I also ran into this today, and fixed it by using `cache.lazy = FALSE` in the setup chunk in my .Rmd.

So what is inside of the first chunk in my R Markdown file looks like this:

    library(knitr)
    knitr::opts_chunk$set(cache = TRUE, warning = FALSE, 
                          message = FALSE, cache.lazy = FALSE)


I am getting the same error in my .rmd file while trying to knit it to pdf.
The incriminated code chunk was cached. 

&gt; Is there a way to bypass that error?

Removing the &#39;cache = TRUE&#39; or setting it to FALSE seems to fix the issue.

Using IntelliJ IDEA 15, I get these constant and annoying documentation popups whenever my mouse is anywhere in the code window for a decompiled class (from a 3rd party jar). It will popup docs for whatever variable/method/class/anything happens to be near my mouse. If my mouse is not near any lines of code, it will popup for the current classfile, so basically I can&#39;t browse code unless I move my mouse to another window. 

It only happens with decompiled classes, not my normal code. How do I stop these?

How to stop annoying documentation popups in IntelliJ IDEA

I investigated performance degradation and tracked it down to slow HashSets.  
I have structs with nullable values that are used as a primary key. For example:

    public struct NullableLongWrapper
    {
        private readonly long? _value;

        public NullableLongWrapper(long? value)
        {
            _value = value;
        }
    }

I noticed that creating a `HashSet&lt;NullableLongWrapper&gt;` is exceptionally slow.

Here&#39;s an example using [BenchmarkDotNet](https://github.com/PerfDotNet/BenchmarkDotNet): (`Install-Package BenchmarkDotNet`)

	using System.Collections.Generic;
	using System.Linq;
	using BenchmarkDotNet.Attributes;
	using BenchmarkDotNet.Configs;
	using BenchmarkDotNet.Jobs;
	using BenchmarkDotNet.Running;

    public class Program
    {
        static void Main()
        {
            BenchmarkRunner.Run&lt;HashSets&gt;();
        }
    }

    public class Config : ManualConfig
    {
        public Config()
        {
            Add(Job.Dry.WithWarmupCount(1).WithLaunchCount(3).WithTargetCount(20));
        }
    }

    public struct NullableLongWrapper
    {
        private readonly long? _value;

        public NullableLongWrapper(long? value)
        {
            _value = value;
        }
    
        public long? Value =&gt; _value;
    }

    public struct LongWrapper
    {
        private readonly long _value;

        public LongWrapper(long value)
        {
            _value = value;
        }

        public long Value =&gt; _value;
    }

    [Config(typeof (Config))]
    public class HashSets
    {
        private const int ListSize = 1000;

        private readonly List&lt;long?&gt; _nullables;
        private readonly List&lt;long&gt; _longs;
        private readonly List&lt;NullableLongWrapper&gt; _nullableWrappers;
        private readonly List&lt;LongWrapper&gt; _wrappers;

        public HashSets()
        {
            _nullables = Enumerable.Range(1, ListSize).Select(i =&gt; (long?) i).ToList();
            _longs = Enumerable.Range(1, ListSize).Select(i =&gt; (long) i).ToList();
            _nullableWrappers = Enumerable.Range(1, ListSize).Select(i =&gt; new NullableLongWrapper(i)).ToList();
            _wrappers = Enumerable.Range(1, ListSize).Select(i =&gt; new LongWrapper(i)).ToList();
        }

        [Benchmark]
        public void Longs() =&gt; new HashSet&lt;long&gt;(_longs);

        [Benchmark]
        public void NullableLongs() =&gt; new HashSet&lt;long?&gt;(_nullables);

        [Benchmark(Baseline = true)]
        public void Wrappers() =&gt; new HashSet&lt;LongWrapper&gt;(_wrappers);

        [Benchmark]
        public void NullableWrappers() =&gt; new HashSet&lt;NullableLongWrapper&gt;(_nullableWrappers);
    }

Result:
&lt;pre&gt;
           Method |          Median |   Scaled
----------------- |---------------- |---------
            Longs |      22.8682 us |     0.42
    NullableLongs |      39.0337 us |     0.62
         Wrappers |      62.8877 us |     1.00
 NullableWrappers | 231,993.7278 us | 3,540.34
&lt;/pre&gt;

Using a struct with a `Nullable&lt;long&gt;` compared to a struct with a `long` is 3540 times slower!  
In my case it made the difference between 800ms and &amp;lt;1ms.

Here is the environment information from BenchmarkDotNet:

&gt; OS=Microsoft Windows NT 6.1.7601 Service Pack 1  
Processor=Intel(R) Core(TM) i7-5600U CPU 2.60GHz, ProcessorCount=4  
Frequency=2536269 ticks, Resolution=394.2799 ns, Timer=TSC  
CLR=MS.NET 4.0.30319.42000, Arch=64-bit RELEASE [RyuJIT]  
GC=Concurrent Workstation  
JitModules=clrjit-v4.6.1076.0

What is the reason performance is this poor? 


Why are HashSets of structs with nullable values incredibly slow?

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 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
<pre><code class="hljs language-php">Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, : 
 long vectors not supported yet: ../../../../R-3.3.1/src/main/connections.c:5600
Calls: &#x3C;Anonymous> ... &#x3C;Anonymous> -> &#x3C;Anonymous> -> lazyLoadDBinsertVariable
Execution halted
</code></pre>
Is there a way to bypass that error?
This seems to be a dupicate of <a href="https://stackoverflow.com/questions/24335692/large-matrices-in-r-long-vectors-not-supported-yet" target="_blank" rel="noopener noreferrer">https://stackoverflow.com/questions/24335692/large-matrices-in-r-long-vectors-not-supported-yet</a>
but the difference is that this only happens when trying to create an Rmd, not in any other case

This question is related to [this one][1]. The two can generate the same functionality, but implementation is slightly different. One significant difference is that a `reactiveValue` is a container that can have several values, like `input$`. In [shiny documentation][2] functionality is usually implemented using `reactive()`, but in most cases I find `reactiveValues()` more convenient. Is there any catch here? Are there any other major differences between the two that I might not be aware off?  Are these two code snippets equivalent?

See the same [example code][2]  implemented using:

1. a reactive expression:

        library(shiny)
        
        ui &lt;- fluidPage( 
          shiny::numericInput(inputId = &#39;n&#39;,label = &#39;n&#39;,value = 2),
          shiny::textOutput(&#39;nthValue&#39;),
          shiny::textOutput(&#39;nthValueInv&#39;)   
        )
        
        fib &lt;- function(n) ifelse(n&lt;3, 1, fib(n-1)+fib(n-2))
        
        server&lt;-shinyServer(function(input, output, session) {   
          currentFib         &lt;- reactive({ fib(as.numeric(input$n)) })  
          output$nthValue    &lt;- renderText({ currentFib() })
          output$nthValueInv &lt;- renderText({ 1 / currentFib() })   
        })
        
        shinyApp(ui = ui, server = server)

2. a reactive value:

        library(shiny)
        
        ui &lt;- fluidPage( 
          shiny::numericInput(inputId = &#39;n&#39;,label = &#39;n&#39;,value = 2),
          shiny::textOutput(&#39;nthValue&#39;),
          shiny::textOutput(&#39;nthValueInv&#39;)  
        )
        
        fib &lt;- function(n) ifelse(n&lt;3, 1, fib(n-1)+fib(n-2))
        
        server&lt;-shinyServer(function(input, output, session) { 
          myReactives &lt;- reactiveValues()  
          observe(  myReactives$currentFib &lt;-  fib(as.numeric(input$n))  ) 
          output$nthValue    &lt;- renderText({ myReactives$currentFib  })
          output$nthValueInv &lt;- renderText({ 1 / myReactives$currentFib  }) 
        })
        
        shinyApp(ui = ui, server = server)


  [1]: https://stackoverflow.com/questions/18324397
  [2]: http://shiny.rstudio.com/articles/reactivity-overview.html

R Shiny: reactiveValues vs reactive

Does someone have an overview with respect to advantages/disadvantages of SparkR vs sparklyr? Google does not yield any satisfactory results and both seem fairly similar. Trying both out, SparkR appears a lot more cumbersome, whereas sparklyr is pretty straight forward (both to install but also to use, especially with the dplyr inputs). Can sparklyr only be used to run dplyr functions in parallel or also &quot;normal&quot; R-Code?

Best 

SparkR vs sparklyr

I would like to have consistent output for a particular R script. In this case, I would like all numeric output to be in scientific notation with exactly two decimal places.

Examples:

    0.05 --&gt; 5.00e-02
    0.05671 --&gt; 5.67e-02
    0.000000027 --&gt; 2.70e-08

I tried using the following options:

    options(scipen = 1)
    options(digits = 2)

This gave me the results:

    0.05 --&gt; 0.05
    0.05671 --&gt; 0.057
    0.000000027 --&gt; 2.7e-08

I obtained the same results when I tried:

    options(scipen = 0)
    options(digits = 2)

Thank you for any advice.

Forcing R output to be scientific notation with at most two decimals

I am getting this error while plotting a bar graph and I am not able to get rid of it, I have tried both qplot and ggplot but still the same error.

Following is my code:

     library(dplyr)
     library(ggplot2)

     #Investigate data further to build a machine learning model
     data_country = data %&gt;%
               group_by(country) %&gt;%
               summarise(conversion_rate = mean(converted))
      #Ist method
      qplot(country, conversion_rate, data = data_country,geom = &quot;bar&quot;, stat =&quot;identity&quot;, fill =   country)
      #2nd method
      ggplot(data_country)+aes(x=country,y = conversion_rate)+geom_bar()

Error:
      
      stat_count() must not be used with a y aesthetic

Data in data_country:

        country conversion_rate
        &lt;fctr&gt;           &lt;dbl&gt;
      1   China     0.001331558
      2 Germany     0.062428188
      3      UK     0.052612025
      4      US     0.037800687

The error is coming in bar chart and not in the dotted chart.


R ggplot2: stat_count() must not be used with a y aesthetic error in Bar graph

I have previously successfully installed rstudio-server with `brew install rstudio-server` on a Mac OS X 10.11.4.

Now, I am trying to login to rstudio-server 0.99.902 without success. From the client side, I get a pop-up window saying -
&gt;&quot;RStudio Initialization Error&quot;, &quot;Unable to connect to service&quot;.

The user I am using has an user id of `1100`, so I do not think the problem is related to account permissions.

While running the daemon, when I try to log-in, the error showing up in `/var/log/system.log` is this:

&gt;rserver[1100]: ERROR system error 61 (Connection refused) [request-uri=/rpc/client_init]; 
OCCURRED AT: void rstudio::core::http::LocalStreamAsyncClient::handleConnect(const boost::system::error_code &amp;) /tmp/rstudio-server-20160803-68705-uhvyws/rstudio-0.99.902/src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp:119; 
LOGGED FROM: void rstudio::server::session_proxy::(anonymous namespace)::logIfNotConnectionTerminated(const rstudio::core::Error &amp;, const http::Request &amp;) 
/tmp/rstudio-server-20160803-68705-uhvyws/rstudio-0.99.902/src/cpp/server/ServerSessionProxy.cpp:308

Crash report: http://pastebin.com/GYkFZ8fT


While running `sudo /usr/local/bin/rserver --server-daemonize=0`, when I try to log-in, no error is output to the console but I do get this error on a pop-up window in the browser: `Error occurred during transmission`.

Crash report: http://pastebin.com/kJMsPh6s


Additional info:

`rstudio-server verify-installation` returns `too many positional options have been specified on the command line`.

Running `sessionInfo()` from R console:

    R version 3.3.0 (2016-05-03)
    Platform: x86_64-apple-darwin13.4.0 (64-bit)
    Running under: OS X 10.11.4 (El Capitan)

    locale:
    [1] C

    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base     




Cannot log-in to rstudio-server

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

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 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

What is the relationship between the functionality of R Markdown, Knitr, Pandoc, and Bookdown?

Specifically what is the &#39;division of labour&#39; between these packages in converting markup documents with embedded R code (e.g. `.Rnw` or `.Rmd`) into final outputs (e.g. `.pdf` or `.html`)?  And if Knitr is used to process RMarkdown, what does the `rmarkdown` package do and how is it different to the `markdown package`?


Relationship between R Markdown, Knitr, Pandoc, and Bookdown

I want my html file to show the code, but not the output of this chunk:

    ```{r echo=True, include=FALSE}
    fun &lt;- function(b)
        {
        for(a in b)
            {print(a)
            return(a * a)}
        }
    y &lt;- fun(b)
    ```

When I run the code, i need the print to see the progress (it is quite a long function in reality).

But in the knitr file, I use the output in a further chunk, so I do not want to see it in this one (and there&#39;s no notion of progress, since the code has already been run).

This `echo=True, include=FALSE` here does not work: the whole thing is hidden (which is the normal behavior of `include=FALSE`).

&lt;b&gt;What are the parameters I could use to hide the prints, but show my code?&lt;/b&gt;

How to show code but hide output in RMarkdown?

I am trying to create a report in R markdown that has sections ordered

1. Section 1 Header
    
    1.1 sub section 1

    1.2 sub section 3

2. Section 2 Header

    2.1 

    2.2 sub section 

          2.2.1 another sub section

Is there a way get R markdown to generate an ordered list like this?
 

Automatically number sections in RMarkdown

for some reason no link in my R markdowns (rmd) is formatted blue. knitting the simple rmd below to pdf is leaving the text color black. only when hovering over it does one realize that it&#39;s actually a link. knitting it to html will make the link blue. of course I can use a latex wrapper but I wonder why that is?

&gt; sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
loaded via a namespace (and not attached):
 knitr_1.15

RStudio 1.0.44

    ---
    title: &quot;R Notebook&quot;
    output:
      pdf_document: default
      html_notebook: default
    ---

    ```{r, echo=F}
    # tex / pandoc options for pdf creation
    x &lt;- Sys.getenv(&quot;PATH&quot;)
    y &lt;- paste(x, &quot;E:\\miktex\\miktex\\bin&quot;, sep=&quot;;&quot;)
    Sys.setenv(PATH = y)
    ```

    [link](www.rstudio.com)

[![enter image description here][1]][1]
  [1]: https://i.stack.imgur.com/awos7.png

Content Type	Original Author	Original Content on Stackoverflow
Question	pachadotdev	View Question on Stackoverflow
Solution 1 - R	Julia Silge	View Answer on Stackoverflow
Solution 2 - R	D-Lorenz	View Answer on Stackoverflow

"long vectors not supported yet" error in Rmd but not in R Script

R Problem Overview

R Solutions

Solution 1 - R

Solution 2 - R

Why are HashSets of structs with nullable values incredibly slow?

How to stop annoying documentation popups in IntelliJ IDEA

Attributions