Small patch to remove TODO for (@@ (guix build-system r) bioconductor-uri)

OpenSubmitted by Kyle Andrews.
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3 participants
  • Kyle Andrews
  • Ricardo Wurmus
  • zimoun
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unassigned
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normal
K
K
Kyle Andrews wrote on 25 Jul 2019 05:13
(address . guix-patches@gnu.org)
92658660d50853e4eec92f536d8b3eb720aab911.camel@gmail.com
Hi,
I am a heavy R user trying to get my feet wet with guix. Here is apatch to remove the hard-coded bioconductor release by adding anoptional 3rd argument to the function with an appropriate defaultvalue. I hope this is helpful.
Regards,
Kyle Andrews
From 729e621cc2175864937b6a4a3e754bd128ac9056 Mon Sep 17 00:00:00 2001From: Kyle Andrews <kyle.c.andrews@gmail.com>Date: Wed, 24 Jul 2019 22:51:20 -0400Subject: [PATCH] NAME and VERSION are not enough for Bioconductor URI. Need RELEASE.
--- guix/build-system/r.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-)
Toggle diff (25 lines)diff --git a/guix/build-system/r.scm b/guix/build-system/r.scmindex fbf08d3aa7..93b2f2f14f 100644--- a/guix/build-system/r.scm+++ b/guix/build-system/r.scm@@ -47,13 +47,14 @@ available via the first URI, the second URI points to the archived version." (string-append "mirror://cran/src/contrib/Archive/" name "/" name "_" version ".tar.gz"))) -(define (bioconductor-uri name version)+(define* (bioconductor-uri name version+ #:optional+ (release (@@ (guix import cran) %bioconductor-version))) "Return a URI string for the R package archive on Bioconductor for the-release corresponding to NAME and VERSION."+release corresponding to NAME, package VERSION, and Bioconductor RELEASE." (list (string-append "https://bioconductor.org/packages/release/bioc/src/contrib/" name "_" version ".tar.gz")- (string-append "https://bioconductor.org/packages/"- (@@ (guix import cran) %bioconductor-version)+ (string-append "https://bioconductor.org/packages/" release "/bioc/src/contrib/Archive/" name "_" version ".tar.gz"))) -- 2.22.0
Z
Z
zimoun wrote on 25 Jul 2019 15:48
(name . Kyle Andrews)(address . kyle.c.andrews@gmail.com)(address . 36805@debbugs.gnu.org)
CAJ3okZ15JPdQETN1G4xS-OGyGV97_4t+Keg0eEfpCk18ir82-g@mail.gmail.com
Dear,
It appears to me nice---if for example one wants to create a channelfor 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
K
K
Kyle Andrews wrote on 26 Jul 2019 06:17
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 36805@debbugs.gnu.org)
8a97ec5ed0d1f657731c22593a1f6696af2434dc.camel@gmail.com
On Thu, 2019-07-25 at 15:48 +0200, zimoun wrote:
Toggle quote (19 lines)> 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 thefile.path function in R to save me from myself a bit with file pathswhile also adding some semantic markup. Perhaps it would also be usefulfor building Guix packages? Users would then seldom have to worry aboutincorrectly including trailing slashes. I created a code snippet withmy naive implementation here:
https://gitlab.com/snippets/1879185
Maybe there is already a guile library for this sort of thing?
Regards,
Kyle
R
R
Ricardo Wurmus wrote on 26 Jul 2019 11:46
(name . Kyle Andrews)(address . kyle.c.andrews@gmail.com)
87pnlx86x2.fsf@elephly.net
Hi Kyle,
Toggle quote (11 lines)> 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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