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

[Andreas Tille]

Hi Heather,

thanks a lot for your quick response.  We do not have any deadline since
Debian 11 was "just" released.

Kind regards

     Andreas.


On Mon, Sep 27, 2021 at 12:01:20PM +0100, Heather Turner wrote:
> Hi Andreas,
> 
> Thanks for forwarding this bug report and thanks to Sébastien for the detailed and accurate analysis. I will need to submit an update to CRAN, which should be feasible in the next week or two. Is there a deadline that I need to work to?
> 
> Best wishes,
> 
> Heather
> 
> On Mon, Sep 27, 2021, at 10:12 AM, Andreas Tille wrote:
> > 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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> >> R-pkg-team at alioth-lists.debian.net
> >> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team
> >
> >
> > -- 
> > http://fam-tille.de
> 

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