GNU bug report logs - #64559
[PATCH] gnu: freesasa: Fix memerr tests.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: David Elsing <david.elsing <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: David Elsing <david.elsing <at> posteo.net>
Subject: [PATCH] gnu: freesasa: Fix memerr tests.
Date: Mon, 10 Jul 2023 18:06:11 +0000

* gnu/packages/chemistry.scm (freesasa)[arguments]: Add
"CFLAGS=-fno-builtin-malloc" to #:configure-flags.
---
 gnu/packages/chemistry.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index cddccf8aea..431b845989 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -703,7 +703,11 @@ (define-public freesasa
       #~(list "--enable-check"
               "--enable-parser-generator"
               "CXXFLAGS=-std=c++17"
-              "--enable-doxygen")
+              "--enable-doxygen"
+              ;; Some tests rely on replacing malloc with a wrapper which
+              ;; fails in a controlled way, but this does not work if the call
+              ;; is replaced.
+              "CFLAGS=-fno-builtin-malloc")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'remove-libc++-linking
-- 
2.40.1

Message #8 received at 64559 <at> debbugs.gnu.org (full text, mbox):

From: Bruno Victal <mirai <at> makinata.eu>
To: David Elsing <david.elsing <at> posteo.net>
Cc: andreas <at> enge.fr, efraim <at> flashner.co.il, 64559 <at> debbugs.gnu.org,
 bavier <at> posteo.net
Subject: Re: [bug#64559] [PATCH] gnu: freesasa: Fix memerr tests.
Date: Fri, 14 Jul 2023 03:33:02 +0100

Hi David,

On 2023-07-10 19:06, David Elsing wrote:
> +              ;; Some tests rely on replacing malloc with a wrapper which
> +              ;; fails in a controlled way, but this does not work if the call
> +              ;; is replaced.
> +              "CFLAGS=-fno-builtin-malloc")

Have you filed an issue with upstream regarding this?
It looks to me that this is something that should be figured out by the
build system or the unit tests.


-- 
Furthermore, I consider that nonfree software must be eradicated.

Cheers,
Bruno.

Message #11 received at 64559 <at> debbugs.gnu.org (full text, mbox):

From: David Elsing <david.elsing <at> posteo.net>
To: Bruno Victal <mirai <at> makinata.eu>
Cc: andreas <at> enge.fr, efraim <at> flashner.co.il, 64559 <at> debbugs.gnu.org,
 bavier <at> posteo.net
Subject: Re: [bug#64559] [PATCH] gnu: freesasa: Fix memerr tests.
Date: Fri, 14 Jul 2023 23:01:46 +0000

Bruno Victal <mirai <at> makinata.eu> writes:

Hello Bruno,

> Have you filed an issue with upstream regarding this?
> It looks to me that this is something that should be figured out by the
> build system or the unit tests.
that's true, I just filed an issue: https://github.com/mittinatten/freesasa/issues/94.

Cheers,
David

Message #14 received at 64559 <at> debbugs.gnu.org (full text, mbox):

From: David Elsing <david.elsing <at> posteo.net>
To: 64559 <at> debbugs.gnu.org
Cc: Bruno Victal <mirai <at> makinata.eu>, 64559-done <at> debbugs.gnu.org
Subject: Re: [bug#64559] [PATCH] gnu: freesasa: Fix memerr tests.
Date: Wed, 14 Feb 2024 19:20:19 +0000

David Elsing <david.elsing <at> posteo.net> writes:

> that's true, I just filed an issue: https://github.com/mittinatten/freesasa/issues/94.

I included this patch in another patch series for rdkit, which was now
applied in commit cc772e7f3172a8014e32c7ea3f6626963d4e9e16. The issue
was also fixed upstream.

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