Re: [Bioc-devel] Error processing scater vignette Mac OS X Sierra

2016-11-30 Thread Leonardo Collado Torres 
Hi Davis,

Update your BiocStyle package to 2.2.1 (release) or 2.3.12 (devel)
which I see you are using at
https://github.com/Bioconductor-mirror/scater/blob/master/DESCRIPTION#L24.
See https://stat.ethz.ch/pipermail/bioc-devel/2016-November/010168.html
for details

Best,
Leo

On Wed, Nov 30, 2016 at 12:33 PM, Davis McCarthy  wrote:
> Hi all
>
>
>
> Since updating to Mac OS X Sierra (the only system change I can think of),
> building the vignette in scater throws an error. It seems to be caused by
> excess arguments to pandoc, but this has never been a problem until now (the
> vignette hasn't changed in any major way for months).
>
>
>
> Has anyone else seen this? Do you know how to fix?
>
>
>
> Details (error messages, session info etc) below.
>
>
>
> Best
> Davis
>
>
>
> The error message reads:
> ```
> Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> unused arguments (self_contained, lib_dir, output_dir)
> Execution halted
> Error: Command failed (1)
> Execution halted
>
> Exited with status 1.
> ```
>
>
>
> Running the vignette outside of R CMD check runs fine until the final step of
> converting the .md file to html, which fails with the  same error as above:
>
> ```
>
> Error in rmarkdown:::pandoc_html_highlight_args(highlight, template =
> "default",  :
>  unused arguments (self_contained, lib_dir, output_dir)
> Calls:  ->  -> overlay -> 
> Execution halted
>
> ```
>
>
>
> Unfortunately there's not really enough information there for me to know
> what's going on.
>
>
>
> Session Info:
>
> ```
>
>> sessionInfo()
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: macOS Sierra 10.12.1
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.8  vipor_0.4.4  plyr_1.8.4
> zlibbioc_1.20.0  viridis_0.3.4
> [6] bitops_1.0-6 tools_3.3.2  biomaRt_2.30.0
> digest_0.6.10rhdf5_2.18.0
> [11] RSQLite_1.0.0tibble_1.2   gtable_0.2.0
> lattice_0.20-34  shiny_0.14.2
> [16] DBI_0.5-1parallel_3.3.2   beeswarm_0.2.3
> gridExtra_2.2.1  stringr_1.1.0
> [21] dplyr_0.5.0  scater_1.1.27S4Vectors_0.12.0
> IRanges_2.8.1stats4_3.3.2
> [26] locfit_1.5-9.1   grid_3.3.2   shinydashboard_0.5.3
> Biobase_2.34.0   data.table_1.9.6
> [31] R6_2.2.0 AnnotationDbi_1.36.0 XML_3.98-1.5
> ggbeeswarm_0.5.0 limma_3.30.4
> [36] reshape2_1.4.2   ggplot2_2.2.0magrittr_1.5
> edgeR_3.16.3 matrixStats_0.51.0
> [41] scales_0.4.1 htmltools_0.3.5  BiocGenerics_0.20.0
> tximport_1.2.0   assertthat_0.1
> [46] mime_0.5 xtable_1.8-2 colorspace_1.3-1
> httpuv_1.3.3 stringi_1.1.2
> [51] RCurl_1.95-4.8   lazyeval_0.2.0   munsell_0.4.3
> rjson_0.2.15 chron_2.3-47
>
> ```
>
>
>
> Output of R CMD check in RStudio:
>
> ```
>
> ==> devtools::check()
>
> Updating scater documentation
> Loading scater
> Loading required package: Biobase
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
>clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>clusterExport, clusterMap, parApply, parCapply, parLapply,
>parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
>IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
>anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
>duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
>is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
>paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
>Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
>unique, unsplit, which, which.max, which.min
>
> Welcome to Bioconductor
>
>Vignettes contain introductory material; view with
>'browseVignettes()'. To cite Bioconductor, see
>'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: ggplot2
> Creating a new generic function for ‘mutate’ in package ‘scater’
> Creating a new generic function for ‘filter’ in package ‘scater’
> Setting env vars
> ---
> CFLAGS  : -Wall -pedantic
> CXXFLAGS: -Wall -pedantic
> Building scater
> 
> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
> \
>  \--no-save --no-restore --quiet CMD build  \
>  '/Users/davis/Dropbox/Projects/scater' --no-resave-data --no-manual
>
> * checking for file ‘/Users/davis/Dropbox/Projects/scater/DESCRIPTION’ ... OK
> *

[Bioc-devel] Error processing scater vignette Mac OS X Sierra

2016-11-30 Thread Davis McCarthy 
Hi all

  

Since updating to Mac OS X Sierra (the only system change I can think of),
building the vignette in scater throws an error. It seems to be caused by
excess arguments to pandoc, but this has never been a problem until now (the
vignette hasn't changed in any major way for months).

  

Has anyone else seen this? Do you know how to fix?

  

Details (error messages, session info etc) below.

  

Best  
Davis

  

The error message reads:  
```  
Error: processing vignette 'vignette.Rmd' failed with diagnostics:  
unused arguments (self_contained, lib_dir, output_dir)  
Execution halted  
Error: Command failed (1)  
Execution halted  
  
Exited with status 1.  
```

  

Running the vignette outside of R CMD check runs fine until the final step of
converting the .md file to html, which fails with the  same error as above:

```

Error in rmarkdown:::pandoc_html_highlight_args(highlight, template =
"default",  :  
 unused arguments (self_contained, lib_dir, output_dir)  
Calls:  ->  -> overlay ->   
Execution halted  

```

  

Unfortunately there's not really enough information there for me to know
what's going on.

  

Session Info:

```

> sessionInfo()  
R version 3.3.2 (2016-10-31)  
Platform: x86_64-apple-darwin13.4.0 (64-bit)  
Running under: macOS Sierra 10.12.1  
  
locale:  
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8  
  
attached base packages:  
[1] stats graphics  grDevices utils datasets  methods   base  
  
loaded via a namespace (and not attached):  
[1] Rcpp_0.12.8  vipor_0.4.4  plyr_1.8.4
zlibbioc_1.20.0  viridis_0.3.4  
[6] bitops_1.0-6 tools_3.3.2  biomaRt_2.30.0
digest_0.6.10rhdf5_2.18.0  
[11] RSQLite_1.0.0tibble_1.2   gtable_0.2.0
lattice_0.20-34  shiny_0.14.2  
[16] DBI_0.5-1parallel_3.3.2   beeswarm_0.2.3
gridExtra_2.2.1  stringr_1.1.0  
[21] dplyr_0.5.0  scater_1.1.27S4Vectors_0.12.0
IRanges_2.8.1stats4_3.3.2  
[26] locfit_1.5-9.1   grid_3.3.2   shinydashboard_0.5.3
Biobase_2.34.0   data.table_1.9.6  
[31] R6_2.2.0 AnnotationDbi_1.36.0 XML_3.98-1.5
ggbeeswarm_0.5.0 limma_3.30.4  
[36] reshape2_1.4.2   ggplot2_2.2.0magrittr_1.5
edgeR_3.16.3 matrixStats_0.51.0  
[41] scales_0.4.1 htmltools_0.3.5  BiocGenerics_0.20.0
tximport_1.2.0   assertthat_0.1  
[46] mime_0.5 xtable_1.8-2 colorspace_1.3-1
httpuv_1.3.3 stringi_1.1.2  
[51] RCurl_1.95-4.8   lazyeval_0.2.0   munsell_0.4.3
rjson_0.2.15 chron_2.3-47  

```

  

Output of R CMD check in RStudio:

```

==> devtools::check()  
  
Updating scater documentation  
Loading scater  
Loading required package: Biobase  
Loading required package: BiocGenerics  
Loading required package: parallel  
  
Attaching package: ‘BiocGenerics’  
  
The following objects are masked from ‘package:parallel’:  
  
   clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,  
   clusterExport, clusterMap, parApply, parCapply, parLapply,  
   parLapplyLB, parRapply, parSapply, parSapplyLB  
  
The following objects are masked from ‘package:stats’:  
  
   IQR, mad, xtabs  
  
The following objects are masked from ‘package:base’:  
  
   anyDuplicated, append, as.data.frame, cbind, colnames, do.call,  
   duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,  
   is.unsorted, lapply, lengths, Map, mapply, match, mget, order,  
   paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,  
   Reduce, rownames, sapply, setdiff, sort, table, tapply, union,  
   unique, unsplit, which, which.max, which.min  
  
Welcome to Bioconductor  
  
   Vignettes contain introductory material; view with  
   'browseVignettes()'. To cite Bioconductor, see  
   'citation("Biobase")', and for packages 'citation("pkgname")'.  
  
Loading required package: ggplot2  
Creating a new generic function for ‘mutate’ in package ‘scater’  
Creating a new generic function for ‘filter’ in package ‘scater’  
Setting env vars
---  
CFLAGS  : -Wall -pedantic  
CXXFLAGS: -Wall -pedantic  
Building scater
  
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
\  
 \--no-save --no-restore --quiet CMD build  \  
 '/Users/davis/Dropbox/Projects/scater' --no-resave-data --no-manual  
  
* checking for file ‘/Users/davis/Dropbox/Projects/scater/DESCRIPTION’ ... OK  
* preparing ‘scater’:  
* checking DESCRIPTION meta-information ... OK  
* cleaning src  
* installing the package to build vignettes  
* creating vignettes ... ERROR  
  
Attaching package: 'BiocGenerics'  
  
The following objects are masked from 'package:parallel':  
  
   clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,  
   clusterExport, clusterMap, parApply, parCapply, parLapply,  
   parLapplyLB,