-html/plotCounts-17.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-17.png" -trim "edgeRexploration_files/figure-html/plotCounts-17.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-18.png" -trim "edgeRexploration_files/figure-html/plotCounts-18.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-18.png" -trim "edgeRexploration_files/figure-html/plotCounts-18.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-19.png" -trim "edgeRexploration_files/figure-html/plotCounts-19.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-19.png" -trim "edgeRexploration_files/figure-html/plotCounts-19.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/plotCounts-20.png" -trim "edgeRexploration_files/figure-html/plotCounts-20.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/plotCounts-20.png" -trim "edgeRexploration_files/figure-html/plotCounts-20.png"' execution failed with error code 4
   inline R code fragments

label: edgeR-BCV (with options) 
List of 2
 $ eval: symbol isEdgeR
 $ echo: language isEdgeR & outputIsHTML

Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/edgeR-BCV-1.png" -trim "edgeRexploration_files/figure-html/edgeR-BCV-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/edgeR-BCV-1.png" -trim "edgeRexploration_files/figure-html/edgeR-BCV-1.png"' execution failed with error code 4
   inline R code fragments

label: edgeR-MDS (with options) 
List of 2
 $ eval: symbol isEdgeR
 $ echo: language isEdgeR & outputIsHTML

Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "edgeRexploration_files/figure-html/edgeR-MDS-1.png" -trim "edgeRexploration_files/figure-html/edgeR-MDS-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "edgeRexploration_files/figure-html/edgeR-MDS-1.png" -trim "edgeRexploration_files/figure-html/edgeR-MDS-1.png"' execution failed with error code 4
   inline R code fragments

label: unnamed-chunk-1 (with options) 
List of 2
 $ child: symbol customCode
 $ eval : symbol hasCustomCode

   inline R code fragments

Warning in `[[.bibentry`(bib, c("edgeR1", "edgeR2", "edgeR5", "edgeR6")) :
  subscript out of bounds
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 348-350 (edgeRexploration.Rmd) 
Error in lapply(x, function(e) sprintf("%o", e)) : 
  reached elapsed time limit
Calls: edgeReport ... Ops.numeric_version -> split -> .encode_numeric_version -> lapply
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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/regionReport.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'regionReport' ...
** R
** 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 'regionReport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'regionReport' as regionReport_1.11.3.zip
* DONE (regionReport)

name	user	system	elapsed
DESeq2Report	33.91	1.75	42.28
derfinderReport	31.89	4.25	38.06
edgeReport	16.33	1.34	18.97
renderReport	88.87	4.13	94.72

name	user	system	elapsed
DESeq2Report	33.54	1.64	36.91
derfinderReport	31.16	3.56	35.90