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 <da...@ebi.ac.uk> 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: <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
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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