By default when one is using install_github
function from devtools
package in R the vignettes of the installed package are not build. I've seen this questio with an answer which shows how to build vignettes if one desires to
Building R package from github: how to disable building vignettes?.
I wrote a package with such vignettes and but I recieve an error what installing directly from github like this:
> devtools::install_github("MarcinKosinski/RTCGA")
Downloading github repo MarcinKosinski/RTCGA@master
Installing RTCGA
'/usr/lib/R/bin/R' --vanilla CMD INSTALL \
'/tmp/RtmpCIboSY/devtools17de96523e5/MarcinKosinski-RTCGA-e47bdf6' \
--library='/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2' \
--install-tests
* installing *source* package ‘RTCGA’ ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCGA)
> browseVignettes("RTCGA")
No vignettes found by browseVignettes("RTCGA")
> ?devtools::install_github
> devtools::install_github("MarcinKosinski/RTCGA", build_vignettes= TRUE)
Downloading github repo MarcinKosinski/RTCGA@master
Installing RTCGA
'/usr/lib/R/bin/R' --vanilla CMD build \
'/tmp/RtmpCIboSY/devtools17de1905fc71/MarcinKosinski-RTCGA-e47bdf6' \
--no-resave-data --no-manual
* checking for file ‘/tmp/RtmpCIboSY/devtools17de1905fc71/MarcinKosinski-RTCGA-e47bdf6/DESCRIPTION’ ... OK
* preparing ‘RTCGA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘RTCGA/ghPage’
Removed empty directory ‘RTCGA/inst’
* building ‘RTCGA_0.99.6.tar.gz’
'/usr/lib/R/bin/R' --vanilla CMD INSTALL \
'/tmp/RtmpCIboSY/RTCGA_0.99.6.tar.gz' \
--library='/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2' \
--install-tests
* installing *source* package ‘RTCGA’ ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
cannot open file '/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2/RTCGA/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing ‘/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2/RTCGA’
* restoring previous ‘/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2/RTCGA’
Error: Command failed (1)
When I build package from source locally there are no errors. Can anyone know what can be a cause of this?
I needed to add
.onLoad <- function(libname, pkgname) {
vig_list = tools::vignetteEngine(package = 'knitr')
vweave <- vig_list[['knitr::knitr']][c('weave')][[1]]
vtangle <- vig_list[['knitr::knitr']][c('tangle')][[1]]
tools::vignetteEngine(pkgname, weave = vweave, tangle = vtangle,
pattern = "[.]Rmd$", package = pkgname)
#register_vignette_engines(pkgname)
}
this function to zzz.R
file in R/
directory and knitr
package to Dependencies in DESCRIPTION
file.
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