[Bioc-devel] KEGGREST is broken and has a long reverse-dependency chain.

[Ali Sajid Imami]

I'll take a look. I rely on KEGGREST a lot.


Regards,
Dr. Ali Sajid Imami
LinkedIn <https://pk.linkedin.com/pub/ali-sajid-imami/50/956/2a6>


On Thu, Sep 21, 2023 at 7:02 PM Charles Plessy <charles.plessy using oist.jp>
wrote:

> Dear all,
>
> yesterday I reported on GitHub that the regression tests of KEGGREST
> fail because the KEGGREST:::.get.tmp.url function can not parse
> www.kegg.jp pages anymore.
>
> https://github.com/Bioconductor/KEGGREST/issues/21
>
> This is a problem in Debian because 1) we do not allow the Bioconductor
> packages that we redistribute to fail their tests and 2) the
> reverse-dependency chain of KEGGREST is heavy.
>
> KEGGREST <- AnnotationDbi <- GenomicFeatures <- lots of other packages
>
> I am not familiar with KEGG enough to grasp what KEGGREST:::.get.tmp.url
> was looking for.  But I was wondering if this bug would be a low-hanging
> fruit for somebody else in this list?
>
> Have a nice day,
>
> Charles Plessy
>
> --
> Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.plessy using oist.jp
> Okinawa  Institute  of  Science  and  Technology  Graduate  University
> Senior staff scientist ~~ Luscombe Unit ~~ https://groups.oist.jp/grsu
> Toots from work - ~~ ~~~~ ~~ - https://fediscience.org/@charles_plessy
>
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