[From nobody Wed Aug 12 05:25:07 2026 Received: (at submit) by bugs.debian.org; 11 Aug 2026 23:16:30 +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, 66; hammy, 150; neutral, 167; 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]:46310) 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 1wtvhu-00CSnT-1E for submit@bugs.debian.org; Tue, 11 Aug 2026 23:16:30 +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 1wtvhv-005MKS-2J for submit@bugs.debian.org; Tue, 11 Aug 2026 23:16:30 +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=9vwrZQCtcYTOfkXdGWb0g8HEpLzymi2ZrXKCfY/b+Lo=; b=fgrTAt8QSB7PzkdBa5WJwy+0sZ UPjXp+XprJyuoNAdB/KTD0yNjCCEhrshXKDW2qpahykzNrqSfFqI7ooYDKt6tn9KXIZ6Q8sTPDT3C cAbq5pHTOGnGPMVjejpei/Q2H7xHXaNmuL95k3X63g7hh5TiZ7WSLku18lGpkFERojcB7KVE84HJR jfClpVMer7DhT4ta45ebiJfTbQT/ug2KB2PD4bA3qYS3i5vnOzNiPNYqCHnHR6RBqMgjbJJxQBDIi hfdUnrB9dbRykS+W4E+rrx4PDZ5QKsOFbXJnWL5ajaM/fYHIuZ1246N4S9ydpdO1B4qAnAf/wAJNK FAZWjpkw==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wtvhu-004iS0-0c for submit@bugs.debian.org; Tue, 11 Aug 2026 23:16:30 +0000 From: Santiago Vila <sanvila@debian.org> To: Debian BTS <submit@bugs.debian.org> Subject: r-bioc-alabaster.base: FTBFS: collect2: error: ld returned 1 exit status X-Debbugs-Cc: sanvila@debian.org Message-Id: <E1wtvhu-004iS0-0c@paradis.debian.org> Date: Tue, 11 Aug 2026 23:16:30 +0000 Delivered-To: submit@bugs.debian.org Package: src:r-bioc-alabaster.base Version: 1.6.1+ds-2 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-alabaster.base, 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 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-alabaster.base/ -O--buildsystem=R I: R Package: alabaster.base Version: 1.6.1 I: Building using R version 4.6.1-4 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Sun, 12 Jan 2025 11:19:49 +0100 mkdir -p /<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library --clean . --built-timestamp="'Sun, 12 Jan 2025 11:19:49 +0100'" * installing *source* package ‘alabaster.base’ ... ** this is package ‘alabaster.base’ version ‘1.6.1’ ** using staged installation ** libs specified C++17 using C++ compiler: ‘x86_64-linux-gnu-g++ (Debian 16.2.0-1) 16.2.0’ using C++17 make[1]: Entering directory '/<<PKGBUILDDIR>>/src' x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c check_csv.cpp -o check_csv.o x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c check_list.cpp -o check_list.o x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c is_rfc3339.cpp -o is_rfc3339.o x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c load_csv.cpp -o load_csv.o x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c load_list.cpp -o load_list.o x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c validate.cpp -o validate.o x86_64-linux-gnu-g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o -fPIC /usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lhdf5_cpp -lcrypto -lcurl -lpthread -lsz -lz -L/usr/lib/R/lib -lR /usr/bin/x86_64-linux-gnu-ld.bfd: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so: No such file or directory collect2: error: ld returned 1 exit status make[1]: *** [/usr/share/R/share/make/shlib.mk:10: alabaster.base.so] Error 1 make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' make[1]: Entering directory '/<<PKGBUILDDIR>>/src' make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' ERROR: compilation failed for package ‘alabaster.base’ * removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-alabaster.base/usr/lib/R/site-library/alabaster.base’ dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library --clean . --built-timestamp="'Sun, 12 Jan 2025 11:19:49 +0100'" returned exit code 1 make: *** [debian/rules:4: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 -------------------------------------------------------------------------------- ]