Debian Bug report logs - #1104334
r-bioc-keggrest: test fail - REFERENCE missing value

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Message #5 received at [email protected] (full text, mbox, reply):

From: "Rebecca N. Palmer" <[email protected]>

To: [email protected]

Subject: r-bioc-keggrest: test fail - REFERENCE missing value

Date: Tue, 29 Apr 2025 10:19:22 +0100

Package: r-bioc-keggrest
Version: 1.46.0+dfsg-2
Severity: serious

The autopkgtest is failing with this error:

ERROR in test_keggGet: Error in if (.self$lastField == "REFERENCE") { :
   missing value where TRUE/FALSE needed

I have not yet investigated why.

Message #10 received at [email protected] (full text, mbox, reply):

From: "Rebecca N. Palmer" <[email protected]>

To: [email protected]

Subject: Re: Bug#1104334: r-bioc-keggrest: test fail - REFERENCE missing value

Date: Wed, 30 Apr 2025 20:49:16 +0100

Control: tags -1 fixed-upstream patch

It looks like this is because the service this connects to started 
adding a blank line between entries, which this can't handle.  This is 
known upstream and easy to fix:

https://github.com/Bioconductor/KEGGREST/commit/b9132b53ecc8ba501e5976994fa7429568cd171c

However, while finding that I also saw the notice that this service 
prohibits non-academic-institution use, meaning we're not actually 
allowed to run these tests.  (The package code itself is open source, 
i.e. anyone is allowed to redistribute it, but not to use its main 
functionality.)

Message #17 received at [email protected] (full text, mbox, reply):

From: Debian FTP Masters <[email protected]>

To: [email protected]

Subject: Bug#1104334: fixed in r-bioc-keggrest 1.46.0+dfsg-3

Date: Thu, 01 May 2025 10:40:18 +0000

[Message part 1 (text/plain, inline)]

Source: r-bioc-keggrest
Source-Version: 1.46.0+dfsg-3
Done: Rebecca N. Palmer <[email protected]>

We believe that the bug you reported is fixed in the latest version of
r-bioc-keggrest, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Rebecca N. Palmer <[email protected]> (supplier of updated r-bioc-keggrest package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])


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Hash: SHA512

Format: 1.8
Date: Wed, 30 Apr 2025 22:08:26 +0100
Source: r-bioc-keggrest
Architecture: source
Version: 1.46.0+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Rebecca N. Palmer <[email protected]>
Closes: 1104334
Changes:
 r-bioc-keggrest (1.46.0+dfsg-3) unstable; urgency=medium
 .
   * Team upload.
   * Don't crash on blank lines between records. (Closes: #1104334)
   * Disable the autopkgtest, as it connects to a restricted-use service.
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