Re: How to sneak in Test-Depends like r-cran-testthat into automated testing for BioC packages
On 2 September 2021 1:13:13 am IST, Andreas Tille <andreas@an3as.eu> wrote:
>On Wed, Sep 01, 2021 at 08:58:45PM +0530, Nilesh Patra wrote:
>>
>> We have the salsa CI results, and it's clear that testthat is getting
>> loaded now as opposed to the last CI.
>>
>> https://salsa.debian.org/r-pkg-team/r-bioc-tximport/-/jobs/1897039
>
>This is in contrast to
>
> https://salsa.debian.org/r-pkg-team/r-bioc-biocparallel/-/jobs/1898498
>
>> BiocGenerics:::testPackage("BiocParallel")
>Error in library("RUnit", quietly = TRUE) :
> there is no package called ‘RUnit’
>Calls: <Anonymous> -> library
>Execution halted
I'm not sure if I understand what you mean?
I don't see any autopkgtest.conf file for biocparallel, so wouldn't that be expected?
I know runit is there in d/tests/control, but probably dependencies are fetched separately for the smoke test (autodep8 one) and the autopkgtest.
Such packages in the past have passed locally for me, but failed in salsa CI, a bit weird. So in these cases I added in a conf file since that doesn't do any harm, after which both my machine and salsa CI were happy.
But that said, I don't know the intricacies of how autodep8 interacts with R packages, and probably Dylan can give better answer here
Nilesh
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