[PATCH] gnu: freesasa: Fix memerr tests.

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2 participants
  • David Elsing
  • Bruno Victal
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unassigned
Submitted by
David Elsing
Severity
normal
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David Elsing wrote on 10 Jul 2023 20:06
(address . guix-patches@gnu.org)(name . David Elsing)(address . david.elsing@posteo.net)
c1869dfdd6a083ccb174e66b46cd53b65b76e966.1689012297.git.david.elsing@posteo.net
* 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(-)

Toggle diff (19 lines)
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
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Bruno Victal wrote on 14 Jul 2023 04:33
(name . David Elsing)(address . david.elsing@posteo.net)
8771e9cf-a653-1156-cc01-e6e737a1658c@makinata.eu
Hi David,

On 2023-07-10 19:06, David Elsing wrote:
Toggle quote (5 lines)
> + ;; 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.
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David Elsing wrote on 15 Jul 2023 01:01
(name . Bruno Victal)(address . mirai@makinata.eu)
861qhajdwl.fsf@posteo.net
Bruno Victal <mirai@makinata.eu> writes:

Hello Bruno,

Toggle quote (3 lines)
> 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
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David Elsing wrote on 14 Feb 20:20 +0100
(address . 64559@debbugs.gnu.org)
86a5o2n98s.fsf@posteo.net
David Elsing <david.elsing@posteo.net> writes:

Toggle quote (2 lines)
> 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.
?