<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>

CC BY-SA 4.0
2018-08-10T20:03:58.310Z
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.
Nikita Vlasenko
CC BY-SA 4.0
2018-08-13T09:18:26.407Z
Are you sure it's not hitting the old system version at compile time?
Matt Bashton
CC BY-SA 4.0
2018-08-13T18:31:01.507Z
Yes, sure. Cluster support fixed it. The issue was related to gcc version, but I am not completely sure what they did.
Nikita Vlasenko
CC BY-SA 4.0
2018-08-13T19:57:19.980Z
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.
Matt Bashton
CC BY-SA 4.0
2018-08-10T08:44:51.043Z
2018-08-10T09:09:44.770Z
2018-08-10T09:09:44.770Z
Matt Bashton
<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>

<r><scrnaseq><rcurl>
RCurl issue when installing SCnorm
# 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:

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.  

---

