Answers.Body: <p>It seems RStudio server doesn't know it's limitations. Currently, Projects are limited to 1GB of RAM. Using <a href="https://github.com/krlmlr/ulimit" rel="nofollow noreferrer">the R package</a> <code>ulimit</code> which mirrors the function of <code>ulimit</code> and allows implementation of memory limits in linux I was able to set my own limitations within the R session. After setting the limit to 1GB I see the <code>ulimit</code> limitation being tripped when invoking <code>ScaleData()</code>. Looks like a case of exceeding available system resources.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-14T18:56:58.607Z
Answers.LastActivityDate: 2018-11-14T18:56:58.607Z
Answers.UserDisplayName: Kohl Kinning
Body: <p>Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the <code>ScaleData()</code> step. The progress bar remains at 0% and hangs, followed by an R crash. I've tried reducing the size for number of genes to scale at in a single computation with the argument <code>block.size</code> with no change. The Seurat S4 object is only ~70mb so I can't imagine I'm exceeding the RStudio Cloud 1gb RAM limitations.</p>
  
  <p>If you'd like to check out the cloud instance I can add you to the workspace temporarily. There is a limit on members allowed in a workspace.</p>
  
  <p>I've been trying to run this tutorial on another remote cluster in RStudio inside of a container (Singularity here vs. Docker in RStudio Cloud) and am hitting the same snag.</p>
  
  <p>I get receive no errors from RStudio Cloud, but in the other evirnment I get this error:</p>
  
  <p><code>ERROR session hadabend; LOGGED FROM: rstudio::core::Error {anonymous}::rInit(const rstudio::r::session::RInitInfo&amp;) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:563</code>.</p>
  
  <p>On <a href="https://github.com/Homebrew/homebrew-science/issues/5504" rel="nofollow noreferrer">this issue thread</a> someone mentions it they receive this error message when hitting their RAM limits.</p>
  
  <p>The source for <code>ScaleData()</code> can be found in the <a href="https://github.com/satijalab/seurat/blob/65b77a9480281ef9ab1aa8816f7c781752092c18/R/preprocessing.R" rel="nofollow noreferrer">Github repo</a>.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-12T14:49:21.953Z
Comments.Text: Are you following the tutorial exactly? I don't see `ScaleData` [in the tutorial](https://satijalab.org/seurat/pbmc3k_tutorial_1_4.html).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-12T16:05:10.897Z
Comments.Text: `RegressOut()` is a deprecated function, regression now happens in the data scaling step. `vars.to.regress` is now passed as an argument to `ScaleData()`. Somehow you've got an old version of the tutorial, see [this tutorial](https://satijalab.org/seurat/pbmc3k_tutorial.html) compiled 22 March, 2018.
Comments.UserDisplayName: Kohl Kinning
Tags: <r><seurat><rstudio>
Title: ScaleData() from Seurat causes crash on RStudio Cloud
ThreadText: # ScaleData() from Seurat causes crash on RStudio Cloud
  
  (Asked by: username_0 on 2018-11-11)
  
  Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the `ScaleData()` step. The progress bar remains at 0% and hangs, followed by an R crash. I've tried reducing the size for number of genes to scale at in a single computation with the argument `block.size` with no change. The Seurat S4 object is only ~70mb so I can't imagine I'm exceeding the RStudio Cloud 1gb RAM limitations.
  
  If you'd like to check out the cloud instance I can add you to the workspace temporarily. There is a limit on members allowed in a workspace.
  
  I've been trying to run this tutorial on another remote cluster in RStudio inside of a container (Singularity here vs. Docker in RStudio Cloud) and am hitting the same snag.
  
  I get receive no errors from RStudio Cloud, but in the other evirnment I get this error:
  
  `ERROR session hadabend; LOGGED FROM: rstudio::core::Error {anonymous}::rInit(const rstudio::r::session::RInitInfo&) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:563`.
  
  On [this issue thread](https://github.com/Homebrew/homebrew-science/issues/5504) someone mentions it they receive this error message when hitting their RAM limits.
  
  The source for `ScaleData()` can be found in the [Github repo](https://github.com/satijalab/seurat/blob/65b77a9480281ef9ab1aa8816f7c781752092c18/R/preprocessing.R).
  
  **Tags:** r, seurat, rstudio
  
  > **Comments:**
  > **username_1**: Are you following the tutorial exactly? I don't see `ScaleData` [in the tutorial](https://satijalab.org/seurat/pbmc3k_tutorial_1_4.html).  
  > **username_0**: `RegressOut()` is a deprecated function, regression now happens in the data scaling step. `vars.to.regress` is now passed as an argument to `ScaleData()`. Somehow you've got an old version of the tutorial, see [this tutorial](https://satijalab.org/seurat/pbmc3k_tutorial.html) compiled 22 March, 2018.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-11-14. Score: 2 | Accepted answer
  
  It seems RStudio server doesn't know it's limitations. Currently, Projects are limited to 1GB of RAM. Using [the R package](https://github.com/krlmlr/ulimit) `ulimit` which mirrors the function of `ulimit` and allows implementation of memory limits in linux I was able to set my own limitations within the R session. After setting the limit to 1GB I see the `ulimit` limitation being tripped when invoking `ScaleData()`. Looks like a case of exceeding available system resources.
  
  
  ---
  
  