[R-pkg-team] Bug#994457: r-cran-gnm autopkgtest needs to be adapted for lapack 3.10

[Sébastien Villemot]

Package: r-cran-gnm
Version: 1.1-1-2
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: needs-update

Dear Maintainer,

Since the upload of lapack 3.10.0-1, the autopkgtest of r-cran-gnm
fails in unstable. See for example:
https://ci.debian.net/data/autopkgtest/unstable/amd64/r/r-cran-gnm/15155026/log.gz

More precisely, test-biplot.R fails, because some results have the
opposite sign compared to the one which is expected.

My understanding is that this comes from the SVD of barleyMatrix in
that test file, which is different between lapack 3.9 and 3.10.
Mathematically, the SVD is not unique, and lapack 3.10 returns a
different (still valid) solution. More precisely, I verified that one
of the right-singular vector of that matrix has the opposite sign in
lapack 3.10. I also verified that the decomposition is correct by
checking that:

  max(abs(barleySVD$u %*% diag(barleySVD$d) %*% t(barleySVD$v) - barleyMatrix))

is a small value (about 2e-14).

Also note that the hardcoded expected values already partially differ 
from those of the original research paper mentioned in that test
(Gabriel (1998): Generalised bilinear regression). More precisely, half
of the values were hardcoded with the opposite sign. It seems that now
all values need to be hardcoded with the opposite sign.

The testsuite of r-cran-gnm thus needs to be adapted, by being more
tolerant to such sign changes.

N.B. : when trying to reproduce the problem, please ensure that your
lapack alternative (as given by “update-alternatives --display
liblapack.so.3-x86_64-linux-gnu) points to /usr/lib/x86_64-linux-
gnu/lapack/liblapack.so.3, and not to the binary provided by either
openblas or atlas (because these two have not yet been recompiled
against lapack 3.10, and thus do not expose the problem).

Best regards,

-- 
⢀⣴⠾⠻⢶⣦⠀  Sébastien Villemot
⣾⠁⢠⠒⠀⣿⡁  Debian Developer
⢿⡄⠘⠷⠚⠋⠀  https://sebastien.villemot.name
⠈⠳⣄⠀⠀⠀⠀  https://www.debian.org

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