[Bioc-devel] how to declare vignette processing properly

[Andrzej Oleś]

Hi Vince,

this is most probably due to missing/incorrect pandoc installation.

Cheers,
Andrzej

On Fri, May 6, 2016 at 6:18 PM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> this is for the current svn version of yriMulti, from 00check.log
>
> * checking re-building of vignette outputs ... WARNING
>
> Error in re-building vignettes:
>
>   ...
>
> Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if
> (grepl("\\.[Rr]rst$",  :
>
>   It seems you should call rmarkdown::render() instead of
> knitr::knit2html() because yriMulti.Rmd appears to be an R Markdown v2
> document.
>
>
> > sessionInfo()
>
> R version 3.3.0 (2016-05-03)
>
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> Running under: CentOS release 6.7 (Final)
>
>
> locale:
>
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>
> [8] methods   base
>
>
> other attached packages:
>
>  [1] yriMulti_0.0.9
>
>  [2] geuvPack_1.3.5
>
>  [3] dsQTL_0.9.4
>
>  [4] GGBase_3.34.0
>
>  [5] snpStats_1.22.0
>
>  [6] Matrix_1.2-6
>
>  [7] survival_2.39-3
>
>  [8] Homo.sapiens_1.3.1
>
>  [9] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
>
> [10] org.Hs.eg.db_3.3.0
>
> [11] GO.db_3.3.0
>
> [12] OrganismDbi_1.14.0
>
> [13] GenomicFeatures_1.24.0
>
> [14] AnnotationDbi_1.34.0
>
> [15] SummarizedExperiment_1.2.0
>
> [16] Biobase_2.32.0
>
> [17] GenomicRanges_1.24.0
>
> [18] GenomeInfoDb_1.8.0
>
> [19] IRanges_2.6.0
>
> [20] S4Vectors_0.10.0
>
> [21] BiocGenerics_0.18.0
>
> [22] gQTLBase_1.4.0
>
>
> loaded via a namespace (and not attached):
>
>  [1] genefilter_1.54.0        ffbase_0.12.3
> VariantAnnotation_1.18.0
>
>  [4] splines_3.3.0            lattice_0.20-33          rtracklayer_1.32.0
>
>
>  [7] base64enc_0.1-3          XML_3.98-1.4             RBGL_1.48.0
>
>
> [10] DBI_0.4                  BiocParallel_1.6.0       foreach_1.4.3
>
>
> [13] stringr_1.0.0            zlibbioc_1.18.0          Biostrings_2.40.0
>
>
> [16] codetools_0.2-14         ff_2.2-13                biomaRt_2.28.0
>
>
> [19] doParallel_1.0.10        BiocInstaller_1.22.1     xtable_1.8-2
>
>
> [22] backports_1.0.2          BSgenome_1.40.0          checkmate_1.7.4
>
>
> [25] graph_1.50.0             annotate_1.50.0          XVector_0.12.0
>
>
> [28] sendmailR_1.2-1          bit_1.1-12               Rsamtools_1.24.0
>
>
> [31] fastmatch_1.0-4          brew_1.0-6               BatchJobs_1.6
>
>
> [34] fail_1.3                 digest_0.6.9             stringi_1.0-1
>
>
> [37] BBmisc_1.9               GenomicFiles_1.8.0       grid_3.3.0
>
>
> [40] tools_3.3.0              bitops_1.0-6             magrittr_1.5
>
>
> [43] RCurl_1.95-4.8           RSQLite_1.0.0            iterators_1.0.8
>
>
> [46] GenomicAlignments_1.8.0
>
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>
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