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Georgios

2021-Jan-22 06:49 UTC

[R] rmarkdown and source call to R file.

Hi!
I'm new in R and this list.
I made a shiny app using R studio.
my files are:
   -server.R
   -ui.R
   -helper.R
   -Report.Rmd.

All the files are on the same directory and helper.R is a file that
contains a lot of functions used in Report.Rmd and server.R

for some reason I cant call from Report.Rmd the file helper.R

My code in Report.Rmd is

   ## Summarize table
   ```{r, echo=FALSE}
   library(knitr)
   source("helper.R", local = knitr::knit_global())
   summarized_table<-give_table(params$ldf_summary)
   kable(summarized_table,"simple")
   ```
If I use absolute path it works but since I want to upload it to 
https://www.shinyapps.io/ I must make it work with relative path.

The message I get is:

   processing file: Report.Rmd
    
   |..........................                                         
                                        |  25%
     ordinary text without R code

    
   |....................................................               
                                        |  50%
   label: unnamed-chunk-1 (with options) 
   List of 1
    $ echo: logi FALSE

   Quitting from lines 13-17 (Report.Rmd) 

   Warning: Error in file: cannot open the connection
     [No stack trace available]


The funny thing is that if I put the cursor inside "" at the beginning
and I press tab I get the option to choose helper.R. So Im guessing
that I'm on the right directory.
Any ideas what I'm missing?

I'm stuck on this lines of code 2 days now.
I would really appreciate
any ideas.


Thanks in advance for your help!!!


ps. I tried all the combinations in Tools->Global Options-> "Evaluate
chunks in directory" with no luck.

Jeff Newmiller

2021-Jan-22 07:57 UTC

head link

[R] rmarkdown and source call to R file.

This is off topic here... please read the Posting Guide about getting help on
contributed packages.  Check out the RStudio forums.

FWIW you should also look carefully at ?knitr::knit_global ... I don't think
it does what you seem to think it does.

On January 21, 2021 10:49:17 PM PST, Georgios via R-help <r-help at
r-project.org> wrote:>Hi!
>I'm new in R and this list.
>I made a shiny app using R studio.
>my files are:
>   -server.R
>   -ui.R
>   -helper.R
>   -Report.Rmd.
>
>All the files are on the same directory and helper.R is a file that
>contains a lot of functions used in Report.Rmd and server.R
>
>for some reason I cant call from Report.Rmd the file helper.R
>
>My code in Report.Rmd is
>
>   ## Summarize table
>   ```{r, echo=FALSE}
>   library(knitr)
>   source("helper.R", local = knitr::knit_global())
>   summarized_table<-give_table(params$ldf_summary)
>   kable(summarized_table,"simple")
>   ```
>If I use absolute path it works but since I want to upload it to 
>https://www.shinyapps.io/ I must make it work with relative path.
>
>The message I get is:
>
>   processing file: Report.Rmd
>    
>   |..........................                                         
>                                        |  25%
>     ordinary text without R code
>
>    
>   |....................................................               
>                                        |  50%
>   label: unnamed-chunk-1 (with options) 
>   List of 1
>    $ echo: logi FALSE
>
>   Quitting from lines 13-17 (Report.Rmd) 
>
>   Warning: Error in file: cannot open the connection
>     [No stack trace available]
>
>
>The funny thing is that if I put the cursor inside "" at the
beginning
>and I press tab I get the option to choose helper.R. So Im guessing
>that I'm on the right directory.
>Any ideas what I'm missing?
>
>I'm stuck on this lines of code 2 days now.
>I would really appreciate
>any ideas.
>
>
>Thanks in advance for your help!!!
>
>
>ps. I tried all the combinations in Tools->Global Options->
"Evaluate
>chunks in directory" with no luck.
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
-- 
Sent from my phone. Please excuse my brevity.

John Kane

2021-Jan-22 15:05 UTC

head link

[R] rmarkdown and source call to R file.

You would be better to try https://community.rstudio.com. Shiny is
basically Tidyverse/Rstudio item and there will be a lot more expertise
there.

On Fri, 22 Jan 2021 at 02:02, Georgios via R-help <r-help at
r-project.org>
wrote:
> Hi!
> I'm new in R and this list.
> I made a shiny app using R studio.
> my files are:
>    -server.R
>    -ui.R
>    -helper.R
>    -Report.Rmd.
>
> All the files are on the same directory and helper.R is a file that
> contains a lot of functions used in Report.Rmd and server.R
>
> for some reason I cant call from Report.Rmd the file helper.R
>
> My code in Report.Rmd is
>
>    ## Summarize table
>    ```{r, echo=FALSE}
>    library(knitr)
>    source("helper.R", local = knitr::knit_global())
>    summarized_table<-give_table(params$ldf_summary)
>    kable(summarized_table,"simple")
>    ```
> If I use absolute path it works but since I want to upload it to
> https://www.shinyapps.io/ I must make it work with relative path.
>
> The message I get is:
>
>    processing file: Report.Rmd
>
>    |..........................
>                                         |  25%
>      ordinary text without R code
>
>
>    |....................................................
>                                         |  50%
>    label: unnamed-chunk-1 (with options)
>    List of 1
>     $ echo: logi FALSE
>
>    Quitting from lines 13-17 (Report.Rmd)
>
>    Warning: Error in file: cannot open the connection
>      [No stack trace available]
>
>
> The funny thing is that if I put the cursor inside "" at the
beginning
> and I press tab I get the option to choose helper.R. So Im guessing
> that I'm on the right directory.
> Any ideas what I'm missing?
>
> I'm stuck on this lines of code 2 days now.
> I would really appreciate
> any ideas.
>
>
> Thanks in advance for your help!!!
>
>
> ps. I tried all the combinations in Tools->Global Options->
"Evaluate
> chunks in directory" with no luck.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
John Kane
Kingston ON Canada

	[[alternative HTML version deleted]]

Yihui Xie

2021-Jan-22 15:17 UTC

head link

[R] rmarkdown and source call to R file.

I don't know the answer (there are multiple possible reasons for the
file not being found), but as the first step to debug the problem, you
may replace this chunk

```{r, echo=FALSE}
   library(knitr)
   source("helper.R", local = knitr::knit_global())
   summarized_table<-give_table(params$ldf_summary)
   kable(summarized_table,"simple")
```

with

```{r}
getwd()
list.files()
```

and see what the working directory is, and which files are available.

Regards,
Yihui


On Fri, Jan 22, 2021 at 1:02 AM Georgios via R-help
<r-help at r-project.org> wrote:>
> Hi!
> I'm new in R and this list.
> I made a shiny app using R studio.
> my files are:
>    -server.R
>    -ui.R
>    -helper.R
>    -Report.Rmd.
>
> All the files are on the same directory and helper.R is a file that
> contains a lot of functions used in Report.Rmd and server.R
>
> for some reason I cant call from Report.Rmd the file helper.R
>
> My code in Report.Rmd is
>
>    ## Summarize table
>    ```{r, echo=FALSE}
>    library(knitr)
>    source("helper.R", local = knitr::knit_global())
>    summarized_table<-give_table(params$ldf_summary)
>    kable(summarized_table,"simple")
>    ```
> If I use absolute path it works but since I want to upload it to
> https://www.shinyapps.io/ I must make it work with relative path.
>
> The message I get is:
>
>    processing file: Report.Rmd
>
>    |..........................
>                                         |  25%
>      ordinary text without R code
>
>
>    |....................................................
>                                         |  50%
>    label: unnamed-chunk-1 (with options)
>    List of 1
>     $ echo: logi FALSE
>
>    Quitting from lines 13-17 (Report.Rmd)
>
>    Warning: Error in file: cannot open the connection
>      [No stack trace available]
>
>
> The funny thing is that if I put the cursor inside "" at the
beginning
> and I press tab I get the option to choose helper.R. So Im guessing
> that I'm on the right directory.
> Any ideas what I'm missing?
>
> I'm stuck on this lines of code 2 days now.
> I would really appreciate
> any ideas.
>
>
> Thanks in advance for your help!!!
>
>
> ps. I tried all the combinations in Tools->Global Options->
"Evaluate
> chunks in directory" with no luck.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

R help - Jan 2021 - rmarkdown and source call to R file.

[R] rmarkdown and source call to R file.

[R] rmarkdown and source call to R file.

[R] rmarkdown and source call to R file.

[R] rmarkdown and source call to R file.