search for: build_vignettes

Displaying 20 results from an estimated 21 matches for "build_vignettes".

2018 Feb 19
4
Include pre-existing PDF files as vignettes in an R package?
...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>...
2018 Feb 19
0
Include pre-existing PDF files as vignettes in an R package?
...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...
2018 Feb 19
2
Include pre-existing PDF files as vignettes in an R package?
.... >> >> 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...
2018 Jul 05
2
Segfault on ubuntu 18.04
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,...
2018 Feb 19
0
Include pre-existing PDF files as vignettes in an R package?
...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/...
2018 Jul 09
3
Parametrized Vignettest in R packages
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...
2018 Jul 09
0
Parametrized Vignettest in R packages
...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...
2018 Feb 19
0
Include pre-existing PDF files as vignettes in an R package?
...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...
2018 Feb 19
2
Include pre-existing PDF files as vignettes in an R package?
...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...
2018 Feb 19
0
Include pre-existing PDF files as vignettes in an R package?
...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...
2018 Jul 10
2
RMarkdown Vignettest in R packages with child is failing in package build
...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...
2018 Jul 09
2
Parametrized Vignettest in R packages
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...
2018 Jul 05
0
Segfault on ubuntu 18.04
...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...
2018 Jul 06
0
Segfault on ubuntu 18.04
...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...
2018 Nov 07
1
Problem building rmarkdown vignettes with child
...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...
2018 Jul 13
1
RMarkdown Vignettest in R packages with child is failing in package build
...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...
2018 Jul 09
2
Parametrized Vignettest in R packages
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. > >
2018 Jul 09
0
Parametrized Vignettest in R packages
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...
2018 Jul 10
0
RMarkdown Vignettest in R packages with child is failing in package build
...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...
2018 Jul 09
0
Parametrized Vignettest in R packages
...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")...