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

[Ramos Perez, Marcel]

Thank you for the fix.
I have updated the package.

Best,

Marcel

On 9/21/23 7:12 PM, Ali Sajid Imami wrote:

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><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><mailto: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<http://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<mailto: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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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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