Your message dated Sun, 13 Jan 2019 16:53:52 +0000 with message-id <e1gij1e-0001v9...@fasolo.debian.org> and subject line Bug#919189: fixed in probabel 0.5.0+dfsg-2 has caused the Debian Bug report #919189, regarding probabel FTBFS on arm64, likely due to Eigen 3 NEON code 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.) -- 919189: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919189 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: probabel Version: 0.5.0+dfsg-1 Severity: serious Tags: ftbfs https://buildd.debian.org/status/fetch.php?pkg=probabel&arch=arm64&ver=0.5.0%2Bdfsg-1&stamp=1538603399&raw=0 ... FAIL: test_bt ============= Analysing BT... BT check: dose vs. dose_fv OK BT check (add model): prob vs. prob_fv OK BT check (domin model): prob vs. prob_fv OK BT check (over_domin model): prob vs. prob_fv OK BT check (recess model): prob vs. prob_fv OK 2c2 < rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 200 0.333517 19 204938 544.518 437.583 -567.387 435.04 1.75239 --- > rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 200 0.333517 19 204938 544.518 > 437.583 -567.388 435.04 1.75239 BT check (2df model): prob vs. prob_fv FAILED FAIL test_bt.sh (exit status: 1) ============================================================================ Testsuite summary for ProbABEL 0.5.0 ============================================================================ # TOTAL: 11 # PASS: 10 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 ============================================================================ See checks/test-suite.log Please report to genabel-de...@r-forge.wu-wien.ac.at ============================================================================ make[4]: *** [Makefile:713: test-suite.log] Error 1 I suspect this might be a problem with the NEON code in Eigen 3, and the fact that this can be fixed with the following workaround makes that even more probable: --- debian/rules.old 2019-01-09 15:07:11.950823327 +0000 +++ debian/rules 2019-01-09 15:17:23.280539016 +0000 @@ -6,6 +6,10 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all +ifeq ($(DEB_HOST_ARCH),arm64) + export DEB_CXXFLAGS_MAINT_APPEND = -march=armv8-a+nosimd +endif + include /usr/share/dpkg/default.mk # Location of the example files, will be converted to the
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--- Begin Message ---Source: probabel Source-Version: 0.5.0+dfsg-2 We believe that the bug you reported is fixed in the latest version of probabel, 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 919...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated probabel 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: Sun, 13 Jan 2019 17:10:41 +0100 Source: probabel Binary: probabel probabel-examples Architecture: source Version: 0.5.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: probabel - Toolset for Genome-Wide Association Analysis probabel-examples - Example files for ProbABEL Closes: 919189 Changes: probabel (0.5.0+dfsg-2) unstable; urgency=medium . * Work around a problem with the NEON code in Eigen 3 for arm64 architecture (Thanks for the patch to Adrian Bunk <b...@debian.org>) CLoses: #919189 * debhelper 12 * Standards-Version: 4.3.0 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target Checksums-Sha1: b6304a1c09712b0524c5979137679d06f24295b2 2175 probabel_0.5.0+dfsg-2.dsc 134f6882d84a7f6334f324b952fa9f3ab7d07804 4992 probabel_0.5.0+dfsg-2.debian.tar.xz 51e9c6d6d6230f2fe1a4f61dc273db374661267e 9097 probabel_0.5.0+dfsg-2_amd64.buildinfo Checksums-Sha256: c7920924254ca7d744292f7d2a1da02e1715a92de223e5ed738c535f1d0955eb 2175 probabel_0.5.0+dfsg-2.dsc 8023d74f8505eadf753294f171994f7169b775e4cf7fcf29c58cc185dafeebe3 4992 probabel_0.5.0+dfsg-2.debian.tar.xz 5a69c83b6b2192618065e30b25fe39f67891467bd5b86ba67f7669fb60c2d160 9097 probabel_0.5.0+dfsg-2_amd64.buildinfo Files: a84ad89cf0d1740fe386841661a8679c 2175 science optional probabel_0.5.0+dfsg-2.dsc a6a31ab0ed0bd6beb2bc57082b376002 4992 science optional probabel_0.5.0+dfsg-2.debian.tar.xz 16346cc4ac42628490f9f14ee71c0424 9097 science optional probabel_0.5.0+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlw7Zl0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFerw//W4U7HgvoSSHz+HjNsd8nzgzaUQKcmy7F GxFzvhSuoTID7EPmKKPf1Go+vQMRGRC2VA9SLdTZ4JM+bkABQjQ5kM8HYCh6TbsZ wVZJBZIfDXnLWRLLJ/Co6OPCXks/tpkxE20vtroln1skvasI9TpjY3iWh/9UYRmI iRG0eXgdIK6VMojCKEWdJ1duAmzKTpBIErxNIrIETHWDGx/CLyrFy4fevqFNl6Zp Tmo+vTTM5ijL9JyW5L9x7udDPyzFCqg23elVi1Qjr1MXX8AtJfAm12hB3uCweKfu Qzs6Qdq+4TH3Q+vDUyvK8GxvJKCBCKacnvuuTDcl6Lr/1aWONEH3ZtGQAYarQ5CM rzPDK6i3orWZwCMbENSR1h/f+NqvoQdTv+JgL5Vs/EdrCCfthYNfQYazXRvtgz6H /7VLeBEQjHacLM793dPDAO5TMnD3ygTYC1Z+lNicMZ8hocLpXdlPj8SGLdhCcUGO DDRoLUcPV2OAoPRl6jOLHCgG/rENdARMmhN/BBmDkoGenL77dij8ESUOhrc0d+0c tNx4/zanPPGQd4dwAZzjutmZzEK4GgdoqQNK+Ld7xzedQJvvhNcb0odcy6bgwYz6 IRDoxmw9pbjNJWP23rK435weq9HYYd4eLpBV5gF0gl4jozjKXBAQy9kiiM/ip9gg 1fhzaFNhHJE= =2IV7 -----END PGP SIGNATURE-----
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