[R-pkg-devel] (no subject)

I'm seeing:

* checking re-building of vignette outputs ... [3s] WARNING
Error in re-building vignettes:
...
Quitting from lines 24-60 (strider.Rmd)
Error: processing vignette 'strider.Rmd' failed with diagnostics:
package 'dplyr' is not installed for 'arch = x64'
Execution halted
I'm a little confused because my vignette avoids loading any packages that
are not available. Is this because the "eval" option is not available in
the version of knitr used by CRAN?

Here's the vignette code:
---
title: "The Strider Package"
author: "Timothy H. Keitt"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Vignette Title}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
```{r include=FALSE}
has_packages = all(c("dplyr", "ggplot2", "microbenchmark") %in%
rownames(installed.packages()))
not_has_packages = !has_packages
```
```{r echo=FALSE, eval=not_has_packages}
cat("Error: You must install dplyr, ggplot2 and microbenchmark to run the
code in this vignette.")
```
```{r include=FALSE, message=FALSE, warning=FALSE, eval=has_packages}
library(dplyr)
library(ggplot2)
library(microbenchmark)
...
This works fine on my computer even if I uninstall dplyr, etc. But it
appears that when CRAN tries to rebuild the vignette, the "eval" flag is
ignored?

Tricky to reproduce as the exact code used to regenerate the vignette is
not part of the output.

THK

http://www.keittlab.org/
Have you put dplyr in 'Suggests'? This should do.

Note that R CMD check runs the code in vignettes twice - once during building and then again the tangled R code file.
So the error may come from the second run. You can check this locally by telling knitr not to clean up after building the vignette and inspecting the generated R file.

I think that in recent versions of knitr there is an option to prevent generating the R file in the first place, so this may solve the problem.

Georgi

--
Dr Georgi Boshnakov               tel: (+44) (0)161 306 3684
School of Mathematics             fax: (+44) (0)161 306 3669
Alan Turing Building 1.125
The University of Manchester      email: Georgi.Boshnakov at manchester.ac.uk
Oxford Road
Manchester M13 9PL
UK

-----Original Message-----
From: R-package-devel [mailto:r-package-devel-bounces at r-project.org] On Behalf Of Tim Keitt
Sent: 10 January 2018 05:49
To: R Package Devel
Subject: [R-pkg-devel] (no subject)

I'm seeing:

* checking re-building of vignette outputs ... [3s] WARNING
Error in re-building vignettes:
...
Quitting from lines 24-60 (strider.Rmd)
Error: processing vignette 'strider.Rmd' failed with diagnostics:
package 'dplyr' is not installed for 'arch = x64'
Execution halted
I'm a little confused because my vignette avoids loading any packages that are not available. Is this because the "eval" option is not available in the version of knitr used by CRAN?

Here's the vignette code:
---
title: "The Strider Package"
author: "Timothy H. Keitt"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Vignette Title}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
```{r include=FALSE}
has_packages = all(c("dplyr", "ggplot2", "microbenchmark") %in%
rownames(installed.packages()))
not_has_packages = !has_packages
```
```{r echo=FALSE, eval=not_has_packages}
cat("Error: You must install dplyr, ggplot2 and microbenchmark to run 
the code in this vignette.") ``` ```{r include=FALSE, message=FALSE, 
warning=FALSE, eval=has_packages}
library(dplyr)
library(ggplot2)
library(microbenchmark)
...
This works fine on my computer even if I uninstall dplyr, etc. But it appears that when CRAN tries to rebuild the vignette, the "eval" flag is ignored?

Tricky to reproduce as the exact code used to regenerate the vignette is not part of the output.

THK

http://www.keittlab.org/

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