search for: build_vignettes

...w if there's a way to include such PDF files as vignettes. We *do* have the source files for the PDF files in question, but it would be tedious to convert those source files to Rmd format. My first thought was simply to add the PDF files to the .../vignettes subdirectory and run the devtools::build_vignettes() function (mentioned in the Broman tutorial), but that doesn't work. I.e., the PDF files don't appear in the list of vignettes for the package. And after running devtools::build_vignettes I see that there's a lot of additional stuff in: ...lib/R/site-library/<package_name>...

...ude such PDF files as vignettes. > > We *do* have the source files for the PDF files in question, but it would be > tedious to convert those source files to Rmd format. > > My first thought was simply to add the PDF files to the .../vignettes > subdirectory and run the devtools::build_vignettes() function (mentioned in > the Broman tutorial), but that doesn't work. I.e., the PDF files don't appear > in the list of vignettes for the package. > > And after running devtools::build_vignettes I see that there's a lot of > additional stuff in: > > ...lib...

.... >> >> We *do* have the source files for the PDF files in question, but it would >> be >> tedious to convert those source files to Rmd format. >> >> My first thought was simply to add the PDF files to the .../vignettes >> subdirectory and run the devtools::build_vignettes() function (mentioned >> in >> the Broman tutorial), but that doesn't work. I.e., the PDF files don't >> appear >> in the list of vignettes for the package. >> >> And after running devtools::build_vignettes I see that there's a lot of >> additi...

I am running R 3.5.1 on ubuntu 18.04, installed via apt. When I run R from the bash prompt, I get (reinstalling r-base doesn't help) > devtools::install_github("goranbrostrom/eha", build_vignettes = TRUE) *** caught segfault *** address 0x68456, cause 'memory not mapped' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(name) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names,...

...clude such PDF files as vignettes. > > We *do* have the source files for the PDF files in question, but it would be > tedious to convert those source files to Rmd format. > > My first thought was simply to add the PDF files to the .../vignettes > subdirectory and run the devtools::build_vignettes() function (mentioned in > the Broman tutorial), but that doesn't work. I.e., the PDF files don't appear > in the list of vignettes for the package. > > And after running devtools::build_vignettes I see that there's a lot of > additional stuff in: > > ...lib/R/...

So far you haven't provided a reproducible example yet. I wonder what exactly the object `sample_analysis` is. Sounds like it is an environment. If that is the case, devtools::build_vignettes() will tangle (for the meaning of "tangle", see ?tools::buildVignette) your vignette into an invalid R script. Environments cannot be represented via dput(), so knitr's purl() (eventually called by the vignette engine) cannot really create a valid R script when your vignette contains...

...MD INSTALL ** installing vignettes 'tr_srm_summary.Rmd' using 'UTF-8' Warning in data(skylineconfig) : data set 'skylineconfig' not found Error in get(data(skylineconfig)) : object 'skylineconfig' not found This problem isn't happening when running devtools::build_vignettes() The Package install works however if I first build the vignettes with devtools::build_vignettes() and than run R CMD INSTALL I will be sending to you a link to a repository with a reproducible example in a separate e-mail. Kind regards Witek On 9 July 2018 at 18:24, Yihui Xie <xie at yihu...

...We *do* have the source files for the PDF files in question, but it would >>> be >>> tedious to convert those source files to Rmd format. >>> >>> My first thought was simply to add the PDF files to the .../vignettes >>> subdirectory and run the devtools::build_vignettes() function (mentioned >>> in >>> the Broman tutorial), but that doesn't work. I.e., the PDF files don't >>> appear >>> in the list of vignettes for the package. >>> >>> And after running devtools::build_vignettes I see that there's...

...ce files for the PDF files in question, but it would >>>> be >>>> tedious to convert those source files to Rmd format. >>>> >>>> My first thought was simply to add the PDF files to the .../vignettes >>>> subdirectory and run the devtools::build_vignettes() function (mentioned >>>> in >>>> the Broman tutorial), but that doesn't work. I.e., the PDF files don't >>>> appear >>>> in the list of vignettes for the package. >>>> >>>> And after running devtools::build_vignette...

...question, but it > would > >>>> be > >>>> tedious to convert those source files to Rmd format. > >>>> > >>>> My first thought was simply to add the PDF files to the .../vignettes > >>>> subdirectory and run the devtools::build_vignettes() function > (mentioned > >>>> in > >>>> the Broman tutorial), but that doesn't work. I.e., the PDF files > don't > >>>> appear > >>>> in the list of vignettes for the package. > >>>> > >>>> And...

...ysis_Empty.Rmd_t" } ``` ```{r includeMissingInOne, child = child_docs} ``` # this is line 351 from the error message which depending on a test outcome includes one or the other Rmarkdown document into the main document. While this report renders executing rmarkdown::render or devtools::build_vignettes, it fails when building the package with devtools::build or R CMD build given the following error: Error in eval(x, envir = envir) : object 'child_docs' not found Warning in readLines(if (is.character(input2)) { : cannot open file './child_docs': No such file or directory Quitti...

Dear Duncan, Following your advice (Thank you for it) I did include into the vignettes params: configuration: !r get(data(sample_analysis)) data: !r get(data(skylineconfig)) And everything seemed (see below) to work fine. devtools::build_vignettes() builds the vignettes. Runs with NO error. By this the .Rmd file, html file and corresponding .R files is being placed into the inst/doc directory. However, when I did want to check the package by running devtools::check(build_args="--no-build-vignettes") The following warning is show...

...Thu, 2018-07-05 at 21:37 +0200, G?ran Brostr?m wrote: >> I am running R 3.5.1 on ubuntu 18.04, installed via apt. When I run >> R >> from the bash prompt, I get (reinstalling r-base doesn't help) >> >> > devtools::install_github("goranbrostrom/eha", build_vignettes = >> TRUE) >> >> *** caught segfault *** >> address 0x68456, cause 'memory not mapped' >> >> Traceback: >> 1: dyn.load(file, DLLpath = DLLpath, ...) >> 2: library.dynam(lib, package, package.lib) >> 3: loadNamespace(name) &gt...

...regards Enrico Quoting G?ran Brostr?m <goran.brostrom at umu.se>: > I am running R 3.5.1 on ubuntu 18.04, installed via apt. When I run > R from the bash prompt, I get (reinstalling r-base doesn't help) > >> devtools::install_github("goranbrostrom/eha", build_vignettes = TRUE) > > *** caught segfault *** > address 0x68456, cause 'memory not mapped' > > Traceback: > 1: dyn.load(file, DLLpath = DLLpath, ...) > 2: library.dynam(lib, package, package.lib) > 3: loadNamespace(name) > 4: doTryCatch(return(expr), name, parentenv, h...

...evel/2018-September/076786.html Finally, I did had some time to create a minimal package to reproduce the problem that vignettes with child can not be build. https://github.com/wolski/RmarkdownVignetteProblem The problem basically is that while all the vignettes can be build by running devtools::build_vignettes or rmarkdown::render they will all fail to build when running devtools::build() or R CMD build except of the ABVignetteWithLocalChild.Rmd for which I did apply the workaround suggested by Duncan in this github issue: https://github.com/yihui/knitr/issues/1540 Best regards Witek -- Witold E...

...gt;> ``` >> # this is line 351 from the error message >> >> which depending on a test outcome includes one or the other Rmarkdown >> document into the main document. >> >> >> While this report renders executing rmarkdown::render or >> devtools::build_vignettes, it fails when building the package with >> devtools::build or R CMD build >> given the following error: >> >> >> Error in eval(x, envir = envir) : object 'child_docs' not found >> Warning in readLines(if (is.character(input2)) { : >> cannot open...

On 09/07/2018 3:24 PM, Witold E Wolski wrote: > Dear Yihui, > > Thank you for the valuable questions. > > sample_analysis is a "tibble" while > configuration is an "R6" class. > But I also have parametrized reports where I pass R reference classes > as arguments. > > This is the Rmd yaml params part corresponding to the error message. > >

Dear Duncan, Was close to giving up to use the parameterized rmarkown as vignettes. But your suggestions to use quote and eval, as well as to use the package parameter in data made it work, with all devtools::install,check,build and build_vignettes as well as with R CMD ... etc. But most importantly it also still works with: rmarkdown::render("vignettes/tr_srm_summary.Rmd", params=list(configuration=skylineconfig, data=sample_analysis )) THANK YOU. This is how my vignette header looks (see below) and it works. --- title: &quot...

...ssingInOne, child = child_docs} > ``` > # this is line 351 from the error message > > which depending on a test outcome includes one or the other Rmarkdown > document into the main document. > > > While this report renders executing rmarkdown::render or > devtools::build_vignettes, it fails when building the package with > devtools::build or R CMD build > given the following error: > > > Error in eval(x, envir = envir) : object 'child_docs' not found > Warning in readLines(if (is.character(input2)) { : > cannot open file './child_docs...

...Wolski wrote: > Dear Duncan, > > Following your advice (Thank you for it) I did include into the vignettes > params: > configuration: !r get(data(sample_analysis)) > data: !r get(data(skylineconfig)) > > And everything seemed (see below) to work fine. > devtools::build_vignettes() builds the vignettes. > > Runs with NO error. By this the .Rmd file, html file and corresponding > .R files is being placed into the inst/doc directory. > > However, when I did want to check the package by running > devtools::check(build_args="--no-build-vignettes")...