Your message dated Thu, 07 Feb 2019 08:40:27 +0000 with message-id <e1grfer-000cpz...@fasolo.debian.org> and subject line Bug#921566: fixed in deepnano 0.0+git20170813.e8a621e-3 has caused the Debian Bug report #921566, regarding deepnano: autopkgtest times out since 2019-01-11 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.) -- 921566: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=921566 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: deepnano Version: 0.0+git20170813.e8a621e-2 Severity: important X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: timeout fails-always Dear maintainers, Since 2019-01-11 your package has failed its autopkgtest on the ci.debian.net infrastructure (both testing and unstable) due to timeouts of autopkgtest (after 10000 seconds). In the past, your test failed in about 1 minute. Could you please investigate and make your autopkgtest more robust against this time out? Please contact me if you need help and you think I can provide that (I am not subscribed to this bug). For now, I have blacklisted deepnano on our infrastructure, I'll remove it when this bug is closed. Paul https://ci.debian.net/data/autopkgtest/testing/amd64/d/deepnano/1834069/log.gz autopkgtest [15:24:56]: test run-test.sh: [----------------------- #1 - deepnano_basecall /usr/lib/python2.7/dist-packages/theano/configdefaults.py:560: UserWarning: DeprecationWarning: there is no c++ compiler.This is deprecated and with Theano 0.11 a c++ compiler will be mandatory warnings.warn("DeprecationWarning: there is no c++ compiler." WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string. WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions. loading template net done loading complement net done loading 2D net done calling read 0/69 test_data/2016_3_4_3507_1_ch120_read240_strand.fast5 calling read 1/69 test_data/2016_3_4_3507_1_ch120_read353_strand.fast5 calling read 2/69 test_data/2016_3_4_3507_1_ch120_read415_strand.fast5 calling read 3/69 test_data/2016_3_4_3507_1_ch120_read418_strand.fast5 calling read 4/69 test_data/2016_3_4_3507_1_ch120_read433_strand.fast5 calling read 5/69 test_data/2016_3_4_3507_1_ch120_read443_strand.fast5 calling read 6/69 test_data/2016_3_4_3507_1_ch120_read505_strand.fast5 calling read 7/69 test_data/2016_3_4_3507_1_ch120_read521_strand.fast5 calling read 8/69 test_data/2016_3_4_3507_1_ch120_read542_strand.fast5 calling read 9/69 test_data/2016_3_4_3507_1_ch120_read586_strand.fast5 calling read 10/69 test_data/2016_3_4_3507_1_ch120_read635_strand.fast5 calling read 11/69 test_data/2016_3_4_3507_1_ch120_read706_strand.fast5 calling read 12/69 test_data/2016_3_4_3507_1_ch120_read83_strand.fast5 calling read 13/69 test_data/2016_3_4_3507_1_ch120_read89_strand.fast5 calling read 14/69 test_data/2016_3_4_3507_1_ch126_read1066_strand.fast5autopkgtest [18:11:36]: ERROR: timed out on command "su -s /bin/bash debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 || true; . ~/.profile >/dev/null 2>&1 || true; buildtree="/tmp/autopkgtest-lxc.fc9prhyw/downtmp/build.lqo/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest-lxc.fc9prhyw/downtmp/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.fc9prhyw/downtmp/autopkgtest_tmp"; export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=2; unset LANGUAGE LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo $$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f /tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; chmod +x /tmp/autopkgtest-lxc.fc9prhyw/downtmp/build.lqo/src/debian/tests/run-test.sh; touch /tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stdout /tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stderr; /tmp/autopkgtest-lxc.fc9prhyw/downtmp/build.lqo/src/debian/tests/run-test.sh 2> >(tee -a /tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stderr >&2) > >(tee -a /tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stdout);" (kind: test) autopkgtest [18:11:37]: test run-test.sh: -----------------------] run-test.sh FAIL timed out
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--- Begin Message ---Source: deepnano Source-Version: 0.0+git20170813.e8a621e-3 We believe that the bug you reported is fixed in the latest version of deepnano, 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 921...@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 deepnano 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: SHA256 Format: 1.8 Date: Thu, 07 Feb 2019 08:25:35 +0100 Source: deepnano Binary: deepnano deepnano-data Architecture: source Version: 0.0+git20170813.e8a621e-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: deepnano - alternative basecaller for MinION reads of genomic sequences deepnano-data - alternative basecaller for MinION reads of genomic sequences (dat Closes: 921566 Changes: deepnano (0.0+git20170813.e8a621e-3) unstable; urgency=medium . * Use less data for autopkgtest Closes: #921566 * debhelper 12 * Standards-Version: 4.3.0 Checksums-Sha1: 54aecb45563ac45c9d819815de6482d4f2974472 2280 deepnano_0.0+git20170813.e8a621e-3.dsc 828ba5c8d62eb19e26cae57cb571ba6a33ba0eb6 5176 deepnano_0.0+git20170813.e8a621e-3.debian.tar.xz Checksums-Sha256: fc5b6786266ec5a2d560f12dcdaf95a337903e69cdbc9464d9a7ca54dd38a52a 2280 deepnano_0.0+git20170813.e8a621e-3.dsc 6fef8a7806b6860d94de8f96ce2c4618857637476d6b6b2c043122de78e38373 5176 deepnano_0.0+git20170813.e8a621e-3.debian.tar.xz Files: 61be4ee555e18d0890d60e69ae116cc6 2280 science optional deepnano_0.0+git20170813.e8a621e-3.dsc 6ccea767c323cbe94cefb224d02f8111 5176 science optional deepnano_0.0+git20170813.e8a621e-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxb5W0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEZ1w//RQI0h9jVvryTLxknIeR5qtrUDivmmVLk EgD7goGHzpoOoE1PNWolbp0gvQyba6dYMaehdW1KlUmn412Cc14jIKzV28iZfua1 9AOw2V+rktZfCCPIIgBEvtvXa02xVVazn0zPDLzZF4CpuxakBNNpUUfYKU8BYJzn SqfZf3dzFjLUO3MfOLcPNRSoQqZowd7Z4u9l3hXWVwpabgW4JlptH9ch4NZHioLa qvM8uVsdQWcJhNTPZEJ6vGru+KBUEfH2KV41+/1tMMToFF5NAEEk3TONCyY49OqO Z3OfzKQ5o+RAWm6fQ/TNoXzv/IT8yi5z0wQzl2IZuO0r/L5fRgpJ32UB/SPcoTiD 5s7eYxf8I3rU0T9t0myG2iOTOGZ+Xu9/vzKzHbSnCQrURbKBF24syrXVi0jtyc1m l9pAZue4n7I7ZhNJJ51p0heGpoqhrXEE23PQwLy0RWcFHWWv8lmsAKCagHjuT7TQ E8GUryA3FQkjMVs9uF7OjLZWy6Z9Mk6Xhp6HPZzvoVsjf2Xji5+3PUXhQ91uo+e9 VQlt5m0CaSsdHE8pfZmlaXQn3CxPrMNRF2v7EPvz3E7ZsJ+BYzZhneJe7ONbdN8V IxvC9Pk8ghevcMeJfFfClaANP/46oEkUjWXZYI7yrCzUh6wzdZ9psODiCLPypwiz fTe827rrGq4= =0f7V -----END PGP SIGNATURE-----
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