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

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: <Anonymous> -> <Anonymous> -> overlay -> <Anonymous>
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_0.6.10        rhdf5_2.18.0
[11] RSQLite_1.0.0        tibble_1.2           gtable_0.2.0
lattice_0.20-34      shiny_0.14.2
[16] DBI_0.5-1            parallel_3.3.2       beeswarm_0.2.3
gridExtra_2.2.1      stringr_1.1.0
[21] dplyr_0.5.0          scater_1.1.27        S4Vectors_0.12.0
IRanges_2.8.1        stats4_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_2.2.0        magrittr_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, parRapply, parSapply, parSapplyLB

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

   IQR, mad, xtabs

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

   Filter, Find, Map, Position, Reduce, anyDuplicated, append,
   as.data.frame, cbind, colnames, do.call, duplicated, eval,
   evalq, get, grep, grepl, intersect, is.unsorted, lapply,
   lengths, mapply, match, mget, order, paste, pmax, pmax.int,
   pmin, pmin.int, rank, rbind, 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")'.


Attaching package: 'scater'

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

   filter

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.

```


Davis McCarthy

NHMRC Early Career Fellow

Stegle Group

EMBL-EBI

www.ebi.ac.uk


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