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

2023-09-25 Thread Ramos Perez, Marcel via Bioc-devel 
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 



On Thu, Sep 21, 2023 at 7:02 PM Charles Plessy 

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

2023-09-21 Thread Ali Sajid Imami 
I'll take a look. I rely on KEGGREST a lot.


Regards,
Dr. Ali Sajid Imami
LinkedIn 


On Thu, Sep 21, 2023 at 7:02 PM Charles Plessy 
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.ple...@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
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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

2023-09-21 Thread Charles Plessy 

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.ple...@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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