Public bug reported:
https://objectstorage.prodstack4-5.canonical.com/v1/AUTH_77e2ada1e7a84929a74ba3b87153c0ac /autopkgtest-hirsute/hirsute/armhf/r/r-bioc- annotationhub/20201120_110208_cc85e@/log.gz ... using temporary cache /tmp/Rtmpd4wQSU/BiocFileCache autopkgtest [10:57:15]: ERROR: timed out on command "su -s /bin/bash ubuntu -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 || true; . ~/.profile >/dev/null 2>&1 || true; buildtree="/tmp/autopkgtest.hNsFPu/build.BwO/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest.hNsFPu/run-unit-test-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest.hNsFPu/run-unit-test-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest.hNsFPu/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest.hNsFPu/autopkgtest_tmp"; export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=4; 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"; export 'ADT_TEST_TRIGGERS=r-base/4.0.3-1'; chmod +x /tmp/autopkgtest.hNsFPu/build.BwO/src/debian/tests/run-unit-test; touch /tmp/autopkgtest.hNsFPu/run-unit-test-stdout /tmp/autopkgtest.hNsFPu/run-unit-test-stderr; /tmp/autopkgtest.hNsFPu/build.BwO/src/debian/tests/run-unit-test 2> >(tee -a /tmp/autopkgtest.hNsFPu/run-unit-test-stderr >&2) > >(tee -a /tmp/autopkgtest.hNsFPu/run-unit-test-stdout);" (kind: test) ... The test passes locally when not using a proxy: using temporary cache /tmp/Rtmp5A5aA8/BiocFileCache snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 snapshotDate(): 2020-04-27 Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid require("xxx_foo") RUNIT TEST PROTOCOL -- Fri Nov 20 12:38:21 2020 *********************************************** Number of test functions: 19 Number of errors: 0 Number of failures:Warning messages: 1: call dbDisconnect() when finished working with a connection 2: download failed hub path: 'bogus/url' cache resource: 'AHInvalid : 5012' reason: all(rtype == "web" | file.exists(fpath)) is not TRUE 3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'xxx_foo' 0 1 Test Suite : AnnotationHub RUnit Tests - 19 test functions, 0 errors, 0 failures Number of test functions: 19 Number of errors: 0 Number of failures: 0 > autopkgtest [12:38:21]: test run-unit-test: -----------------------] autopkgtest [12:38:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-test PASS ... Maybe this is related to changes in R 4.0.3. https://stat.ethz.ch/pipermail/r-announce/2020/000662.html ... NEW FEATURES: ... * The default value for options("timeout") can be set from enviromnent variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting to 60 (seconds) if that is not set or invalid. ... ** Affects: r-bioc-annotationhub (Ubuntu) Importance: Undecided Status: New -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1905031 Title: autopkgtest fails in hirsute on armhf To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/r-bioc-annotationhub/+bug/1905031/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
