Installation Issues On A HPC Associated With TAR

[yr542]

I git cloned the Github repository on my HPC but when I tried to do the following installation:

Command:

devtools::install_github("aschluter/ClinPrior")

Error:

Downloading GitHub repo aschluter/ClinPrior@HEAD
sh: 1: /usr/bin/tar: not found
sh: 1: /usr/bin/tar: not found
Error: Failed to install 'ClinPrior' from GitHub:
  error in running command
In addition: Warning messages:
1: In system(cmd) : error in running command
2: In utils::untar(tarfile, ...) :
  ‘path/to/tar -xf '/path/to/file##e#########.tar.gz' -C '/path/to/remotes##e##ae##eac'’ returned error code 127

• Where the # stand for certain numbers.

I do have the ability to use tar on the HPC just not via an R script.

Questions:

1. Is there a recommended work around given HPC issues?
2. Is there another way to install that you can recommend?
3. Do you perchance have a docker/singularity (the docker would need to be converted to singularity image format) that I could use as HPCs often limit access to the internet to protect human data/information?

[aschluter]

Hi yr542,

Thank you for submitting this issue. Unfortunately ClinPrior installations haven't been tested on HPC. As you suggest I will try to build ClinPrior in a docker container and convert it to a singularity image and get back to you soon.

Agatha

[aschluter]

Hi yr542

Now ClinPrior is available as docker image/singularity.

You can download the ClinPrior Docker image here:

docker pull aschluterclinprior/clinprior:latest

To create and run a new container from the clinprior image:

sudo docker run -it clinprior bash

or the singularity image here:

singularity pull --arch amd64 library://aschluter/clinprior/clinprior_latest:latest

You will need to install the singularity package. Please, let me know if the images are working well.

Best,

Agatha

[yr542]

Dr. @aschluter I seem to be having trouble with the command I cannot seem to find your docker link.

Main Question:

1) Would it be possible to have the docker link as I cannot seem to pull down the singularity and I am sure it is some small change in the way the aschluter clinprior link is mentioned in docker.

• If I see it on docker I might be able to figure out a work around?

[aschluter]

Hi yr542,

Here is the ClinPrior docker link:

https://hub.docker.com/r/aschluterclinprior/clinprior

You need singularity package to convert it.

Agatha