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BUILD report for CNPBayes on malbec2

This page was generated on 2019-10-16 12:07:46 -0400 (Wed, 16 Oct 2019).

Package 307/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.14.0
Jacob Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CNPBayes
Branch: RELEASE_3_9
Last Commit: 547ab1b
Last Changed Date: 2019-05-02 11:53:58 -0400 (Thu, 02 May 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  ERROR  skipped  skipped 

Summary

Package: CNPBayes
Version: 1.14.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CNPBayes
StartedAt: 2019-10-15 21:38:52 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 21:42:28 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 216.3 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CNPBayes
###
##############################################################################
##############################################################################


* checking for file ‘CNPBayes/DESCRIPTION’ ... OK
* preparing ‘CNPBayes’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
duplicated vignette title:
  ‘Overview of CNPBayes package’

--- re-building ‘Convergence.Rmd’ using rmarkdown
Quitting from lines 44-48 (Convergence.Rmd) 
Error: processing vignette 'Convergence.Rmd' failed with diagnostics:
1 components of `...` had unexpected names.

We detected these problematic arguments:
* `values`

Did you misspecify an argument?
Backtrace:
     x
  1. +-tools::buildVignettes(dir = ".", tangle = TRUE)
  2. | +-base::tryCatch(...)
  3. | | \-base:::tryCatchList(expr, classes, parentenv, handlers)
  4. | |   \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. | |     \-base:::doTryCatch(return(expr), name, parentenv, handler)
  6. | \-engine$weave(file, quiet = quiet, encoding = enc)
  7. |   \-knitr:::vweave_rmarkdown(...)
  8. |     \-rmarkdown::render(...)
  9. |       \-knitr::knit(...)
 10. |         \-knitr:::process_file(text, output)
 11. |           +-base::withCallingHandlers(...)
 12. |           +-knitr:::process_group(group)
 13. |           \-knitr:::process_group.block(group)
 14. |             \-knitr:::call_block(x)
 15. |               \-knitr:::block_exec(params)
 16. |                 +-knitr:::in_dir(...)
 17. |                 \-knitr:::evaluate(...)
 18. |                   \-evaluate::evaluate(...)
 19. |                     \-evaluate:::evaluate_call(...)
 20. |                       +-evaluate:::timing_fn(...)
 21. |                       +-base:::handle(...)
 22. |                       +-base::withCallingHandlers(...)
 23. |                       +-base::withVisible(eval(expr, envir, enclos))
 24. |                       \-base::eval(expr, envir, enclos)
 25. |                         \-base::eval(expr, envir, enclos)
 26. +-CNPBayes::ggChains(model)
 27. \-CNPBayes::ggChains(model)
 28.   \-CNPBayes:::.ggMultiBatchPooledChains(model)
 29.     +-CNPBayes:::gatherChains(model)
 30.     \-CNPBayes:::gatherChains(model)
 31.       \-CNPBayes:::.meltMultiBatchPooledChains(object)
 32.         +-gather(th, key = "variable", values = -c(param, iter)) %>% as.tibble
 33.         | \-base::eval(lhs, parent, parent)
 34.         |   \-base::eval(lhs, parent, parent)
 35.         \-tidyr::gather(th, key = "variable", values = -c(param, iter))
 36.           \-ellipsis::check_dots_unnamed()
 37.             \-ellipsis:::action_dots(...)
--- failed re-building ‘Convergence.Rmd’

--- re-building ‘Implementation.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/home/biocbuild/bbs-3.9-bioc/R/libra
ry/BiocStyle/resources/tex/Bioconductor',
               but the package provides `Bioconductor'.
Package geometry Warning: Over-specification in `h'-direction.
    `width' (384.1122pt) is ignored.
Package Fancyhdr Warning: \fancyhead's `E' option without twoside option is use
less on input line 173.
--- finished re-building ‘Implementation.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

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

    count

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

-- Attaching packages ------------------------------------ tidyverse 1.2.1 --
v tibble  2.1.3     v purrr   0.3.2
v readr   1.3.1     v stringr 1.4.0
v tibble  2.1.3     v forcats 0.4.0
-- Conflicts --------------------------------------- tidyverse_conflicts() --
x ggplot2::Position()  masks BiocGenerics::Position(), base::Position()
x dplyr::collapse()    masks IRanges::collapse()
x Biobase::combine()   masks dplyr::combine(), BiocGenerics::combine()
x matrixStats::count() masks dplyr::count()
x dplyr::desc()        masks IRanges::desc()
x tidyr::expand()      masks S4Vectors::expand()
x dplyr::filter()      masks stats::filter()
x dplyr::first()       masks S4Vectors::first()
x dplyr::lag()         masks stats::lag()
x purrr::reduce()      masks GenomicRanges::reduce(), IRanges::reduce()
x dplyr::rename()      masks S4Vectors::rename()
x purrr::simplify()    masks DelayedArray::simplify()
x dplyr::slice()       masks IRanges::slice()
Loading required package: VanillaICE
Welcome to VanillaICE version 1.46.0
Quitting from lines 72-77 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
1 components of `...` had unexpected names.

We detected these problematic arguments:
* `values`

Did you misspecify an argument?
Backtrace:
     x
  1. +-tools::buildVignettes(dir = ".", tangle = TRUE)
  2. | +-base::tryCatch(...)
  3. | | \-base:::tryCatchList(expr, classes, parentenv, handlers)
  4. | |   \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. | |     \-base:::doTryCatch(return(expr), name, parentenv, handler)
  6. | \-engine$weave(file, quiet = quiet, encoding = enc)
  7. |   \-knitr:::vweave_rmarkdown(...)
  8. |     \-rmarkdown::render(...)
  9. |       \-knitr::knit(...)
 10. |         \-knitr:::process_file(text, output)
 11. |           +-base::withCallingHandlers(...)
 12. |           +-knitr:::process_group(group)
 13. |           \-knitr:::process_group.block(group)
 14. |             \-knitr:::call_block(x)
 15. |               \-knitr:::block_exec(params)
 16. |                 +-knitr:::in_dir(...)
 17. |                 \-knitr:::evaluate(...)
 18. |                   \-evaluate::evaluate(...)
 19. |                     \-evaluate:::evaluate_call(...)
 20. |                       +-evaluate:::timing_fn(...)
 21. |                       +-base:::handle(...)
 22. |                       +-base::withCallingHandlers(...)
 23. |                       +-base::withVisible(eval(expr, envir, enclos))
 24. |                       \-base::eval(expr, envir, enclos)
 25. |                         \-base::eval(expr, envir, enclos)
 26. +-CNPBayes::ggChains(model)
 27. \-CNPBayes::ggChains(model)
 28.   \-CNPBayes:::.ggMultiBatchChains(model)
 29.     +-CNPBayes:::gatherChains(model)
 30.     \-CNPBayes:::gatherChains(model)
 31.       \-CNPBayes:::.meltMultiBatchChains(object)
 32.         +-gather(th, key = "variable", values = -c(param, iter)) %>% as.tibble
 33.         | \-base::eval(lhs, parent, parent)
 34.         |   \-base::eval(lhs, parent, parent)
 35.         \-tidyr::gather(th, key = "variable", values = -c(param, iter))
 36.           \-ellipsis::check_dots_unnamed()
 37.             \-ellipsis:::action_dots(...)
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Convergence.Rmd’ ‘Overview.Rmd’

Error: Vignette re-building failed.
Error: Duplicate vignette titles.
  Ensure that the %\VignetteIndexEntry lines in the vignette sources
  correspond to the vignette titles.
Execution halted