I&#39;m struggling to create a reproducible example for this, but I suspect others will know what I mean.  Why does R sometimes seem to get stuck with a backlog of warnings/error messages that it repeats again after subsequent commands?  E.g. you get some warning message `Bad whatever system choking` after running some code, which repeats again after you enter an innocuous instruction like `x &lt;- 5`. This sometimes happens after several entries of `x &lt;- 5`, although it normally stops after one or two.

R has been like this for me for at least 5 years, across many versions on both Windows and Mac.  Am I alone?  Does anyone know if it has been identified as a bug?  I normally work with RStudio so I wonder if it&#39;s related to the IDE.

-----------------------

Edit. Pretty sure this *is* related to RStudio.

Persistent warnings from earlier commands with RStudio

Update R using RStudio

I am using Rstudio and not sure how options &quot;run&quot; and &quot;source&quot; are different.

I tried googling these terms but &#39;source&#39; is a very common word and wasn&#39;t able to get good search results :(

![enter image description here][1]


  [1]: http://i.stack.imgur.com/2GHjV.jpg

Rstudio difference between run and source

I would like to set the working directory to the path of current script programmatically but first I need to get the path of current script.


So I would like to be able to do: &lt;br&gt;

    current_path = ...retrieve the path of current script ...
    setwd(current_path) 

Just like the RStudio menu does:
[![RStudio set working directory][1]][1]

So far I tried:

    initial.options &lt;- commandArgs(trailingOnly = FALSE)
    file.arg.name &lt;- &quot;--file=&quot;
    script.name &lt;- sub(file.arg.name, &quot;&quot;, initial.options[grep(file.arg.name, initial.options)])
    script.basename &lt;- dirname(script.name)

&gt; script.name **returns NULL**

    source(&quot;script.R&quot;, chdir = TRUE)

&gt; **Returns**:
&gt; Error in file(filename, &quot;r&quot;, encoding = encoding) : cannot open the
&gt; connection In addition: Warning message: In file(filename, &quot;r&quot;,
&gt; encoding = encoding) : cannot open file &#39;/script.R&#39;: No such file or
&gt; directory


    dirname(parent.frame(2)$ofile)

&gt; **Returns**: Error in dirname(parent.frame(2)$ofile) : a character vector argument expected
&gt; *...because parent.frame is null*


    frame_files &lt;- lapply(sys.frames(), function(x) x$ofile)
    frame_files &lt;- Filter(Negate(is.null), frame_files)
    PATH &lt;- dirname(frame_files[[length(frame_files)]])

&gt; **Returns**: Null because frame_files is a list of 0

    thisFile &lt;- function() {
        cmdArgs &lt;- commandArgs(trailingOnly = FALSE)
        needle &lt;- &quot;--file=&quot;
        match &lt;- grep(needle, cmdArgs)
        if (length(match) &gt; 0) {
            # Rscript
            return(normalizePath(sub(needle, &quot;&quot;, cmdArgs[match])))
        } else {
            # &#39;source&#39;d via R console
            return(normalizePath(sys.frames()[[1]]$ofile))
        }
    }

 &gt; **Returns**: Error in path.expand(path) : invalid &#39;path&#39; argument 

Also I saw all answers from [here][2], [here][3], [here][4] and [here][5].
No joy.

Working with `RStudio 1.1.383`

&gt; **EDIT:** It would be great if there was no need for an external library to achieve this.


  [1]: https://i.stack.imgur.com/2Gxf0.png
  [2]: https://stackoverflow.com/questions/3452086/getting-path-of-an-r-script
  [3]: https://stackoverflow.com/questions/1815606/rscript-determine-path-of-the-executing-script
  [4]: https://stackoverflow.com/questions/26519172/command-for-set-working-directory-to-source-file-location
  [5]: https://stackoverflow.com/questions/28550711/r-set-working-directory-to-folder

Get the path of current script

I have a simple script file called `test.R`. It&#39;s saved in the working directory. When I go to `File &gt; Open &gt; test.R`, it opens the file in the editor (without executing the code, which is what I want). 

How do I do this by typing a command in the console window? To be clear, I just want to open (**not** execute) the file.

How do I open a script file in RStudio using an R command?

I would like to output a progress indicator during my lengthy running algorithms. I can easily &quot;bubble up&quot; a progress value from within my algorithm (e.g. via invoking a provided function callback specifically for this purpose), but the difficulty is in the actual text output process. Every call to `print` creates a new line, and each prefixed with `[1]`.

**Is there a way to print at different moments in time, without introducing line breaks?**

To be concrete, I want to achieve an &quot;animation&quot; that would look like the following if observed at two different times.

    0%...

...

    0%...2%...4%...



How to output text in the R console without creating new lines?

`setwd` in an Rmd file in RStudio does not appear to change the directory in subsequent chunks.  Is there a way to set the working directory for good?

Example:

    ```{r}
    setwd(&quot;/tmp&quot;)
    getwd()
    ```
    
    ```{r}
    getwd()
    ```

Output:

    setwd(&quot;/tmp&quot;)
    getwd()
    ## [1] &quot;/private/tmp&quot;

    getwd()
    ## [1] &quot;/Users/me/src&quot;

This is on Mac OS 10.8.5 using RStudio 0.97.551, R version 3.0.2 and knitr version 1.5.

I wish to set the directory once for all subsequent chunks.



In RStudio/RMarkdown, how to setwd?

I am running R on Windows, not as an administrator. When I install a package, the following command doesn&#39;t work:

    &gt; install.packages(&quot;zoo&quot;)
    Installing package(s) into ‘C:/Program Files/R/R-2.15.2/library’
    (as ‘lib’ is unspecified)
    Warning in install.packages :
      &#39;lib = &quot;C:/Program Files/R/R-2.15.2/library&quot;&#39; is not writable

To install a package, I have to specify a library location:

    install.packages(&quot;zoo&quot;, lib=&quot;C:/software/Rpackages&quot;)

To load a package, I also have to specify the library location:

    library(&quot;zoo&quot;, lib.loc=&quot;C:/software/Rpackages&quot;)

All of this is OK, but I wanted to see if I could add `C:/software/Rpackages` to the library path somehow and thus not have to type it each time.

As I searched online, I found that one way to do this is to edit the `Rprofile.site` file and to add the line

    .libPaths(&quot;C:/software/Rpackages&quot;)

However, after doing this, and starting RStudio, this is the output that I get

    &gt; .libPaths()
    [1] &quot;C:/Program Files/R/R-2.15.2/library&quot; &quot;C:/Program Files/RStudio/R/library&quot; 

The `.libPaths` command that I added to the `Rprofile.site` doesn&#39;t seem to have had any effect! Why is this the case? Or more importantly, how can I fix the problem so that I can install and load packages without typing in the library location?

Note: if I start RStudio the `.libPaths()` command seems to work as it is supposed to

    .libPaths(&quot;C:/software/Rpackages&quot;)
    &gt; .libPaths()
    [1] &quot;C:/software/Rpackages&quot;               &quot;C:/Program Files/R/R-2.15.2/library&quot;

Isn&#39;t that strange?

Change R default library path using .libPaths in Rprofile.site fails to work

I have been using Knitr via R-Studio, and think it is pretty neat. I have a minor issue though. When I source a file in an R-Chunk, the knitr output includes external comments as follows: 


    + FALSE Loading required package: ggplot2
    + FALSE Loading required package: gridExtra
    + FALSE Loading required package: grid
    + FALSE Loading required package: VGAM
    + FALSE Loading required package: splines
    + FALSE Loading required package: stats4
    + FALSE Attaching package: &#39;VGAM&#39;
    + FALSE The following object(s) are masked from &#39;package:stats4&#39;:

I have tried to set R-chunk options in various ways but still didn&#39;t seem to avoid the problem: 

    ```{r echo=FALSE, cache=FALSE, results=FALSE, warning=FALSE, comment=FALSE, warning=FALSE} 
    source(&quot;C:/Rscripts/source.R&quot;);
    
    ```

Is there any way to comment out these messages?



R - Markdown avoiding package loading messages

I am trying to understand at a high level what the differences between `R Markdown` and `R NoteBook`. I know they are interrelated but I would like to figure out how they are related. My understanding is this:

I know R Notebooks are really R Markdown documents but I am confused about the terminologies.

RStudio new file option has both `R Markdown` and `R NoteBook` and selecting either of them opens an `R Markdown` file but with minor differences. **So just trying to figure out why are there two options and what is the difference between the two?** 

[![enter image description here][1]][1]


  [1]: https://i.stack.imgur.com/oyKmv.png

I understand R Notebooks are newly introduced and R Markdown has been there for a while. Part of the confusion could be because I never used `R Markdown` before R Notebook was introduced so my related or more specific question is

**What is R NoteBook doing differently than just using R MarkDown or what new capabilities is R NoteBook bringing?**
 
All my hits on web search are pointing that R Notebook uses R Markdown but I did not find any help on what is specifically different between the two. 


Difference between R MarkDown and R NoteBook

I recently &quot;upgraded&quot; from OSX Mountain Lion to Yosemite and from R 3.1.3 to 3.2. Immediately after the upgrade, when I opened R or RStudio I got a pop-up message saying that I needed to install Java 6. In addition, loading `rJava` or any package that depends on rJava (e.g., `xlsx`) caused RStudio to crash (R also crashed when I tried this by opening `R.app` directly). 

After trying a few fixes found on Stack Overflow and elsewhere (more details below), I am at a point where loading `rJava` or any package that depends on `rJava` no longer causes R to crash, but results in the following error:

    library(rJava)
    Error : .onLoad failed in loadNamespace() for &#39;rJava&#39;, details:
      call: dyn.load(file, DLLpath = DLLpath, ...)
      error: unable to load shared object &#39;/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so&#39;:
      dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
      Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so
      Reason: image not found
    Error: package or namespace load failed for ‘rJava’

However, if I invoke R from the command line and then load `rJava` or any package that depends on `rJava`, it seems to work (or at least I don&#39;t get any error messages).

I&#39;ve tried a number of different attempted fixes, some of them a few times, and can&#39;t quite remember exactly what I did in what order (didn&#39;t realize this would be such a morass and wasn&#39;t really keeping track), but here&#39;s the gist of it:

- Added the following to my `.bash_profile` (per [this SO answer](https://stackoverflow.com/a/30068890/496488)):

    &gt;export JAVA_HOME=&quot;/usr/libexec/java_home -v 1.8&quot;  
    &gt;export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/server

- Reconfigured java from the command line as follows:

    &gt;sudo R CMD javareconf -n  

- Checked `options(&quot;java.home&quot;)` and discovered this was set to  `NULL`. I tried setting it to the following (per [this SO question](https://stackoverflow.com/questions/28133360/rjava-is-not-picking-up-the-correct-java-version)):

    &gt;options(&quot;java.home&quot;=&quot;/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre&quot;)

- Installed the latest Java Development Kit and reinstalled `rJava` from source (can&#39;t remember where I found that one).

At some point while trying all of these, I was able to load `rJava` without crashing R, but instead got the error message posted above. In addition, when I quit RStudio, it would seem to close normally, but then an &quot;RStudio quit unexpectedly&quot; message would pop up, indicating that the program had crashed while trying to close. 

I finally decided to install [Java for OS X 2014-001](https://support.apple.com/kb/DL1572?locale=en_US) (Java 6), as I seemed to be running out of options. Now, when I opened R or RStudio the &quot;This software needs Java 6&quot; pop-up message no longer appeared. However, I was still getting the `.onLoad failed in loadNamespace() for &#39;rJava&#39;` error message posted above. 

In reviewing some of the posts I&#39;d already looked at, I noticed [another SO answer](https://stackoverflow.com/a/30581550/496488) that I&#39;d missed before, which recommended opening RStudio with the following command line code that gives RStudio the correct path to java:

&gt;LD_LIBRARY_PATH=$(/usr/libexec/java_home)/jre/lib/server: open -a RStudio

That opened an RStudio window and I was also able to load `rJava` and packages that depend on it without getting an error.

Lastly, I tried running R from the command line (which I hadn&#39;t done before). It turns out that on the command line, loading `rJava` or any package that depends on `rJava` works and does not throw any errors.

So, I can now get `rJava` to work if I open RStudio from the command line with the code that gives RStudio the java path (as noted above). However, I&#39;d like to find a way to fix the underlying problem, whatever it may be, so that RStudio can be opened in the usual Mac way, without needing a command line kludge. I&#39;m also concerned that having an old version of Java installed could cause problems down the road. 

Does anyone have any ideas about how to diagnose and solve this issue?

rJava load error in RStudio/R after &quot;upgrading&quot; to OSX Yosemite

I am using RStudio for writing markdown documents and want to add Table of Contents (TOC) at top of the documents so that the user could click the relevant section for reading. There were some relevant examples on rpubs but now I can&#39;t seem to find them. Please note that I don&#39;t use `pandoc` and am quite new to `Rmd` &amp; `knitr`. Is there any way to add TOCs without using `pandoc`? If using `pandoc` is must then which functions are relevant?

# EDIT

Here&#39;s a small sample page:

    ---
    title: &quot;Sample Document&quot;
    output:
      html_document:
        toc: true
        theme: united
    ---

    Header 1
    ---------------
    This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see &lt;http://rmarkdown.rstudio.com&gt;.
        
    ## Header 2
    When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
        
    ```{r}
    summary(cars)
    ```
    
    You can also embed plots, for example:
    
    ```{r, echo=FALSE}
    plot(cars)
    ```
    ### Header 3
    Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

I tried running this in RStudio v 0.98.864 and it worked! but sadly it didn&#39;t work on 0.98.501 and 0.98.507. I am working on my thesis in 0.98.501 and after updating RStudio, some of my analyses didn&#39;t work. So, I reverted back to 0.98.501.
What should I do now? I really want TOCs but without harming the outputs of other analyses.


How to add table of contents in Rmarkdown?

I wonder how to use `rmarkdown` to generate a pdf which has both portrait and landscape layout in the same document. If there is a pure `rmarkdown` option that would be even better than using latex.

Here&#39;s a small, reproducible example. First, rendering this `.Rmd` in RStudio (press **Knit PDF** button) results in a pdf with all pages in landscape layout:

    ---
    title: &quot;All pages landscape&quot;
    output: pdf_document
    classoption: landscape
    ---
      
    ```{r}
    summary(cars)
    ```
    
    \newpage
    ```{r}
    summary(cars)
    ```

Then an attempt to create a document which mixes portrait and landscape layout. The basic setup in the `YAML` is done according to the &#39;Includes&#39; section [**here**](http://rmarkdown.rstudio.com/pdf_document_format.html). The `in_header` file &#39;header.tex&#39; only contains `\usepackage{lscape}`, a package suggested for `knitr` landscape layout [**here**](https://github.com/yihui/knitr-examples/blob/master/030-landscape.Rnw). The `.tex` file is in the same directory as the `.Rmd` file.  

    ---
    title: &quot;Mixing portrait and landscape&quot;
    output:
        pdf_document:
            includes:
                in_header: header.tex
    ---
    
    Portrait:
    ```{r}
    summary(cars)
    ```
    
    \newpage
    \begin{landscape}
    Landscape:
    ```{r}
    summary(cars)
    ```
    \end{landscape}
    
    \newpage
    More portrait:
    ```{r}
    summary(cars)
    ```

However, this code results in an error:

    # ! You can&#39;t use `macro parameter character #&#39; in horizontal mode.
    # l.116 #
    
    # pandoc.exe: Error producing PDF from TeX source
    # Error: pandoc document conversion failed with error 43

Any help is much appreciated.

Rstudio rmarkdown: both portrait and landscape layout in a single PDF

I have a strange issue with Rstudio: If a script calls ggplot2 functions to display a plot, then using *Source* to run the script does not produce the plots. If I select the whole script with `Ctrl+A`, then *Run the current line or selection* (`Ctrl+Enter`), then the plot *does* display. Likewise, typing plotting commands into the console produces correct output.

For example:

    library(ggplot2)

    p = ggplot(mtcars, aes(wt, mpg))
    p + geom_point()

Will only produce output if pasted into console, not if sourced.

There are other questions about this, but neither is helpful:

* https://stackoverflow.com/q/16472935/1042555 falsely claims the issue is fixed in newer versions, it has not.
* https://stackoverflow.com/q/16489570/1042555 was closed as a duplicate, yet not only is it not a duplicate, but the `dev.off()` workaround doesn&#39;t work (&quot;`Error in dev.off() : cannot shut down device 1 (the null device)`&quot;)

How can I get Rstudio to display plots when a script is sourced? I am using Rstudio  0.98.1062 and R 3.1.1.

ggplot plots in scripts do not display in Rstudio

Is there any possibilities for auto-formatting code in RStudio?

I found [this][1], but it is not connected with RStudio.

Also it is desirable that it be customizable formatting.

  [1]: https://stackoverflow.com/questions/3017877/tool-to-auto-format-r-code

Auto-format R code in RStudio

Consider the following trivial Dockerfile:



    FROM debian:testing
    RUN  adduser --disabled-password --gecos &#39;&#39; docker
    RUN  adduser --disabled-password --gecos &#39;&#39; bob 

in a working directory with nothing else. Build the docker image: 

    docker build -t test .

and then run a bash script on the container, linking the working directory into a new subdir on bob&#39;s home directory:

    docker run --rm -it -v $(pwd):/home/bob/subdir test 

Who owns the contents of `subdir` on the container? On the container, run:
    
    cd /home/bob/subdir
    ls -l

ad we see:

    -rw-rw-r-- 1 docker docker 120 Oct 22 03:47 Dockerfile

Holy smokes! `docker` owns the contents!  Back on the host machine outside the container, we see that our original user still owns the `Dockerfile`. Let&#39;s try and fix the ownership of `bob`&#39;s home directory. On the container, run:

    chown -R bob:bob /home/bob
    ls -l 

and we see: 

    -rw-rw-r-- 1 bob bob 120 Oct 22 03:47 Dockerfile

But wait! outside the container, we now run `ls -l`

    -rw-rw-r-- 1 1001 1001 120 Oct 21 20:47 Dockerfile

we no longer own our own file.  Terrible news!  

----------

If we had only added one user in the above example, everything would have gone more smoothly.  For some reason, Docker seems to be making any home directory owned by the _first_ non-root user it encounters (even if that user is declared on an earlier image).  Likewise, this _first_ user is the one that corresponds to the same ownership permissions as my home user. 

**Question 1** Is that correct?  Can someone point me to documentation of this, I&#39;m just conjecturing based on the above experiment. 

**Question 2**: Perhaps this is just because they both have the same numerical value on the kernel, and if I tested on a system where my home user was not id `1000` then permissions would get changed in every case?

**Question 3**: The real question is, of course, &#39;what do I do about this?&#39; If `bob` is logged in as `bob` on the given host machine, he should be able to run the container as `bob` and not have file permissions altered under his host account.  As it stands, he actually needs to run the container as user `docker` to avoid having his account altered.  


I hear you asking _Why do I have such a weird Dockerfile anyway?_. I wonder too sometimes. I am writing a container for a webapp (RStudio-server) that permits different users to log in, which simply uses the user names and credentials from the linux machine as the valid user names.  This brings me the perhaps unusual motivation of wanting to create multiple users.  I can get around this by creating the user only at runtime and everthing is fine.  However, I use a base image that has added a single `docker` user so that it can be used interactively without running as root (as per best practice).  This ruins everything since that user becomes the _first_ user and ends up owning everything, so attempts to log on as other users fail (the app cannot start because it lacks write permissions).  Having the startup script run `chown` first solves this issue, but at the cost of linked volumes changing permissions (obviously only a problem if we are linking volumes).  

Understanding user file ownership in docker: how to avoid changing permissions of linked volumes

So I&#39;m using RStudio and storing my files on Google Drive (the version with folders on your system, acting like Dropbox). I&#39;m using it because it provides a lot more space for free than Dropbox, and I need that space for the projects I&#39;m working on.

When I attempt to write any document at all -- an R script, an RMarkdown file, etc... -- I get the error mentioned in the title. This doesn&#39;t happen using Dropbox. I have found answers for this question for Dropbox, but the solution (tell Dropbox not to sync the Rproj file) doesn&#39;t seem applicable to Google Drive (if it is, please correct me). 

Currently, I&#39;m pausing Google Drive, which is fine, but I often forget to resume it and that causes headaches.

Thanks for your help!

Rstudio and Google Drive Syncing Problems: &quot;The process cannot access the file because it is being used by another process&quot;

I have code to clear the workspace: `rm(list=ls())` and code to clear the console: `cat(&quot;\014&quot;)`

Is there code to clear all plots from Rstudio?


Code to clear all plots in RStudio

I would like to create an automated knitr report that will produce histograms for each numeric field within my dataframe. My goal is to do this without having to specify the actual fields (this dataset contains over 70 and I would also like to reuse the script). 

I&#39;ve tried a few different approaches:

- saving the plot to an object, `p`, and then calling `p` after the loop
  - This only plots the final plot
- Creating an array of plots, `PLOTS &lt;- NULL`,  and appending the plots within the loop `PLOTS &lt;- append(PLOTS, p)`
  - Accessing these plots out of the loop did not work at all
- Even tried saving each to a `.png` file but would rather not have to deal with the overhead of saving and then re-accessing each file
 
I&#39;m afraid the intricacies of the plot devices are escaping me. 

## Question
How can I make the following chunk output each plot within the loop to the report? Currently, the best I can achieve is output of the final plot produced by saving it to an object and calling that object outside of the loop.

R markdown chunk using `knitr` in RStudio:

    ```{r plotNumeric, echo=TRUE, fig.height=3}
    suppressPackageStartupMessages(library(ggplot2))
    FIELDS &lt;- names(df)[sapply(df, class)==&quot;numeric&quot;]
    for (field in  FIELDS){
      qplot(df[,field], main=field)  
    }
    ```

From this point, I hope to customize the plots further. 

R knitr Markdown: Output Plots within For Loop

I want to print a long string to the RStudio console so that it does not get truncated.

    &gt; paste(1:300, letters, collapse=&quot; &quot;)
    [1] &quot;1 a 2 b 3 c 4 d 5 e 6 f 7 g 8 h 9 i 
    ...
    181 y 182 z 183 a 184 b... &lt;truncated&gt;

I supposed this should be fairly simple, but I cannot figure out how. I tried 

    options(max.print = 10000)

and looked through the args on the `print` help pages. Still no luck. 

**What parameter / settings to I have to change to achieve this?**

avoid string printed to console getting truncated (in RStudio)

**What commands are run when pressing &quot;Knit HTML&quot; on an R Markdown file in Rstudio 0.96?**

My motivation is that I might want to run the same command when I&#39;m in another text editing environment or I might want to combine the command in a larger `makefile`.

How to convert R Markdown to HTML? I.e., What does &quot;Knit HTML&quot; do in Rstudio 0.96?

I&#39;m trying to follow [this pandoc example](http://johnmacfarlane.net/pandoc/demo/example9/pandocs-markdown.html#yaml-metadata-block) to add multiple authors to an Rmarkdown file in the [yaml metadata block](http://rmarkdown.rstudio.com/authoring_pandoc_markdown.html#yaml-metadata-block). The pdf will generate in RStudio (Version 0.98.932), but there is no author information. 

    ---
    title:  &#39;This is the title: it contains a colon&#39;
    author:
    - name: Author One
      affiliation: University of Somewhere
    - name: Author Two
      affiliation: University of Nowhere
    date: &quot;`r format(Sys.time(), &#39;%d %B %Y&#39;)`&quot;
    tags: [nothing, nothingness]
    abstract: |
      This is the abstract.
    
      It consists of two paragraphs.
    output: pdf_document
    ---

I&#39;d also like to customize the heading a bit more and add a subtitle. Possible?

multiple authors and subtitles in Rmarkdown yaml

I am operating matrices with R 3.1 and RStudio 0.99.

I have my R Script and with cmd+enter it works without problem. 

I created an Rmd for reporting but I have this error

    Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  : 
      long vectors not supported yet: ../../../../R-3.3.1/src/main/connections.c:5600
    Calls: &lt;Anonymous&gt; ... &lt;Anonymous&gt; -&gt; &lt;Anonymous&gt; -&gt; lazyLoadDBinsertVariable
    Execution halted

Is there a way to bypass that error?

This seems to be a dupicate of https://stackoverflow.com/questions/24335692/large-matrices-in-r-long-vectors-not-supported-yet

but the difference is that this only happens when trying to create an Rmd, not in any other case


&quot;long vectors not supported yet&quot; error in Rmd but not in R Script

I am using R on Windows 7. Apparently R somehow found evidence that I speak languages besides English, and stubbornly insists on giving output in the console in my own language. For a variety of reasons, this is undesirable, and I want R to be English.

What works
----------

I am able to use `LANGUAGE=en` as a command line option for the R console desktop shortcut, but the language is still wrong in Rstudio, which launches the R executable directly and hence ignores the command line arguments in the shortcut.

What doesn&#39;t work
-----------------

I have tried creating an `.Renviron` file under `C:\Users\[MY_NAME]\Documents`, which is the path returned for the working directory by `getwd()`, with `LANGUAGE=en` in it. R ignores this. My `R_ENVIRON` and `R_ENVIRON_USER` variables show up as `&quot;&quot;` so `.Renviron` should be the correct filename.

I have also tried creating `.Renviron` under `R_HOME\etc` (`R_HOME` points to `C:/PROGRA~1/R/R-215~1.0`) and R also ignores it.

I was somewhat successful with adding `Sys.setenv(LANGUAGE=&quot;en&quot;)` in `R_HOME\etc` - this made all output from the R console English, except for the initial copyright information.

The question
--------

How can I make R default to English such that this is propagated to RStudio?

The R console is in my native language, how can I set R to English?

Related, but only talks about the allocated plot space in general, not how to directly set the plot image size and *then* scale it to fill the desired space

- https://stackoverflow.com/questions/17204735/shiny-chart-space-allocation

---

I&#39;m creating a shiny web app and would like to set the size of the plot *and* scale. What I mean by that is I&#39;m looking for a way to set a finite height/width for my plot, and *then* scale that set sized image to the `mainPanel( plotOutput ())` area.

Take this as an example/analogous situation outside of `shiny`.

    x &lt;- 1:10
    y &lt;- x^2
    png(&quot;~/Desktop/small.png&quot;, width = 600, height = 400)
    plot(x, y)
    dev.off()

    png(&quot;~/Desktop/big.png&quot;, width = 1200, height = 800)
    plot(x, y)
    dev.off()

I can&#39;t upload images to SO and set a size, so I&#39;ll include a browser screenshot of each using the following html:

    &lt;img src=&quot;file:///home/jwhendy/Desktop/file.png&quot; width = &quot;800px&quot; /&gt;

This is a full width screenshot on my 1600 x 900 px laptop.

**Small**
![smaller picture][1]

**Big**
![bigger picture][2]

I&#39;d like to control the size of the image itself, as I find the `ggplot2` legends when using options like `colour = var` and `size = var` to be pretty small. Note the difficulty of reading axis labels for the bigger picture as well. I realize I may get into a situation where the size of the image doesn&#39;t scale well due to limited pixels, but I think I at least have *some* room to travel before I run into that.

Any suggestions? I&#39;ve tried playing with the following so far, but without luck:

**ui.R**
---
    
    shinyUI(pageWithSidebar(
    
    headerPanel(&quot;Title&quot;),
      
      sidebarPanel(),
    
      mainPanel(
      
         plotOutput(outputId = &quot;main_plot&quot;, width = &quot;100%&quot;))
      
      ))

**server.R**
---

    shinyServer(function(input, output) {
    
      x &lt;- 1:10
      y &lt;- x^2
    
      output$main_plot &lt;- renderPlot({
    
        plot(x, y) }, height = 400, width = 600 )
    } )

It seems that the height/width options specified in `server.R` override whatever I have set in the `plotOutput` section of `ui.R`.

Is there a way to keep the size of the plot image smaller to maintain readability while still filling the desired `mainPanel` area?

  [1]: http://i.stack.imgur.com/hDLBg.png
  [2]: http://i.stack.imgur.com/KPlaV.png

Scale and size of plot in RStudio shiny

**Update:**

I&#39;ve written a brief walkthrough guide to [installing Rtools on windows](http://thecoatlessprofessor.com/programming/rcpp/install-rtools-for-rcpp/).

**Original:**

I am trying to build an R package using RStudio on Windows 7. When I attempt to build the package via RStudio&#39;s Build panel I receive:

    WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
    
    http://cran.rstudio.com/bin/windows/Rtools/

Loading `library(devtools)` and running `find_rtools(T)` gives:

    Scanning path...
    ls : F:\Rtools\bin\ls.exe 
    Scanning registry...
    Found F:/Rtools for 3.1 
    VERSION.txt
    Rtools version 3.1.0.1936 
    [1] TRUE

The Path variable is set as:

    F:\Rtools\bin;F:\Rtools\gcc-4.6.3\bin;F:\Rtools\perl\bin;F:\Rtools\MinGW\bin;F:\Program Files\R\R-3.0.2\bin\x64;F:\Program Files (x86)\HTML Help Workshop;F:\Program Files\MiKTeX 2.9\miktex\bin\x64\;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program Files (x86)\Common Files\Microsoft Shared\Windows Live;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Windows Live\Shared;C:\Program Files\Microsoft Network Monitor 3\;F:\Program Files (x86)\QuickTime\QTSystem\

I&#39;ve also restarted several times, yet the error persists. I&#39;m a bit confused as to why this is occurring.

Output when R access system variable Path:

    &gt; Sys.getenv()[&#39;PATH&#39;]
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     PATH 
    &quot;F:\\Program Files\\R\\R-3.0.2\\bin\\x64;F:\\Rtools\\bin;F:\\Rtools\\gcc-4.6.3\\bin;F:\\Rtools\\perl\\bin;F:\\Rtools\\MinGW\\bin;F:\\Program Files\\R\\R-3.0.2\\bin\\x64;F:\\Program Files (x86)\\HTML Help Workshop;F:\\Program Files\\MiKTeX 2.9\\miktex\\bin\\x64\\;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\Program Files\\Common Files\\Microsoft Shared\\Windows Live;C:\\Program Files (x86)\\Common Files\\Microsoft Shared\\Windows Live;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\Windows Live\\Shared;C:\\Program Files\\Microsoft Network Monitor 3\\;F:\\Program Files (x86)\\QuickTime\\QTSystem\\&quot; 

The R version I am using is: R version 3.0.2 (2013-09-25) -- &quot;Frisbee Sailing.&quot;

The Rstudio Version I am using is: 0.97.551. When I check for updates, I&#39;m told that this is the latest patch.

    &gt; Sys.which(&quot;ls.exe&quot;)
                       ls.exe 
    &quot;F:\\Rtools\\bin\\ls.exe&quot; 
    &gt; Sys.which(&quot;gcc.exe&quot;)
    gcc.exe 
         &quot;&quot; 

Rtools not being detected by R

I&#39;m trying to come up with a good system for generating slides and accompanying handouts. The ideal system would have the following properties:

* beautiful in both presentation (PDF/HTML) and handout (PDF) layouts (handouts should have room for taking notes)
* embedded R chunks, figures, other JPG/PNG pictures, etc.
* easy to compose
* build using command-line tools
* bibliography support
* `pandoc` slide separator format (automatically generate a new slide after headers of a specified level) is preferred
* I can live with a little bit of additional processing (e.g. via `sed`), but would prefer not to write a huge infrastructure
* **two-column layouts**: there is a [SO post on how to get multi-column slides from pandoc](https://stackoverflow.com/questions/15142134/slides-with-columns-in-pandoc), but it is LaTeX- rather than HTML-oriented.
* ability to adjust sizes of embedded images (other than R-generated figures) and column widths on the fly

Here&#39;s what I&#39;ve discovered so far about the various options:
 
* *Slidify*: 
    * doesn&#39;t do `pandoc` slide separator format, although [there is a workaround](https://github.com/ramnathv/slidify/issues/15‎)
	* the suggestion for creating handouts is to print to PDF; I&#39;d like to leave room for notes etc. (I could probably figure out a way to do that using something like [PDFtk](http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/) or `psnup` ...)
* `RStudio` presentations (`.Rpres` files): 
    * does lots of things nicely, including multi-columns with specified widths
    * doesn&#39;t support `pandoc` slide separator format 
    * I can&#39;t figure out what&#39;s going on under the hood. There is [RStudio documentation](http://www.rstudio.com/ide/docs/r_markdown) that describes the translation process for regular HTML, but it doesn&#39;t seem to cover the R presentation format (which isn&#39;t quite the same). (I have previously invested some effort in [figuring out how to get RStudio-like output via pandoc](http://ms.mcmaster.ca/~bolker/misc/pandoc_diffs.html) ...), which means I can&#39;t generate slides etc. from the command line.
* [RStudio&#39;s Development Version](http://www.rstudio.com/ide/download/preview) (as of March 2014) comes bundled with Pandoc and version 2 of `rmarkdown`. It addresses many of the above issues with the `.Rpres` format.
* `pandoc`: may be the only markdown-translator that has features such as footnotes, bibliography support, etc..  I can also use `pandoc` to generate LaTeX using the [tufte-handout class](http://code.google.com/p/tufte-latex/), which meets my criteria of beauty. 
    * Unfortunately, it seems not to have built-in two-column format support. [Yihui Xie&#39;s HTML5 example](http://yihui.name/knitr/demo/slides/) doesn&#39;t show any two-column examples, and it claims (on slide 5) that clicking the &quot;Knit HTML&quot; button in RStudio is equivalent to `pandoc -s -S -i -t dzslides --mathjax knitr-slides.md -o knitr-slides.html`, but it doesn&#39;t seem to be ...
* LaTeX/beamer: I could simply compose in `Rnw` (knitr-dialect Sweave) rather than R markdown to begin with.  This would give me ultimate flexibility ...
    * despite many years of LaTeX use I do find LaTeX composition more of a pain than markdown composition.  

After all that, my specific question is: *what&#39;s the best (easiest) way to generate a two-column layout for HTML output*?

Any other advice will also be appreciated.



two-column layouts in RStudio presentations/slidify/pandoc

I&#39;ve seen similar questions on Stack Overflow but virtually no conclusive answers, and certainly no answer that worked for me.

What is the easiest way to access and use objects (regression fits, data frames, other objects) that are located in the global R environment in the Markdown (Rstudio) script.

I find it surprising that there is no easy solution to this, given the tendency of the RStudio team to make things comfortable and effective.

Thanks in advance.

How to use objects from global environment in Rstudio Markdown

### TL;DR ###
What are the (possibly unwanted) side-effects of using `knit()`/`knit2pdf()` instead of the &quot;Compile PDF&quot;&lt;sup&gt;1&lt;/sup&gt; button in RStudio?

## Motivation ##

Most users of `knitr` seem to write their documents in RStudio and compile the documents using the &quot;Compile PDF&quot; / &quot;Knit HTML&quot; button. This works smoothly most of the time, but every once a while there are special requirements that cannot be achieved using the compile button. In these cases, the solution is usually to call `knit()`/`knit2pdf()`/`rmarkdown::render()` (or similar functions) directly.

 Some examples:

 - [How to knit/Sweave to a different file name?](https://stackoverflow.com/questions/21883761/how-to-knit-sweave-to-a-different-file-name)
 - [Is there a way to knitr markdown straight out of your workspace using RStudio?](https://stackoverflow.com/questions/11155182/is-there-a-way-to-knitr-markdown-straight-out-of-your-workspace-using-rstudio?lq=1)
 - [Insert date in filename while knitting document using RStudio Knit button](https://stackoverflow.com/questions/32377291/insert-date-in-filename-while-knitting-document-using-rstudio-knit-button)
 
Using `knit2pdf()` instead of the &quot;Compile PDF&quot; button usually offers a simple solution to such questions. However, this comes at a price: There is the fundamental difference that &quot;Compile PDF&quot; processes the document [in a separate process and environment](https://support.rstudio.com/hc/en-us/articles/200552056-Using-Sweave-and-knitr) whereas `knit2pdf()` and friends don&#39;t. 
 
*This has implications and the problem is that not all of these implications are obvious.* Take the fact that `knit()` uses objects from the global environment (whereas &quot;Compile PDF&quot; does not) as an example. This might be obvious and the desired behavior in cases like the second example above, but it is an *unexpected consequence* when `knit()` is used to overcome problems like in example 1 and 3. 
 
 Moreover, there are more subtle differences:

  - The [working directory](https://stackoverflow.com/questions/33555002/difference-between-compile-pdf-and-knit2pdf) might not be set as expected. 
  - [Packages need to be loaded](https://stackoverflow.com/questions/31856298/function-is-not-found-in-knitr).
  - Some options that are usually set by RStudio may have [unexpected values](https://stackoverflow.com/questions/33969024/knitr-gives-error-message).

## The Question and it&#39;s goal ##
Whenever I read/write the advice to use `knit2pdf()` instead of &quot;Compile PDF&quot;, I think *&quot;correct, but the user should understand the consequences …&quot;*. 

Therefore, the question here is:

&gt; What are the (possibly unwanted) side-effects of using `knit()`/`knit2pdf()` instead of the &quot;Compile PDF&quot; button in RStudio?

If there was a comprehensive (community wiki?) answer to this question, it could be linked in future answers that suggest using `knit2pdf()`.

## Related Questions ##

There are dozens of related questions to this one. However, they either propose only code to (more or less) reproduce the behavior of the RStudio button or they explain what &quot;basically&quot; happens without mentioning the possible pitfalls. Others look like being very similar questions but turn out to be a (very) special case of it. Some examples:

  - [Knit2html not replicating functionality of Knit HTML button in R Studio](https://stackoverflow.com/questions/11275255/knit2html-not-replicating-functionality-of-knit-html-button-in-r-studio?lq=1): Caching issue.
  - [HTML outputs are different between using knitr in Rstudio &amp; knit2html in command line](https://stackoverflow.com/questions/25576095/html-outputs-are-different-between-using-knitr-in-rstudio-knit2html-in-command): Markdown versions.
  - [How to convert R Markdown to HTML? I.e., What does “Knit HTML” do in Rstudio 0.96?](https://stackoverflow.com/questions/10646665/how-to-convert-r-markdown-to-html-i-e-what-does-knit-html-do-in-rstudio-0-9): Rather superficial answer by Yihui (explains what &quot;basically&quot; happens) and some options how to reproduce the behavior of the RStudio button. Neither the [suggested](https://stackoverflow.com/a/10654295/2706569) `Sys.sleep(30)` nor [the &quot;Compile PDF&quot; log](https://stackoverflow.com/a/17515963/2706569) are insightful (both hints point to the same thing).
  - [What does “Knit HTML” do in Rstudio 0.98?](https://stackoverflow.com/questions/27881289/what-does-knit-html-do-in-rstudio-0-98): Reproduce behavior of button.
  
## About the answer ##

I think this question raised many of the issues that should be part of an answer. However, there might be many more aspects I don&#39;t know about which is the reason why I am reluctant to self-answer this question (though I might try if nobody answers).

 Probably, an answer should cover three main points:

  - The new session vs. current session issue (global options, working directory, loaded packages, …).
  - A consequence of the first point: The fact that `knit()` uses objects from the calling environment (default: `envir = parent.frame()`) and implications for reproducibility. I tried to tackle the issue of preventing `knit()` from using objects from outside the document in [this answer](https://stackoverflow.com/a/34017805/2706569) (second bullet point).
  - Things RStudio secretly does …
     - … when starting an interactive session ([example](https://stackoverflow.com/a/33970452/2706569)) --&gt; Not available when hitting &quot;Compile PDF&quot;
     - … when hitting &quot;Compile PDF&quot; (anything special besides the new session with the working directory set to the file processed?)


I am not sure about the right perspective on the issue. I think both, &quot;What happens when I hit &#39;Compile PDF&#39; + implications&quot; as well as &quot;What happens when I use `knit()` + implications&quot; is a good approach to tackle the question. 


----------
&lt;sup&gt;&lt;sup&gt;1&lt;/sup&gt; The same applies to the &quot;Knit HTML&quot; button when writing RMD documents.&lt;/sup&gt;

Difference: &quot;Compile PDF&quot; button in RStudio vs. knit() and knit2pdf()

Such as margins, orientations and such...

`dev.off()` does not work for me. I am often using RStudio, with its inbuilt graphics device. I then have plotting functions, which I want to plot either in the default RStudio graphics device, or if I called `X11()`, before in a new window.

This behaviour doesn&#39;t work with `dev.off()`. If my plotting function always calls `dev.off()`, it might inadvertently close the `X11()` window and instead plot in the RStudio device. If I always call `dev.off()` followed by `X11()`, it would always plot in a new window, even if I wanted to plot in the RStudio device.

Ordinarily that could be solved with `getOption(&quot;device&quot;)`, however, that always returns `RStudioGD`.


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