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BUILD report for pRoloc on tokay2

This page was generated on 2019-04-09 12:01:28 -0400 (Tue, 09 Apr 2019).

Package 1234/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pRoloc 1.23.2
Laurent Gatto
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/pRoloc
Branch: master
Last Commit: 12e9698
Last Changed Date: 2019-03-15 05:37:41 -0400 (Fri, 15 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK [ ERROR ] skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: pRoloc
Version: 1.23.2
Command: chmod a+r pRoloc -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pRoloc
StartedAt: 2019-04-08 21:53:27 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:00:47 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 440.0 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r pRoloc -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pRoloc
###
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* checking for file 'pRoloc/DESCRIPTION' ... OK
* preparing 'pRoloc':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'v01-pRoloc-tutorial.Rmd' using rmarkdown
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plotdist1-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plotdist1-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/dendro-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/dendro-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plotavrprof-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plotavrprof-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plot2d-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plot2d-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plot2dorg-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plot2dorg-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/scree-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/scree-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plotfoi-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plotfoi-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/qsep-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/qsep-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/qsep-2.png" -trim "v01-pRoloc-tutorial_files/figure-html/qsep-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plot2dnull-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plot2dnull-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plotKmeans-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plotKmeans-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plotHclust-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plotHclust-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/plotPam-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/plotPam-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/params-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/params-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/params-2.png" -trim "v01-pRoloc-tutorial_files/figure-html/params-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/predscores-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/predscores-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/svmres-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/svmres-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/pdres-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/pdres-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v01-pRoloc-tutorial_files/figure-html/pdres2-1.png" -trim "v01-pRoloc-tutorial_files/figure-html/pdres2-1.png"' execution failed with error code 4
Warning: The label(s) fig:params not found
Warning: The label(s) fig:params not found
--- finished re-building 'v01-pRoloc-tutorial.Rmd'

--- re-building 'v02-pRoloc-ml.Rmd' using rmarkdown
Warning in lapply(X = X, FUN = FUN, ...) :
  NaNs found in 'precision' with hyperparameters cost:1 sigma:1.
Warning in lapply(X = X, FUN = FUN, ...) :
  NaNs found in 'precision' with hyperparameters cost:2 sigma:1.
--- finished re-building 'v02-pRoloc-ml.Rmd'

--- re-building 'v03-pRoloc-bayesian.Rmd' using rmarkdown
--- finished re-building 'v03-pRoloc-bayesian.Rmd'

--- re-building 'v04-pRoloc-goannotations.Rmd' using rmarkdown
Loading required namespace: GO.db

Retaining 80 out of 549 in GOAnnotations
Retaining 79 out of 80 in GOAnnotations
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v04-pRoloc-goannotations_files/figure-html/visualiseRes-1.png" -trim "v04-pRoloc-goannotations_files/figure-html/visualiseRes-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "v04-pRoloc-goannotations_files/figure-html/visualiseRes-2.png" -trim "v04-pRoloc-goannotations_files/figure-html/visualiseRes-2.png"' execution failed with error code 4
--- finished re-building 'v04-pRoloc-goannotations.Rmd'

--- re-building 'v05-pRoloc-transfer-learning.Rmd' using rmarkdown
Quitting from lines 143-147 (v05-pRoloc-transfer-learning.Rmd) 
Error: processing vignette 'v05-pRoloc-transfer-learning.Rmd' failed with diagnostics:
biomaRt error: looks like we're connecting to incompatible version of BioMart suite.
--- failed re-building 'v05-pRoloc-transfer-learning.Rmd'

SUMMARY: processing the following file failed:
  'v05-pRoloc-transfer-learning.Rmd'

Error: Vignette re-building failed.
Execution halted