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
