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Oefenweb / ansible-r

Ansible role to set up (the latest version of) R in Ubuntu systems
MIT License
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enable bioconductor-3.8 #37

Closed lecorguille closed 4 years ago

lecorguille commented 5 years ago

Hi, Nice jobs, thanks a lot. Here is a little hack to install bioconductor packages since the 3.8

tersmitten commented 5 years ago

Thanks for your contribution. Can you make it similar to the logic we use for r_packages_from_github?

lecorguille commented 5 years ago

Still need to figure out what does that mean:

r_packages_from_github: "{{ r_packages | selectattr('type', 'defined') | selectattr('type', 'equalto', 'github') | map(attribute='name') | list | length > 0 }}"

I have just submitted a second try. I don't know if this alternative sounds better for you?

lecorguille commented 5 years ago

AH!

    "stderr": "Error: package ‘BiocManager’ is not available (for R version 3.4.4)\nExecution halted",

Indeed!

Need to do something around {{ r_version_35 | ternary('-cran35', '') }}/" ?

lecorguille commented 5 years ago

Sorry for the hesitation, I'm rather newbie in Ansible. I take the liberty to mv r_packages_from_github in vars because for me as user you dn't need to touch this and it's a scary syntax.

If it's what you expected, I will have to deal with the issue of bioconductor 3.x (biocLite) vs 3.8 (BiocManager)

tersmitten commented 5 years ago

I take the liberty to mv r_packages_from_github in vars because for me as user you didn't need to touch this and it's a scary syntax.

Good call

tersmitten commented 5 years ago

The changes look good so far

tersmitten commented 5 years ago

I will have to deal with the issue of bioconductor 3.x (biocLite) vs 3.8 (BiocManager)

That's a tricky one

lecorguille commented 5 years ago

Just tested in real with a couple of package on our infrastructure and it works finally :)

tersmitten commented 5 years ago

I think we're almost done!

lecorguille commented 5 years ago

The failed test seems to not come from this PR. `WARNING: The following packages cannot be authenticated!\n r-base-core``

Should we just add:

-  apt:
    allow_unauthenticated: yes
FanchTheSystem commented 4 years ago

I re-order the package workflow to be as it is on master:

Also I rebase this branch on master. And remove the retrie part added on some task

Please @tersmitten, could you say what is missing now for merge ?

lecorguille commented 4 years ago

Many thanks @tersmitten and @FanchTheSystem