[Debian-med-packaging] Bug#1092510: python-freecontact: FTBFS: ImportError: /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0: undefined symbol: PyObject_DelAttr

[Lucas Nussbaum]

Source: python-freecontact
Version: 1.1-8
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20250107 ftbfs-trixie

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> make[1]: Entering directory '/build/reproducible-path/python-freecontact-1.1'
> PYBUILD_SYSTEM=custom \
> PYBUILD_TEST_ARGS="{interpreter} /build/reproducible-path/python-freecontact-1.1/test/test01.py" \
>     dh_auto_test
> dh_auto_test: warning: warning: pybuild does not support building out of source tree. In source building enforced.
> 	pybuild --test -i python{version} -p "3.12 3.13"
> I: pybuild base:311: python3.12 /build/reproducible-path/python-freecontact-1.1/test/test01.py
> Traceback (most recent call last):
>   File "/build/reproducible-path/python-freecontact-1.1/test/test01.py", line 18, in <module>
>     import freecontact
> ImportError: /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0: undefined symbol: PyObject_DelAttr
> E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: python3.12 /build/reproducible-path/python-freecontact-1.1/test/test01.py
> I: pybuild base:311: python3.13 /build/reproducible-path/python-freecontact-1.1/test/test01.py
> ..will use 1 OMP threads
> SSE2 veczweight, wchunk = 64
> total weight (variation) of alignment = 620.777515304633
> 
> seq weight loop for 1000 seqs took 0.003128 secs
> will use 1 OMP threads
> calculated column aa frequencies, gap cols = 4
> calculated pair frequency table in 0.090502 secs
> collected apc_mean[MI] = 0.174031486973761
> aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606
> formed covariance matrix (122/126,4)
> LU factorization took 3.70552 secs, inverted matrix (incl LUf) in 11.638 secs
> density of inverse covariance matrix = 1 (cksum 346842.2)
> went back to gapped (126) wwi matrix
> collected apc_mean[l1norm] = 117.987054769839
> collected apc_mean[fro] = 3.35437751555787
> all done in 11.9483 secs
> will use 1 OMP threads
> SSE2 veczweight, wchunk = 64
> total weight (variation) of alignment = 561.595172234625
> 
> seq weight loop for 1000 seqs took 0.003001 secs
> will use 1 OMP threads
> calculated column aa frequencies, gap cols = 4
> calculated pair frequency table in 0.070504 secs
> collected apc_mean[MI] = 0.165528914074767
> aa freq sum (cell) = 0.999993945475299, pairfreq sum (cell) = 0.999988196197513
> formed covariance matrix (126/126,4)
> cov matrix Cholesky... not positive definite, dmean dev: 0.0457782
> cov matrix Cholesky... not positive definite, dmean dev: 0.0412004
> cov matrix Cholesky... not positive definite, dmean dev: 0.0370804
> cov matrix Cholesky... not positive definite, dmean dev: 0.0333723
> cov matrix Cholesky... not positive definite, dmean dev: 0.0300351
> cov matrix Cholesky... not positive definite, dmean dev: 0.0270316
> cov matrix Cholesky... not positive definite, dmean dev: 0.0243284
> cov matrix Cholesky... not positive definite, dmean dev: 0.0218956
> cov matrix Cholesky... not positive definite, dmean dev: 0.019706
> cov matrix Cholesky... not positive definite, dmean dev: 0.0177354
> cov matrix Cholesky... not positive definite, dmean dev: 0.0159619
> cov matrix Cholesky... not positive definite, dmean dev: 0.0143657
> cov matrix Cholesky... not positive definite, dmean dev: 0.0129291
> cov matrix Cholesky...
> shrank covariance matrix in 4.89104 secs
> will try rho 0.00178064, exact solution
>  iteration =   1 iteration =   2 iteration =   3will use 1 OMP threads
> SSE2 veczweight, wchunk = 64
> total weight (variation) of alignment = 620.777515304633
> will use 1 OMP threads
> calculated column aa frequencies, gap cols = 4
> calculated pair frequency table in 0.06468 secs
> collected apc_mean[MI] = 0.174031486973761
> aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606
> formed covariance matrix (122/126,4)
> LU factorization took 3.53366 secs, inverted matrix (incl LUf) in 12.7405 secs
> density of inverse covariance matrix = 1 (cksum 346842.2)
> went back to gapped (126) wwi matrix
> collected apc_mean[l1norm] = 117.987054769839
> collected apc_mean[fro] = 3.35437751555787
> .
> ----------------------------------------------------------------------
> Ran 3 tests in 32.032s
> 
> OK
> 	rm -fr -- /tmp/dh-xdg-rundir-zIZR6E00
> dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.13" returned exit code 13


The full build log is available from:
http://qa-logs.debian.net/2025/01/07/python-freecontact_1.1-8_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20250107;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250107&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.