[From nobody Wed Aug 12 07:07:09 2026 Received: (at submit) by bugs.debian.org; 11 Aug 2026 23:16:32 +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=-121.0 required=4.0 tests=ALL_TRUSTED,BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,FROMDEVELOPER,HAS_PACKAGE, PP_MIME_FAKE_ASCII_TEXT,USER_IN_DKIM_WELCOMELIST,X_DEBBUGS_CC autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 6; hammy, 150; neutral, 145; spammy, 0. spammytokens: hammytokens:0.000-+--pkgbuilddir, 0.000-+--PKGBUILDDIR, 0.000-+--HTo:N*Debian, 0.000-+--forky, 0.000-+--H*F:U*sanvila Return-path: <sanvila@debian.org> Received: from muffat.debian.org ([2607:f8f0:614:1::1274:33]:46324) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wtvhw-00CSnz-1I for submit@bugs.debian.org; Tue, 11 Aug 2026 23:16:32 +0000 Received: via submission from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=paradis.debian.org, EMAIL=hostmaster@paradis.debian.org (verified) by muffat.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wtvhx-005MKW-2N for submit@bugs.debian.org; Tue, 11 Aug 2026 23:16:32 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.paradis; h=Date:Message-Id:Subject:To:From:Reply-To:Cc: MIME-Version:Content-Type:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=jlsBqzOJsHo/GyUkzugNHHYYWu0dPiSwnG3hf8/Cqc4=; b=EwzNAxYtqzZhHRgh8owX+YOIjW HNaanRO10r4L8mtAKSdiIBBMhWMHbVkKjlHj3Sy+YdY1U6kylJt1pvB0ftvltJ1UwKBUdV/kMijtw T4NxZn6l4itrqlBIutMGlD8buPlLfQap5EdakG/dFxTiF8hfZ76ap7+lwGPH4O1aHQb4knWezOxX1 xgIrBB3YgdMMhTutulUV8u0DBgTIziRQiGBh5MfM12jtBP/1rhlZCxWmUN/4saQeyl+OkwjJQinYw 1ojpqo8qVsVdamSK3tN68DLx5Zkoc4gFL0ofAwqvnpmFeMmzN3ah8h2K+wAdG02CJE92m161QvHFX c1H15Rsg==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wtvhw-004iS6-0f for submit@bugs.debian.org; Tue, 11 Aug 2026 23:16:32 +0000 From: Santiago Vila <sanvila@debian.org> To: Debian BTS <submit@bugs.debian.org> Subject: r-bioc-genomicalignments: FTBFS: dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library --clean . --built-timestamp="'Tue, 04 Aug 2026 16:12:48 +0200'" returned exit code 1 X-Debbugs-Cc: sanvila@debian.org Message-Id: <E1wtvhw-004iS6-0f@paradis.debian.org> Date: Tue, 11 Aug 2026 23:16:32 +0000 Delivered-To: submit@bugs.debian.org Package: src:r-bioc-genomicalignments Version: 1.48.0-1 Severity: serious Tags: ftbfs forky sid Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202608/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:r-bioc-genomicalignments, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem R dh: warning: Implicitly activating single-binary dh addon for backwards compatibility. In compat 14+, dh: warning: this fallback will *not* happen automatically via dh_auto_install will instead use a dh: warning: different default for --destdir unless the single-binary add-on is active, dh: warning: which can cause the source to produce an empty binary package dh: warning: dh: warning: To keep the existing behaviour (compat 13), please activate the single-binary addon explicitly. dh: warning: This can be done by adding "dh-sequence-single-binary" to Build-Depends or passing dh: warning: --with=single-binary to dh. dh: warning: dh: warning: If you have solved this issue differently (e.g., by passing --destdir explicitly to dh: warning: dh_auto_install or not using dh_auto_install at all) and want to silence this warning dh: warning: without activating the addon, you can do that by passing --without=single-binary to dh dh: warning: to explicitly acknowledge the change. dh: warning: dh: warning: Please see the description of the "single-binary" in "man dh" for more details of what dh: warning: it does and why this is changing from implicit behaviour to explicitly opt-in. dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh: warning: Implicitly activating single-binary dh addon for backwards compatibility. In compat 14+, dh: warning: this fallback will *not* happen automatically via dh_auto_install will instead use a dh: warning: different default for --destdir unless the single-binary add-on is active, dh: warning: which can cause the source to produce an empty binary package dh: warning: dh: warning: To keep the existing behaviour (compat 13), please activate the single-binary addon explicitly. dh: warning: This can be done by adding "dh-sequence-single-binary" to Build-Depends or passing dh: warning: --with=single-binary to dh. dh: warning: dh: warning: If you have solved this issue differently (e.g., by passing --destdir explicitly to dh: warning: dh_auto_install or not using dh_auto_install at all) and want to silence this warning dh: warning: without activating the addon, you can do that by passing --without=single-binary to dh dh: warning: to explicitly acknowledge the change. dh: warning: dh: warning: Please see the description of the "single-binary" in "man dh" for more details of what dh: warning: it does and why this is changing from implicit behaviour to explicitly opt-in. dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-genomicalignments/ -O--buildsystem=R I: R Package: GenomicAlignments Version: 1.48.0 I: Building using R version 4.6.1-4 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Tue, 04 Aug 2026 16:12:48 +0200 mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library --clean . --built-timestamp="'Tue, 04 Aug 2026 16:12:48 +0200'" ERROR: dependency ‘cigarillo’ is not available for package ‘GenomicAlignments’ Perhaps try a variation of: install.packages('cigarillo') * removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library/GenomicAlignments’ dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library --clean . --built-timestamp="'Tue, 04 Aug 2026 16:12:48 +0200'" returned exit code 1 make: *** [debian/rules:4: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 -------------------------------------------------------------------------------- ]