taskManeage - Tasks: task #16641, Autoconf/configure related...

 
 

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task #16641: Autoconf/configure related reproducibility

Submitter:  Boud Roukema <boud>
Submitted:  Sat 22 Mar 2025 01:54:46 PM UTC
   
 
Should Start On:  Sat 22 Mar 2025 12:00:00 AM UTC Should be Finished on:  Tue 19 Jan 2038 03:14:07 AM UTC
Category:  None Priority:  5 - Normal
Status:  None Privacy:  Public
Assigned to:  None Percent Complete:  0%
Open/Closed:  Open Effort:  0.00

Sun 23 Mar 2025 03:33:03 PM UTC, comment #2: 

My point here at task #16641 is for the general task of keeping an eye on reproducibility flaws in autotools.

I agree that the specific bug is useful as a Maneage bug report: done: bug #66942 . I set it to 'closed', because there's a hack that worked for me; a hack that should work; and a long-term solution that is presumably already implemented.

https://savannah.nongnu.org/bugs/index.php?66942

Boud Roukema <boud>
Group Member
Sat 22 Mar 2025 08:15:37 PM UTC, comment #1: 

Thanks for raising this point Boud. It is a very valuable lesson!

To help future users find this bug and use your experience it may be better to define this as a "bug" (not a "task") and set the title to something like this: "Old M4 and Binutils fail due to mismatch between host cc and configure checks".

A more dirty solution is to update the problematic software (especially in 'basic.mk' which will most likely not change the analysis results).

Mohammad Akhlaghi <makhlaghi>
Group administrator
Sat 22 Mar 2025 01:54:46 PM UTC, original submission:  

This task aims to collect together notes on autoconf/configure related to the hoped-for long-term (10-50 years) reproducibility. It starts with one particular reproducibility flaw found for the software pipeline for a published paper.

Point 3 [1] in the reproducibility test of [2] appears to be solved for the purposes of reproducibility by updating 'autoconf' to a version such as 2.72 and running it to generate new 'configure' files, or doing a hack in existing 'configure' files, based on a suggestion at [3] and described in [4]. The bug is that older 'autoconf' versions considered it a fatal error if any of the gcc version options failed, whereas in reality, '-V' and '-qversion' were apparently deprecated (still work but should not be used) a long time ago, and in gcc 12.1.0 have become obsolete (will fail). The hack fix is to pass the test if at least one version option is found. I haven't actually tested the more modular approach of autoconf 2.72 - I'm just guessing that it would avoid fatal errors if running a modern version of gcc.

[1] https://codeberg.org/boud/subpoisson/commit/365a2e846757ce5f5a91877c79a0a0d880651610

[2] "Anti-clustering in the national SARS-CoV-2 daily infection counts", 2021, PeerJ, 9:e11856, by B. F. Roukema - ArXiv:2007.1179 - doi:10.7717/peerj.11856 - doi:10.5281/zenodo.5262698

[3] https://superuser.com/questions/846768/gcc-unrecognized-command-line-options-v-and-qversion-with-autoconf

[4] https://codeberg.org/boud/subpoisson/commit/22a13cd3986af9baf9745a4d33b49f5de7f97a44

Boud Roukema <boud>
Group Member

 

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