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 <h...@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...@lists.debian.org >> > > User: debian...@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-t...@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
