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

[Andreas Tille]

Control: tags -1 upstream
Control: forwarded -1 Heather Turner <ht at heatherturner.net>

Hi Heather,

the Debian packaged gnm recieved a bug report about a failing test in
connection with the upgrade to lapack 3.10.0 on the machine running the
test.  Please read the bug report below.

We admit we need your help to solve this issue that might affect
other systems as well.

Kind regards

    Andreas.

On Thu, Sep 16, 2021 at 10:59:19AM +0200, Sébastien Villemot wrote:
> 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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