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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

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.

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This is a bug affecting the curl compile, it's been reported here and also here, I suggest trying to compile from the newer release of the libcurl source rather than the .deb you linked.

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  • $\begingroup$ I tried reinstalling libcurl from here: curl.haxx.se, and it did not help. I see that the R is using the newly reinstalled version, and giving the same error. $\endgroup$
    – Nikita Vlasenko
    Aug 10, 2018 at 20:03
  • $\begingroup$ Are you sure it's not hitting the old system version at compile time? $\endgroup$
    – Matt Bashton
    Aug 13, 2018 at 9:18
  • $\begingroup$ Yes, sure. Cluster support fixed it. The issue was related to gcc version, but I am not completely sure what they did. $\endgroup$
    – Nikita Vlasenko
    Aug 13, 2018 at 18:31
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    $\begingroup$ 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. $\endgroup$
    – Matt Bashton
    Aug 13, 2018 at 19:57

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