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

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

[Tobias Geerinckx-Rice]

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Guix,

guix-commits@gnu.org wrote:
> nckx pushed a commit to branch master
> in repository guix.
>
> commit 0971f8bd884b6e92b77d9e12030cd58279699183
> Author: Tobias Geerinckx-Rice <me@tobias.gr>
> Date:   Mon Jul 8 16:09:46 2019 +0200
>
>     gnu: Remove r-biocinstaller.
>     
>     It requires R < 3.6 and is no longer supported.
>     
>     * gnu/packages/bioinformatics.scm (r-biocinstaller): Define 
>     as
>     deprecated in favour of r-biocmanager.
> ---
>  gnu/packages/bioinformatics.scm | 18 +-----------------
>  1 file changed, 1 insertion(+), 17 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.scm 
> b/gnu/packages/bioinformatics.scm
> index b6f5a35..62d1cbd 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -7238,23 +7238,7 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
>      (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:
   2874:4 19 (define-module* _ #:filename _ #:pure _ #:version _ 
   #:imports _ #:exports _ #:replacements _ #:re-exports _ 
   #:autoloads _ #:duplicates _ #:transformer _)
  2887:24 18 (_)
   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 _)
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 (_)
   2312:4  3 (save-module-excursion #<procedure 2d7be10 at 
   ice-9/boot-9.scm:2995:21 ()>)
  3014:26  2 (_)
In unknown file:
           1 (primitive-load-path "gnu/packages/bioinformatics" 
           #<procedure 2dbe700 at ice-9/boot-9.scm:3001:37 ()>)
In gnu/packages/bioinformatics.scm:
  7246:22  0 (_)

gnu/packages/bioinformatics.scm:7246:16: error: r-biocmanager: 
unbound variable
--8<---------------cut here---------------end--------------->8---

Replacing DEPRECATED-PACKAGE with the more explicit (and 
desperate)

--8<---------------cut here---------------start------------->8---
 (define-public r-biocinstaller
  ;; DEPRECATED-PACKAGE can only refer to a package variable 
  within the calling
  ;; 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.

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.

Kind regards,

T G-R

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

[Ricardo Wurmus]

Tobias Geerinckx-Rice <me@tobias.gr> writes:

>>   (define-public r-biocinstaller
>
> […]
>
>> +  (deprecated-package "r-biocinstaller" r-biocmanager))
>
> This breaks things […]

In this case I think it’s fine to just remove it and not set up the
deprecation redirection to r-biocmanager.

--
Ricardo