Dear organisers,
I have just received an error message from Express Lane (challenge 1):
500 Server Error: Internal Server Error for url: http+docker://localunixsocket/v1.24/containers/363c3817419a024c9f87408407338853c729f69c7e10193c6c348ea0aa2c9f5b/start ("invalid header field value "oci runtime error: container_linux.go:247: starting container process caused \"exec: \\\"/score_sc1.sh\\\": permission denied\"\n"")
My submission was just the provided example docker, so I am not sure if this is your server problem or I missed anything?
Thanks.
Regards,
Thuc.
Created by Thuc Le thucmi Hi Tom,
This is the docker file (I downloaded from the example).
Thanks.
Thuc.
FROM ubuntu
RUN apt-get update
RUN apt-get -y install r-base
## Install dependencies
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("plyr")'
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN Rscript -e "install.packages('data.table')"
## Copy files over to Docker image
COPY run-mm-sc1.R /run-mm-sc1.R
COPY score_sc1.sh /score_sc1.sh
COPY model-state-metadata.Rd /model-state-metadata.Rd
Dear Thuc,
Can you show me the line in your docker file where you are installing plyr?
Best,
Tom Thanks, Tom.
My submission name: syn10739256
submission ID: 9634474.
Regards,
Thuc. Dear Thuc,
First, it is important that you are installing the correct version of R that you want or else some of the packages that you want won't be installed due to older version of R.
Second, the Dockerfile shouldn't finish building if its not able to install the R packages. What exactly are the errors that you are getting? Is there a submissionId that you can share with me?
Best,
Tom Thanks, Tom for your reply.
I have done all of that, but the error message says the R packages are not available. It seems that the Dockerfile fails to install the required R packages.
Do you have suggestions of how to fix this?
Many thanks.
Regards,
Thuc.
Dear Thuc,
Please make sure that the first line of your shell script has:
`#!/bin/bash`
and that your shell script has the right permissions. `chmod 770 score_sc1.sh`
Best,
Tom