[From nobody Mon Sep 28 04:21:04 2026 Received: (at submit) by bugs.debian.org; 19 Aug 2026 09:51:02 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-112.3 required=4.0 tests=ALL_TRUSTED,BAYES_00, DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,FOURLA, FROMDEVELOPER,FUZZY_CPILL,PGPSIGNATURE,SPF_HELO_NONE,SPF_PASS, USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 34; hammy, 150; neutral, 115; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <terceiro@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:46392) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <terceiro@debian.org>) id 1wwcwo-001Y99-1X for submit@bugs.debian.org; Wed, 19 Aug 2026 09:51:02 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Type:MIME-Version:Message-ID: Subject:To:From:Date:Reply-To:Cc:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=KQJ9qbrKlaRrOUH21NpMAATZ8rB4FzPAJEzjSR2utwk=; b=DSqV4ClpPDK9zXTMqc6/N+5ZKu +ypG/XujN6COIsSAMXQHvpL8cWN7Wzdt+/5Eh+oT7D8PYcvRcZ2gyfIN2G78ewFv19cwKEWYAERTi df/i1IHL89v4ollV15ZfcwtsPw+EneZrS+9HFSYpSdrF/sCf4tMqQ1/rBnsYYV9bVmih5+Hj4ahAd ZZ6+tDEkAPEuhRnRP1Vq918VDCZVTXG9Jgo6HTDL9NuxhtiVpBEaBNzfQUt9S8yHy8MqpL6PSmqPA MIV8d8NIxxJwXlXbjRoXhhdA7mvSmBCAFYamgSQH7Iq+L1IdHy5Mrnj8dG6X6CNB+V9XNL8la/VQB M71zXPuQ==; Received: from authenticated-user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_X25519__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <terceiro@debian.org>) id 1wwcwl-009hj1-2E for submit@bugs.debian.org; Wed, 19 Aug 2026 09:51:01 +0000 Received: from localhost (ava [IPv6:2804:14d:7224:88bd:b38e:cd50:1e1d:e09a]) by vps.terceiro.xyz (Postfix) with ESMTPSA id 1D4144083C for <submit@bugs.debian.org>; Wed, 19 Aug 2026 06:50:57 -0300 (-03) Date: Wed, 19 Aug 2026 06:50:56 -0300 From: Antonio Terceiro <terceiro@debian.org> To: submit@bugs.debian.org Subject: ncbi-entrez-direct: autopkgtest fails under incus-lxc: run-unit-test FAIL non-zero exit status 1 Message-ID: <aoV8gJuEkgWj3CGr@debian.org> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="zQUuW9eWHZvsH+J2" Content-Disposition: inline X-Debian-User: terceiro Delivered-To: submit@bugs.debian.org --zQUuW9eWHZvsH+J2 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Source: ncbi-entrez-direct Version: 24.0.20250523+dfsg-2 Severity: important Justification: fails autopkgtest on Debian CI infrastructure Tags: forky sid User: debian-ci@lists.debian.org Usertags: lxc Hi, Debian CI is switching away from lxc containers in favor of incus Container= s. This is motivated by security concerns from us; incus is based on lxc, but orchestrates containers substantially different: containers are not privile= ged (so root in the container is not uid 0 outside of it, and incus imposes a stricter isolation from the host system. ncbi-entrez-direct passes its tests under lxc, but fails under incus. The relevant part of the failure is (hopefully): > =1B[93m=1B[1mTest 12: word-at-a-time=1B[0m > a > about > again > all > almost > also > although > always > among > an > =1B[92m=1B[1mPassed=1B[0m >=20 > =1B[93m=1B[1mTest 13: xml2tbl=1B[0m > >Feature AF068625.2 > 1 200 source > organism Mus musculus > mol_type mRNA > db_xref taxon:10090 > chromosome 12 > map 4.0 cM > 1 200 gene > gene Dnmt3a > =1B[92m=1B[1mPassed=1B[0m >=20 > =1B[93m=1B[1mTest 14: xtract=1B[0m >=20 > =1B[0m=1B[31m=1B[1m=1B[7m ERROR: =1B[0m=1B[31m=1B[1m Input data from both= stdin and file 'sample_query.xml', mode is 'prw-------'=1B[0m > autopkgtest [21:01:16]: test run-unit-test: -----------------------] > autopkgtest [21:01:16]: test run-unit-test: - - - - - - - - - - results = - - - - - - - - - - > run-unit-test FAIL non-zero exit status 1 The full autokpgtest logs are available at: https://ci.debian.net/experiments/8/regressions/ (please beware of pagination) Common types of failure and suggested fixes are being documented at: https://wiki.debian.org/ContinuousIntegration/LxcToIncus Note that for the time being, ncbi-entrez-direct is still being tested unde= r lxc to avoid disturbing its testing migration test results. If you decide to add the `isolation-machine` restriction to get this package tested under qemu, please mention that explicitly when closing this bug (it= 's fine to do that only in the package changelog entry that closes the bug) so that we can configure your package for qemu on ci.debian.net. --zQUuW9eWHZvsH+J2 Content-Type: application/pgp-signature; name=signature.asc -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEst7mYDbECCn80PEM/A2xu81GC94FAmqFfIAACgkQ/A2xu81G C96c8BAAghnGRz17eLGsGCsn/vzCTbagf1+ZjZJCQn0fY+pFP+Um4jqrBFWi15mR rDLJlAlhaFf6YCpLFUQtNDbWVNEeJ4B/S9ujV3gPm8zuNhk6mxxaI/c1o+o6mK+d NQKE6jDrNFacvf4m3eG5KIo8trD8YH+HleaQO2Jsh6OQvXp7FQmgbt+J6/FCwIO7 gh9/FC67nQaeR8Fn6C/MvS6H+XEy2Uvv3hC3YIMpODT/obOHUVJXl2yD4kDc7lzo iB6PtZWW0Vyd4wvPLF1UnguYQUSTkzFTtAf7qK1XUdzysAMNEt470e5/l1Ex/cdq 5bKb0rGGrVkd8WWQaEPaXA6KffxXnCtSGJX8aJrVgcu2gAO+EtpzUt34B8NYyW0p yMtqPl3eExIxCz6XwbAhOfg36J9lcc7OG8T2pzG5J7yO9vxxHX3BZmQJoMtkY/M9 GezwXbALbcMm9yENV1TSX8b0HEI9rf6MBNPi3HGMgw3sgc1W8dxA/fEeEQcgCF8O c/ZVhUEFTMN+zpZo0Xo66HxWPeaT6fsQCZm4bbs92mG9INbp6+8g7Qdo8hPw2g3h TpT8V19LNk91wWXba6eHPGNUGP774461i6rzV6M3Ekyw9APFU7rXDE2T1fzJLh8o 4dLZZw7qSsi14S0MXiU65SGvBoxzz6vmaOgbw4EoWbS74Tg1/sg= =u34L -----END PGP SIGNATURE----- --zQUuW9eWHZvsH+J2-- ]