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

[Heather Turner]

Dear Sébastien,

Thanks for the patch, that will certainly do the job till I get this fixed in the next gnm release - sorry I've not got to it yet.

Best wishes,

Heather

On Mon, Oct 11, 2021, at 5:14 PM, Sébastien Villemot wrote:
> Dear Heather,
>
> Please find attached the patch that I am going to apply to r-cran-gnm
> in Debian.
>
> With this patch applied, the test now works with both lapack 3.9 and
> 3.10.
>
> Feel free to use it (or not) for the next release of gnm.
>
> Best wishes,
>
> Le lundi 27 septembre 2021 à 12:01 +0100, Heather Turner a écrit :
>> 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
>> > > 
>> > 
>> > 
>> > 
>> > > _______________________________________________
>> > > R-pkg-team mailing list
>> > > R-pkg-team at alioth-lists.debian.net
>> > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team
>> > 
>> > 
>> > -- 
>> > http://fam-tille.de
>
> -- 
> ⢀⣴⠾⠻⢶⣦⠀  Sébastien Villemot
> ⣾⠁⢠⠒⠀⣿⡁  Debian Developer
> ⢿⡄⠘⠷⠚⠋⠀  https://sebastien.villemot.name
> ⠈⠳⣄⠀⠀⠀⠀  https://www.debian.org
>
>
> Attachments:
> * lapack-3.10.patch
> * signature.asc