[Bug] bash errors during packer build

[dcloud9]

Hi, We hit these bash errors when packer is ran

    amazon-ebs:   Installing : 1:gmp-devel-6.0.0-15.amzn2.0.2.x86_64                        1/1
    amazon-ebs:   Verifying  : 1:gmp-devel-6.0.0-15.amzn2.0.2.x86_64                        1/1
    amazon-ebs:
    amazon-ebs: Installed:
    amazon-ebs:   gmp-devel.x86_64 1:6.0.0-15.amzn2.0.2
    amazon-ebs:
    amazon-ebs: Complete!
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: -bash: R: command not found
==> amazon-ebs: Stopping the source instance...
    amazon-ebs: Stopping instance
==> amazon-ebs: Waiting for the instance to stop...
==> amazon-ebs: Creating AMI <redacted> from instance i-0fd869a2af80d736f
    amazon-ebs: AMI: ami-071a7ab923fbc1348
==> amazon-ebs: Waiting for AMI to become ready...
==> amazon-ebs: Terminating the source AWS instance...
==> amazon-ebs: Cleaning up any extra volumes...
==> amazon-ebs: No volumes to clean up, skipping
==> amazon-ebs: Deleting temporary security group...
==> amazon-ebs: Deleting temporary keypair...
Build 'amazon-ebs' finished.

==> Builds finished. The artifacts of successful builds are:
--> amazon-ebs: AMIs were created:
eu-west-2: ami-071a7ab923fbc1348

I think because of R is not in the PATH var? Below are the bash commands in the provision-rstudio.sh script.

sudo yum install -y gmp-devel-6.0.*                           # GNU MP arbitrary precision library

#Additional R Packages
sudo su - -c "R -e \"install.packages('tidyverse', version='1.3.1', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('devtools', version='2.4.0', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('kableExtra', version='1.3.4', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('survival', version='3.2.10', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('survminer', version='0.4.9', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('MASS', version='7.3.53.1', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('quantreg', version='5.85', repos='http://cran.rstudio.com/')\""
sudo su - -c "R -e \"install.packages('DescTools', version='0.99.41', repos='http://cran.rstudio.com/')\""

# Wipe out all traces of provisioning files
sudo rm -rf "/tmp/rstudio"
sudo rm -rf "/tmp/libgit2"
sudo rm -rf "/tmp/R"

[travberk]

I found this problem a couple of days ago, and just found out the root cause. The script provision-rstudio.sh on line 7 tries to install a very specific version of a library, namely libcurl-devel-7.76.1. Unfortunately, it's companion library, libcurl, is already installed at version 7.79.1 in the base image. Therefore, this library install fails, which causes the R installation to fail, and everything falls apart afterward. To fix it, you can simply change the specific library version to be libcurl-devel-7.79.1, save, and redeploy. The build then ran successfully for me in 52 minutes. I have not yet tested just having it install whatever version is current by not specifying version numbers. As the base image continues to update, this problem could come up again.

[dcloud9]

Agreed. Shall we raise a PR for this? Or there's already a much better future-proofing route in the roadmap?

[travberk]

I have no idea what is on their roadmap. If you want to raise a PR, I'll go in with you. I'm not sure if they would rather use another specific version, as I suggested above, or just leave the version off to use whatever is the latest. I have not tested the latter.

[manikandan-thangavelu-rl]

Fixed the issue in the PR #11 and closing the issue

[BoPeng]

I continue to have the same problem with the master branch. I am trying again with the version of libcurl removed.