GNU bug report logs - #36805
Small patch to remove TODO for (@@ (guix build-system r) bioconductor-uri)

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Kyle Andrews <kyle.c.andrews <at> gmail.com>
To: guix-patches <at> gnu.org
Subject: Small patch to remove TODO for (@@ (guix build-system r)
 bioconductor-uri)
Date: Wed, 24 Jul 2019 23:13:46 -0400

[Message part 1 (text/plain, inline)]

Hi,

I am a heavy R user trying to get my feet wet with guix. Here is a
patch to remove the hard-coded bioconductor release by adding an
optional 3rd argument to the function with an appropriate default
value. I hope this is helpful.

Regards,

Kyle Andrews

[0001-NAME-and-VERSION-are-not-enough-for-Bioconductor-URI.patch (text/x-patch, attachment)]

Message #8 received at 36805 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Kyle Andrews <kyle.c.andrews <at> gmail.com>
Cc: 36805 <at> debbugs.gnu.org
Subject: Re: [bug#36805] Small patch to remove TODO for (@@ (guix build-system
 r) bioconductor-uri)
Date: Thu, 25 Jul 2019 15:48:15 +0200

Dear,

It appears to me nice---if for example one wants to create a channel
for Bioconductor 3.6 or older.
This eases the automation of such channel.

I am using the package `cytofkit`, removed in the last release:
https://bioconductor.org/about/removed-packages/

Append strings to build the uri is not really nice.
https://github.com/zimoun/guix-bimsb/blob/master/bimsb/packages/staging.scm#L2895-L2941

Thank you for this suggestion.


All the best,
simon

Message #11 received at 36805 <at> debbugs.gnu.org (full text, mbox):

From: Kyle Andrews <kyle.c.andrews <at> gmail.com>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 36805 <at> debbugs.gnu.org
Subject: Re: [bug#36805] Small patch to remove TODO for (@@ (guix
 build-system r) bioconductor-uri)
Date: Fri, 26 Jul 2019 00:17:05 -0400

On Thu, 2019-07-25 at 15:48 +0200, zimoun wrote:
> Dear,
> 
> It appears to me nice---if for example one wants to create a channel
> for Bioconductor 3.6 or older.
> This eases the automation of such channel.
> 
> I am using the package `cytofkit`, removed in the last release:
> https://bioconductor.org/about/removed-packages/
> 
> Append strings to build the uri is not really nice.
> https://github.com/zimoun/guix-bimsb/blob/master/bimsb/packages/stagi
> ng.scm#L2895-L2941
> 
> Thank you for this suggestion.
> 
> 
> All the best,
> simon

Hi Simon,

I find it sometimes convenient to use a modified version of the
file.path function in R to save me from myself a bit with file paths
while also adding some semantic markup. Perhaps it would also be useful
for building Guix packages? Users would then seldom have to worry about
incorrectly including trailing slashes. I created a code snippet with
my naive implementation here:

https://gitlab.com/snippets/1879185

Maybe there is already a guile library for this sort of thing?

Regards,

Kyle

Message #14 received at 36805 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Kyle Andrews <kyle.c.andrews <at> gmail.com>
Cc: 36805 <at> debbugs.gnu.org, zimoun <zimon.toutoune <at> gmail.com>
Subject: Re: [bug#36805] Small patch to remove TODO for (@@ (guix build-system
 r) bioconductor-uri)
Date: Fri, 26 Jul 2019 11:46:33 +0200

Hi Kyle,

> I find it sometimes convenient to use a modified version of the
> file.path function in R to save me from myself a bit with file paths
> while also adding some semantic markup. Perhaps it would also be useful
> for building Guix packages? Users would then seldom have to worry about
> incorrectly including trailing slashes. I created a code snippet with
> my naive implementation here:
>
> https://gitlab.com/snippets/1879185
>
> Maybe there is already a guile library for this sort of thing?

There is, but it’s a little heavier:

    https://gitlab.com/brandoninvergo/guile-file-names

-- 
Ricardo

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