Unable to install EnhancedVolcano: non-zero exit status

Question

[phoenix.sum13]

Hi everyone,

I'm unable to install R package EnhancedVolcano. I end up getting warning messages mentioning several packages with non-zero exit status.

How do I proceed from here?

[Kevin Blighe]

It seems to be unrelated to EnhancedVolcano (I am the EnhancedVolcano maintainer). What were the error messages for these other packages, such as textshaping?

Which command are you using to [try to] install?

[phoenix.sum13]

Hi sir, sorry for the late reply. I'm still not able to install any of these missing packages. This is an example of 'textshaping'.

[Kevin Blighe]

Can you please read through the error messages and follow the provided advice? For example, read from [ANTICONF]

It seems that you need to install some libraries outside of RStudio

Answer 1

[ATpoint]

The procedure with compilation errors is always the same. Go to the first error message, try to manually compile that tool, address the errors that come up, then try to compile the actual tool you want again. Repeat this until you have success. Usually it comes down to some kind of missing system libraries or dependencies.

Bioconductor also provides a Docker container with all dependencies installed to compile any Bioc tool, see https://github.com/Bioconductor/bioconductor_docker/blob/master/Dockerfile#L33

If you see an error due to missing dependencies and you cannot google-out what the exact lib is that is missing go through this linked Docker file which lists all relevant dependencies, maybe that helps narrowing it down, but usually just googling the error message is enough, as usually a thousand others had the same problem before as well, so there is usually a StackOverflow post addressing this.