Your message dated Mon, 11 Oct 2021 17:09:00 +0000 with message-id <e1mzynm-0006y0...@fasolo.debian.org> and subject line Bug#994457: fixed in r-cran-gnm 1.1-1-3 has caused the Debian Bug report #994457, regarding r-cran-gnm autopkgtest needs to be adapted for lapack 3.10 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 994457: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=994457 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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
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--- Begin Message ---Source: r-cran-gnm Source-Version: 1.1-1-3 Done: Sébastien Villemot <sebast...@debian.org> We believe that the bug you reported is fixed in the latest version of r-cran-gnm, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 994...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Sébastien Villemot <sebast...@debian.org> (supplier of updated r-cran-gnm package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 11 Oct 2021 18:03:30 +0200 Source: r-cran-gnm Architecture: source Version: 1.1-1-3 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net> Changed-By: Sébastien Villemot <sebast...@debian.org> Closes: 994457 Changes: r-cran-gnm (1.1-1-3) unstable; urgency=medium . * Team upload. * lapack-3.10.patch: new patch, fixes autopkgtest against lapack 3.10 (Closes: #994457) Checksums-Sha1: 351ec7ef928e7dd969e0de27b4fb1239409e0bb9 2084 r-cran-gnm_1.1-1-3.dsc c3b2704464081c0e2fe6ae0f2eae55fb36130a4c 5040 r-cran-gnm_1.1-1-3.debian.tar.xz c61daf7f5a96eae8a1f800bb9549f48d39003a17 10804 r-cran-gnm_1.1-1-3_amd64.buildinfo Checksums-Sha256: e754218347557cb4526b175bc4a5f2c22fa844a21a5ed4ed916d9288e68987d3 2084 r-cran-gnm_1.1-1-3.dsc a7f5afe549e1a519f3cbf74cbf181268262d546710300a941c875192f683b6ae 5040 r-cran-gnm_1.1-1-3.debian.tar.xz 32bb3c39e164bac9d10cbea9fa8555800cfe1c3ea423652f9694cec33c986e3a 10804 r-cran-gnm_1.1-1-3_amd64.buildinfo Files: 27cff92a7583cc5a139d5b299a715a72 2084 gnu-r optional r-cran-gnm_1.1-1-3.dsc e9451514e850cf5259bc0fe341c1ad75 5040 gnu-r optional r-cran-gnm_1.1-1-3.debian.tar.xz c4b12b65e3e3ac0eec9f9d0020d13a16 10804 gnu-r optional r-cran-gnm_1.1-1-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEU5UdlScuDFuCvoxKLOzpNQ7OvkoFAmFkZYgACgkQLOzpNQ7O vkoa1w/+IUuZvNHj6jHJonOQPAYaoLqRc/Tk5xknrVFaavhRGO6VT9WvYy3zHSJI qm1nrkLR89V3B0QMtdWNdKP2CQt8pbTGqRjxSOwIO97huW+mEovqmo7xhbeqDKvt fhrr4ZKKzDd4VfPYr/1bcjNzBiGe3IhRm0KrR7K6aZRirmCUDEoTZqPxaNLXte21 9uJoDUgYW1u8tg3enyDHDgFZ+PT1K+kw6Vd50XxfwLsZYQxmh1aVMcDf6RtfttWj /SE8PfQJml9FQz6p62nK4oNpYme2wS+hKurgwE37QdSmsX1bOvP8Gkp02xuC2O18 0zBwRxTYYD3wT/CWxa9RsVb/Gz+Ka3mpxF0HzrCLkOw/d+1MAfgTIEYF6/NJnwLY dFWzwyCqhzhKQlJnJ5z9zSNNJqmQk24sA/SEImnprMBjmp+xeG+pFSsKwB4fjdg7 XYTsYf29SGahkgk6bMXRhT6mgJoXfhVYC2XgtzE+uWjuxUHWMSXh8t29Y+XToC1Y wrxmptITM1rpWCZoskgt4kVGghhsUv3qdL/H6gT206VsGq7BWgbchqc+til3r+Gn FHdpMnmKWvmTHbGXtxrFmMKaCD6BuYRyftHyo9TVBczP/eHWLaXDQMiMw8/+nE2Y TII5GFLgbQCRfOADRX3+nSWT0yUcv6Yh80vmROknsvTjvabrVBk= =BeS2 -----END PGP SIGNATURE-----
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