[Bioc-devel] how to declare vignette processing properly

Fri May 6 19:15:47 CEST 2016

Is pandoc-citeproc installed?

----- Original Message -----
> From: "Vincent Carey" <stvjc at channing.harvard.edu>
> To: "Andrzej Oleś" <andrzej.oles at gmail.com>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, May 6, 2016 9:44:06 AM
> Subject: Re: [Bioc-devel] how to declare vignette processing properly

> Thanks Andrzej, can you give a bit more diagnosis?  Is 1.13.1 too old?
> 
> %derby01> pandoc -v
> 
> pandoc 1.13.1
> 
> Compiled with texmath 0.8, highlighting-kate 0.5.11.
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> Default user data directory: /udd/stvjc/.pandoc
> 
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> 
> Web:  http://johnmacfarlane.net/pandoc
> 
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> On Fri, May 6, 2016 at 12:30 PM, Andrzej Oleś <andrzej.oles at gmail.com>
> wrote:
> 
>> 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
>>>
>>>         [[alternative HTML version deleted]]
>>>
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>>>
>>
>>
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