[From nobody Mon Sep 28 03:21:08 2026 Received: (at submit) by bugs.debian.org; 17 May 2026 10:48:37 +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=-121.5 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, 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, 60; hammy, 149; neutral, 76; spammy, 1. spammytokens:0.987-1--knit hammytokens:0.000-+--pkgbuilddir, 0.000-+--PKGBUILDDIR, 0.000-+--forky, 0.000-+--HTo:N*Debian, 0.000-+--H*F:U*sanvila Return-path: <sanvila@debian.org> Received: from muffat.debian.org ([2607:f8f0:614:1::1274:33]:43946) 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 1wOZ2z-0028Pm-2B for submit@bugs.debian.org; Sun, 17 May 2026 10:48:37 +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 1wOZ30-000tOj-1A for submit@bugs.debian.org; Sun, 17 May 2026 10:48:37 +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=nyJZgyicXdwsENlSnf+Y5hujIsCL9alViuVk3xeXetI=; b=hA3a+G0/e/FpH0lhRogVQbHBlc zk9FOdiBFO6Wel+m6cwFdMbPXeWjiru8ygXswVmlzNh7eqpzMf8axeSUAeQ7DABWnA5y7zwdgcnPM KbFC+QlN85uOaI+1UjWYA499KxEjbeuja8BsTgLHdQT2fiKeSPO1nYEjc8QUK6aTnLdoHxGZvg0CP tn3vr9bF6X7zB84HpFkf+Vg/0rJWWCc3MjQQPlppyPec8LUddbVsMD1C1RsZmijyMpB+f7ufmh3aS 3I83kBrKuCLf5ys9mPtZYtxAlUUuu9IjSUxda7/q538xBrLNZvF8Dlv6bc4ViMMOtdBb50QNnPM4Y E1KxqgzQ==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wOZ2z-000t9g-1Y for submit@bugs.debian.org; Sun, 17 May 2026 10:48:37 +0000 From: Santiago Vila <sanvila@debian.org> To: Debian BTS <submit@bugs.debian.org> Subject: r-bioc-ioniser: FTBFS: Detected bibliography in YAML (IONiseR.md) but the rbibutils package is unavailable. X-Debbugs-Cc: sanvila@debian.org Message-Id: <E1wOZ2z-000t9g-1Y@paradis.debian.org> Date: Sun, 17 May 2026 10:48:37 +0000 Delivered-To: submit@bugs.debian.org Package: src:r-bioc-ioniser Version: 2.30.0+dfsg-3 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/202605/ 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-ioniser, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem R 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_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R dh_auto_configure -O--buildsystem=R dh_auto_build -O--buildsystem=R debian/rules execute_after_dh_auto_build make[1]: Entering directory '/<<PKGBUILDDIR>>' cd inst/doc && Rscript -e "require(knitr); require(markdown); knit('IONiseR.Rmd', 'IONiseR.md'); markdownToHTML('IONiseR.md', 'IONiseR.html', options=c('use_xhtml', 'base64_images'));" && rm -f IONiseR.md Loading required package: knitr Loading required package: markdown processing file: IONiseR.Rmd 1/37 2/37 [style] 3/37 4/37 [loadLibs] 5/37 6/37 [readData] 7/37 8/37 [loadData] 9/37 10/37 [exampleData] 11/37 12/37 [extractData1] 13/37 14/37 [extractData2] 15/37 16/37 [summaryPlots1] 17/37 18/37 [readCategories] 19/37 20/37 [summaryPlots2] 21/37 22/37 [numReads] 23/37 24/37 [heatmapExample] 25/37 26/37 [channelActivity] 27/37 28/37 [pentamerCorrelation] 29/37 30/37 [combinedplots] 31/37 32/37 [writefastq] 33/37 34/37 [writefastq2] 35/37 36/37 [fast5toFastq] 37/37 output file: IONiseR.md [1] "IONiseR.md" Error in mark(..., format = "html", template = template) : Detected bibliography in YAML (IONiseR.md) but the rbibutils package is unavailable. Please make sure it is installed (and declared in Suggests if bibliography is used in package vignettes). Calls: markdownToHTML -> mark_html -> mark Execution halted make[1]: *** [debian/rules:7: execute_after_dh_auto_build] Error 1 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:4: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 -------------------------------------------------------------------------------- ]