kenhanscombe
commented
3 years ago By default devtools::github_install should not build the vignettes: build_manual = FALSE, build_vignettes = FALSE. The vignette is written in rmarkdown, which is declared as a dependency.
Maybe try creating a dedicated conda environment then try installing into that environment?
Hi
devtools::install_github("kenhanscombe/ukbtools", dependencies = TRUE)
When I use the above command I am getting the following error:
E> checking for file ‘/nvme/pbs/tmpdir/pbs.202087.flashmgr2/RtmpCkMHkl/remotes615da87bc05/kenhanscombe-ukbtools-3dca23a/DESCRIPTION’ ... OK E> preparing ‘ukbtools’: E> checking DESCRIPTION meta-information ... OK E> installing the package to process help pages E> * creating vignettes ... ERROR E> Warning in engine$weave(file, quiet = quiet, encoding = enc) : E> Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1. E> Error: processing vignette 'explore-ukb-data.Rmd' failed with diagnostics: E> The 'markdown' package should be installed and declared as a dependency of the 'ukbtools' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'markdown' package. Please see https://github.com/yihui/knitr/issues/1864 for more information. E> Execution halted
I do not have pandoc in the cluster.
How can I solve this problem?
Regards,
Sathish