| Message ID | 92658660d50853e4eec92f536d8b3eb720aab911.camel@gmail.com |
|---|---|
| State | Accepted |
| Headers | show |
| Series | [bug#36805] Small patch to remove TODO for (@@ (guix build-system r) bioconductor-uri) | expand |
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
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
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
From 729e621cc2175864937b6a4a3e754bd128ac9056 Mon Sep 17 00:00:00 2001 From: Kyle Andrews <kyle.c.andrews@gmail.com> Date: Wed, 24 Jul 2019 22:51:20 -0400 Subject: [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(-) diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm index 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