Answers.Body: <p>This is a bug affecting the curl compile, it's been reported <a href="https://github.com/curl/curl/issues/846" rel="nofollow noreferrer">here</a> and also <a href="https://github.com/curl/curl/pull/1404" rel="nofollow noreferrer">here</a>, I suggest trying to compile from the newer release of the libcurl source rather than the <code>.deb</code> you linked. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-10T20:03:58.310Z
Answers.Text: I tried reinstalling `libcurl` from here: https://curl.haxx.se/, and it did not help. I see that the `R` is using the newly reinstalled version, and giving the same error.
Answers.UserDisplayName: Nikita Vlasenko
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Answers.CreationDate: 2018-08-13T09:18:26.407Z
Answers.Text: Are you sure it's not hitting the old system version at compile time?
Answers.UserDisplayName: Matt Bashton
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-13T18:31:01.507Z
Answers.Text: Yes, sure. Cluster support fixed it. The issue was related to gcc version, but I am not completely sure what they did.
Answers.UserDisplayName: Nikita Vlasenko
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-13T19:57:19.980Z
Answers.Text: Glad it got fixed, although if you find out exactly it would be good to post and answer since this will help others with the same issue.
Answers.UserDisplayName: Matt Bashton
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-10T08:44:51.043Z
Answers.LastActivityDate: 2018-08-10T09:09:44.770Z
Answers.LastEditDate: 2018-08-10T09:09:44.770Z
Answers.UserDisplayName: Matt Bashton
Body: <p>I am working on the <code>Rivanna</code> cluster that is of <code>SLURM</code>-type. Because of that I do not have write permissions and need to install the newest <code>R</code> version myself locally, and use it. For it to be successfully built from source, I needed to also build from source <code>libcurl4-openssl-dev</code>, so I downloaded <code>tar.gz</code> file from here:</p>
  
  <p><a href="https://packages.debian.org/ru/jessie/libcurl4-openssl-dev" rel="nofollow noreferrer">https://packages.debian.org/ru/jessie/libcurl4-openssl-dev</a></p>
  
  <p>and did:</p>
  
  <pre><code>mkdir build 
  ./configure --prefix=/scratch/nv4e/curl/build
  make
  make install
  </code></pre>
  
  <p>Then, in the same way I built from source <code>R</code> <code>3.5.1</code>, the latest current version. It was compiled without any errors, but with some warnings. Then, I submitted the <code>R</code> script that uses <code>SCnorm</code> package:</p>
  
  <p><a href="https://bioconductor.org/packages/release/bioc/html/SCnorm.html" rel="nofollow noreferrer">https://bioconductor.org/packages/release/bioc/html/SCnorm.html</a></p>
  
  <p>Inside of the script I am having:</p>
  
  <pre><code>source("https://bioconductor.org/biocLite.R")
  biocLite("SCnorm")
  biocLite("SingleCellExperiment")
  library(SCnorm)
  library(SingleCellExperiment) 
  </code></pre>
  
  <p>Of course, I am submitting it through <code>.slurm</code> file where I have the main command:</p>
  
  <pre><code>Rscript --vanilla scnorm.R
  </code></pre>
  
  <p>It fails, apparently because <code>SCnorm</code> requires <code>RCurl</code>, but it can not get one, even though in the log file it is trying to access it correctly:</p>
  
  <p><a href="https://i.sstatic.net/cjKur.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cjKur.png" alt="enter image description here"></a></p>
  
  <p>The <code>libcurl</code> library was built from source in the <code>/scratch/nv4e/curl/build</code> folder. The only suspicion that I have here is that maybe its version is wrong and <code>SCnorm</code> needs another <code>libcurl</code> version? Any suggestions would be greatly appreciated.</p>
  
  <blockquote>
    <p>Update</p>
  </blockquote>
  
  <p>I tried reinstalling <code>libcurl</code> library from the official website, using the latest version:</p>
  
  <p><a href="https://curl.haxx.se/" rel="nofollow noreferrer">https://curl.haxx.se/</a></p>
  
  <p>But it did not fix the issue. I have also tried using <code>libcurl</code> from <code>Anaconda</code> but it gave the same error. So, neither <code>7.61.0</code> (latest), nor <code>7.29.0</code> (<code>Anaconda</code>), nor <code>7.38.0</code> (<code>Debian</code> link) are working.</p>
  
Tags: <r><scrnaseq><rcurl>
Title: RCurl issue when installing SCnorm
ThreadText: # RCurl issue when installing SCnorm
  
  (Asked by: username_0 on 2018-08-10)
  
  I am working on the `Rivanna` cluster that is of `SLURM`-type. Because of that I do not have write permissions and need to install the newest `R` version myself locally, and use it. For it to be successfully built from source, I needed to also build from source `libcurl4-openssl-dev`, so I downloaded `tar.gz` file from here:
  
  <https://packages.debian.org/ru/jessie/libcurl4-openssl-dev>
  
  and did:
  
  ```
  mkdir build 
  ./configure --prefix=/scratch/nv4e/curl/build
  make
  make install
  
  ```
  
  Then, in the same way I built from source `R` `3.5.1`, the latest current version. It was compiled without any errors, but with some warnings. Then, I submitted the `R` script that uses `SCnorm` package:
  
  <https://bioconductor.org/packages/release/bioc/html/SCnorm.html>
  
  Inside of the script I am having:
  
  ```
  source("https://bioconductor.org/biocLite.R")
  biocLite("SCnorm")
  biocLite("SingleCellExperiment")
  library(SCnorm)
  library(SingleCellExperiment) 
  
  ```
  
  Of course, I am submitting it through `.slurm` file where I have the main command:
  
  ```
  Rscript --vanilla scnorm.R
  
  ```
  
  It fails, apparently because `SCnorm` requires `RCurl`, but it can not get one, even though in the log file it is trying to access it correctly:
  
  [![enter image description here](https://i.sstatic.net/cjKur.png)](https://i.sstatic.net/cjKur.png)
  
  The `libcurl` library was built from source in the `/scratch/nv4e/curl/build` folder. The only suspicion that I have here is that maybe its version is wrong and `SCnorm` needs another `libcurl` version? Any suggestions would be greatly appreciated.
  
  > Update
  
  I tried reinstalling `libcurl` library from the official website, using the latest version:
  
  <https://curl.haxx.se/>
  
  But it did not fix the issue. I have also tried using `libcurl` from `Anaconda` but it gave the same error. So, neither `7.61.0` (latest), nor `7.29.0` (`Anaconda`), nor `7.38.0` (`Debian` link) are working.
  
  **Tags:** r, scrnaseq, rcurl
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-08-10. Score: 1
  
  This is a bug affecting the curl compile, it's been reported [here](https://github.com/curl/curl/issues/846) and also [here](https://github.com/curl/curl/pull/1404), I suggest trying to compile from the newer release of the libcurl source rather than the `.deb` you linked.
  
  > **Comments:**
  > **username_0**: I tried reinstalling `libcurl` from here: https://curl.haxx.se/, and it did not help. I see that the `R` is using the newly reinstalled version, and giving the same error.  
  > **username_1**: Are you sure it's not hitting the old system version at compile time?  
  > **username_0**: Yes, sure. Cluster support fixed it. The issue was related to gcc version, but I am not completely sure what they did.  
  > **username_1**: Glad it got fixed, although if you find out exactly it would be good to post and answer since this will help others with the same issue.  
  
  ---
  
  