From: zimoun <zimon.toutoune@gmail.com>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: 48792@debbugs.gnu.org
Subject: bug#48792: CRAN/bioconductor updater downloads tarballs twice
Date: Fri, 04 Nov 2022 13:27:39 +0100 [thread overview]
Message-ID: <87mt96aoqs.fsf@gmail.com> (raw)
In-Reply-To: <87pmx4uury.fsf@elephly.net> (Ricardo Wurmus's message of "Wed, 02 Jun 2021 17:54:25 +0200")
Hi,
On mer., 02 juin 2021 at 17:54, Ricardo Wurmus <rekado@elephly.net> wrote:
> When upgrading packages with “guix refresh -t bioconductor -u” Guix downloads
> tarballs for every package twice.
It can be worse with 3 downloads.
--8<---------------cut here---------------start------------->8---
$ ./pre-inst-env guix refresh -u r-rhdf5lib
Starting download of /tmp/guix-file.IjNx2z
From https://bioconductor.org/packages/release/bioc/src/contrib/Rhdf5lib_1.20.0.tar.gz...
…20.0.tar.gz 14.0MiB 96.9MiB/s 00:00 [##################] 100.0%
gnu/packages/bioconductor.scm:14362:13: r-rhdf5lib: updating from version 1.18.2 to version 1.20.0...
Starting download of /tmp/guix-file.NmqLjM
From https://bioconductor.org/packages/release/bioc/src/contrib/Rhdf5lib_1.20.0.tar.gz...
…20.0.tar.gz 14.0MiB 97.3MiB/s 00:00 [##################] 100.0%
Starting download of /tmp/guix-file.ytAuK3
From https://bioconductor.org/packages/release/bioc/src/contrib/Rhdf5lib_1.20.0.tar.gz...
…20.0.tar.gz 14.0MiB 103.3MiB/s 00:00 [##################] 100.0%
guix refresh: r-rhdf5lib: consider adding this input: zlib
gnu/packages/bioconductor.scm:14431:5: r-rhdf5lib: consider removing this native input: hdf5-source
gnu/packages/bioconductor.scm:14429:5: r-rhdf5lib: consider removing this propagated input: hdf5
gnu/packages/bioconductor.scm:14429:5: r-rhdf5lib: consider removing this propagated input: zlib
--8<---------------cut here---------------end--------------->8---
Cheers,
simon
PS: Noted when upgrading from 3.15 to 3.16 with this change.
--8<---------------cut here---------------start------------->8---
diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
index 620822b870..9b360ae581 100644
--- a/guix/build-system/r.scm
+++ b/guix/build-system/r.scm
@@ -61,7 +61,7 @@ (define* (bioconductor-uri name version #:optional type)
"/src/contrib/"
name "_" version ".tar.gz")
;; TODO: use %bioconductor-version from (guix import cran)
- (string-append "https://bioconductor.org/packages/3.15"
+ (string-append "https://bioconductor.org/packages/3.16"
type-url-part
"/src/contrib/"
name "_" version ".tar.gz"))))
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 4e1ce7c010..cdc6b806b2 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -156,9 +156,9 @@ (define %cran-url "https://cran.r-project.org/web/packages/")
(define %cran-canonical-url "https://cran.r-project.org/package=")
(define %bioconductor-url "https://bioconductor.org/packages/")
-;; The latest Bioconductor release is 3.15. Bioconductor packages should be
+;; The latest Bioconductor release is 3.16. Bioconductor packages should be
;; updated together.
-(define %bioconductor-version "3.15")
+(define %bioconductor-version "3.16")
(define* (bioconductor-packages-list-url #:optional type)
(string-append "https://bioconductor.org/packages/"
--8<---------------cut here---------------end--------------->8---
prev parent reply other threads:[~2022-11-04 12:29 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-06-02 15:54 bug#48792: CRAN/bioconductor updater downloads tarballs twice Ricardo Wurmus
2021-06-09 14:21 ` zimoun
2022-11-04 12:27 ` zimoun [this message]
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