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 | |
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### Running command:
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### chmod a+r CNPBayes -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data CNPBayes
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* 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
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `Implementation_files/figure-latex/graph-marginal-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `Implementation_files/figure-latex/mapping-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `Implementation_files/figure-latex/ggMixture-1.pdf'.
Warning: LaTeX Warning: You have requested package `C:/Users/biocbuild/bbs-3.9-bioc/R/li
brary/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