trouble finding file source in .rmd chunk when knitting .rmd from master .R file
knitr, r
Solution
@Yihui: Perhaps you can make `../` an absolute path using `normalizePath('../')`. A relative working directory can be confusing to reason about (at least my head hurts after I read too many levels of relative paths :). BTW, when you Knit HTML in RStudio, RStudio first changes the working directory to the input Rmd file.
Me: yes! using just `opts_knit$set(root.dir=normalizePath('../'))` works for knitting the `.rmd` file from `master.R` and knitting to html or running all chunks from within the `.rmd`. I updated the github example. `test-b.rmd` now shows this. thanks!
Problem
Let's say I have a project directory called `testknit` (and I do, see github for MRE), and inside this I have several subdirectories, including `scripts` where I keep `.R` and `.rmd` files. In RStudio, I create a project and select this `testknit` directory so that when I open the project, the working directory is `mypath/testknit`. Inside `testknit/scripts` I have a `master.R` file. If I want to source a file called `testsource1.R`, which is also in `testknit/scripts`, I can run `source("scripts/testsource1.R")` from within `master.R`. ``` library(knitr) getwd() # [1] "mypath/testknit" source("scripts/testsource1.R") ``` So far so good. But let's say I also want to knit a `.rmd` file called `test.rmd` that is located in `testknit/scripts`. I can run `knit("scripts/test.rmd")` from `master.R`. My `test.rmd` file does the following: ```` ```{r setup} library(knitr) opts_knit$set(root.dir='../') ``` ```{r option1} source("scripts/testsource2.R") ``` ```{r option2} source("testsource2.R") ``` ```` Since `test.rmd` exists within `testknit/scripts`, I specify `opts_knit$set(root.dir='../')` in the first chunk so knitr knows that my root directory is really one level up. When I open `test.rmd` in RStudio and click `knit HTML`, predictably, the `option1` chunk works and the `option2` chunk does not. But when I try to knit `test.rmd` by running `knit("scripts/test.rmd")` from `master.R` instead of knitting from within the `.rmd` file, neither chunk option works. Both return an error that there is no file by that name. What am I doing wrong? Why can't R find `testsource2.R` when knitting the `.rmd` file from the master `.R`? See github link above for reproducible example. Update: As I noted below in the comments, I tried adding `wd <- getwd()` just before `opts_knit$set` and changed `(root.dir='../')` to `(root.dir=wd)`. So when I run `knit("scripts/test.rmd")` from `master.R`, the option2 chunk runs because the `wd` I added gets set to `mypath/testknit/scripts`. But if i open the `.rmd` file and run all chunks, `wd` is set to the root directory, `mypath/testknit`, and the option1 chunk runs. I need the working directory to remain the project root. This does not seem like an elegant solution to me, but changing: ```` ```{r setup} library(knitr) opts_knit$set(root.dir='../') ``` ```` to ```` ```{r setup} library(knitr) wd <- ifelse(basename(getwd())=="scripts", gsub("/scripts", "", getwd()), getwd()) opts_knit$set(root.dir=wd) ``` ```` lets me run all chunks when in the `.rmd` file or `knit("scripts/test.rmd")` from `master.R`. It works, but it feels like I am taking the wrong approach.