Re: 02/02: gnu: Remove r-biocinstaller does not evaluate

[Tobias Geerinckx-Rice]

Guix,

guix-comm...@gnu.org wrote:

nckx pushed a commit to branch master
in repository guix.

commit 0971f8bd884b6e92b77d9e12030cd58279699183
Author: Tobias Geerinckx-Rice <m...@tobias.gr>
Date:   Mon Jul 8 16:09:46 2019 +0200

    gnu: Remove r-biocinstaller.

    deprecated in favour of r-biocmanager.
---
 gnu/packages/bioinformatics.scm | 18 +-----------------
 1 file changed, 1 insertion(+), 17 deletions(-)


index b6f5a35..62d1cbd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7238,23 +7238,7 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")

It requires R < 3.6 and is no longer supported. * gnu/packages/bioinformatics.scm (r-biocinstaller): Define as diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) (define-public r-biocinstaller

[…]

+  (deprecated-package "r-biocinstaller" r-biocmanager))

This breaks things like:

--8<---------------cut here---------------start------------->8---
~ λ guix refresh -l grpc
Backtrace:
In ice-9/boot-9.scm:

 2887:24 18 (_)

In ice-9/threads.scm:
   390:8  7 (_ _)
In ice-9/boot-9.scm:
 2726:13  6 (_)
In ice-9/threads.scm:
   390:8  5 (_ _)
In ice-9/boot-9.scm:
 2994:20  4 (_)

 3014:26  2 (_)
In unknown file:

In gnu/packages/bioinformatics.scm:
 7246:22  0 (_)


--8<---------------cut here---------------end--------------->8---



--8<---------------cut here---------------start------------->8---
(define-public r-biocinstaller

 ;; module.  r-biocmanager is in (gnu packages cran).
 (package
   (inherit r-biocmanager)
   (name "r-biocinstaller")
   (properties `((superseded . ,r-biocmanager)))))
--8<---------------cut here---------------end--------------->8---

didn't help.



Kind regards,

T G-R

2874:4 19 (define-module* _ #:filename _ #:pure _ #:version _ #:imports _ #:exports _ #:replacements _ #:re-exports _ #:autoloads _ #:duplicates _ #:transformer _) 222:29 17 (map1 (((guix licenses) #:prefix license:) ((guix packages)) ((guix download)) ((guix git-download)) ((guix utils)) ((guix build-system r)) ((gnu packages algebra)) ((gnu packages base)) ((gnu packages #)) (#) …)) 222:29 16 (map1 (((guix packages)) ((guix download)) ((guix git-download)) ((guix utils)) ((guix build-system r)) ((gnu packages algebra)) ((gnu packages base)) ((gnu packages bioinformatics)) ((gnu packages c)) ((# …)) …)) 222:29 15 (map1 (((guix download)) ((guix git-download)) ((guix utils)) ((guix build-system r)) ((gnu packages algebra)) ((gnu packages base)) ((gnu packages bioinformatics)) ((gnu packages c)) ((gnu packages #)) ((…)) …)) 222:29 14 (map1 (((guix git-download)) ((guix utils)) ((guix build-system r)) ((gnu packages algebra)) ((gnu packages base)) ((gnu packages bioinformatics)) ((gnu packages c)) ((gnu packages compression)) ((gnu # #)) # …)) 222:29 13 (map1 (((guix utils)) ((guix build-system r)) ((gnu packages algebra)) ((gnu packages base)) ((gnu packages bioinformatics)) ((gnu packages c)) ((gnu packages compression)) ((gnu packages curl)) ((gnu # #)) # …)) 222:29 12 (map1 (((guix build-system r)) ((gnu packages algebra)) ((gnu packages base)) ((gnu packages bioinformatics)) ((gnu packages c)) ((gnu packages compression)) ((gnu packages curl)) ((gnu packages databases)) # …)) 222:29 11 (map1 (((gnu packages algebra)) ((gnu packages base)) ((gnu packages bioinformatics)) ((gnu packages c)) ((gnu packages compression)) ((gnu packages curl)) ((gnu packages databases)) ((gnu packages #)) ((# …)) …)) 222:29 10 (map1 (((gnu packages base)) ((gnu packages bioinformatics)) ((gnu packages c)) ((gnu packages compression)) ((gnu packages curl)) ((gnu packages databases)) ((gnu packages fontutils)) ((gnu packages gcc)) (#) …)) 222:17 9 (map1 (((gnu packages bioinformatics)) ((gnu packages c)) ((gnu packages compression)) ((gnu packages curl)) ((gnu packages databases)) ((gnu packages fontutils)) ((gnu packages gcc)) ((gnu packages geo)) (#) …)) 2800:17 8 (resolve-interface (gnu packages bioinformatics) #:select _ #:hide _ #:prefix _ #:renamer _ #:version _) 2312:4 3 (save-module-excursion #<procedure 2d7be10 at ice-9/boot-9.scm:2995:21 ()>) 1 (primitive-load-path "gnu/packages/bioinformatics" #<procedure 2dbe700 at ice-9/boot-9.scm:3001:37 ()>) gnu/packages/bioinformatics.scm:7246:16: error: r-biocmanager: unbound variable Replacing DEPRECATED-PACKAGE with the more explicit (and desperate) ;; DEPRECATED-PACKAGE can only refer to a package variable within the calling I half-understand why this is a problem (every single use of DEPRECATED-PACKAGE in Guix is intra-module, it's obviously not meant to span modules like this), but not the root cause or how to fix it without moving things around & breaking part of the backwards compatibility that DEPRECATED-PACKAGE is there to provide.

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