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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