[From nobody Wed Oct 7 05:43:08 2026 Received: (at submit) by bugs.debian.org; 1 May 2026 23:14:37 +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=-121.1 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, 68; hammy, 150; neutral, 176; spammy, 0. spammytokens: hammytokens:0.000-+--pkgbuilddir, 0.000-+--PKGBUILDDIR, 0.000-+--forky, 0.000-+--H*F:U*sanvila, 0.000-+--HTo:N*Debian Return-path: <sanvila@debian.org> Received: from muffat.debian.org ([2607:f8f0:614:1::1274:33]:59504) 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 1wIx49-000Esg-1X for submit@bugs.debian.org; Fri, 01 May 2026 23:14:37 +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 1wIx4A-0004Fo-1H for submit@bugs.debian.org; Fri, 01 May 2026 23:14:37 +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=GvSkWwB9QNBvybFGc6SJ7dWwyvKHuF6Vsh/UgQVb1rc=; b=F+31RWw9O7T976xBuwHF1Oy1O6 soCOxf43KTIyNGdZ4PjHVgL4Zsvrjs5TmIsPG6FiptwI7UMid6owEX/DkP8HxSZxiAi0Q2SapZLDI Ed6xPTw1m32sSQyzMg/3Pqm2mfYpodtbZIa9Hvfqhs4oiWFdc9u31MCqQInZ3I1VuqhiBFqYt/M86 tUhPOWdK08I+QjwxrWQjiWsAJuNM4GAXVRefOUEmbxWuzpGQoltQ7p23q5xPBsDMBYdDba8un25LX CqsJHVs9c9IK1GO4AS7R3vE3tEvE9DF9mUycPIHCNKSaAiGKOZtB2SxYLDon7j5pYnqcxAR9HJj3D h3HWOY7g==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1wIx49-0005WC-0t for submit@bugs.debian.org; Fri, 01 May 2026 23:14:37 +0000 From: Santiago Vila <sanvila@debian.org> To: Debian BTS <submit@bugs.debian.org> Subject: r-bioc-hdf5array: FTBFS: h5mread_startscounts.c:405:29: error: implicit declaration of function 'DATAPTR'; did you mean 'DATAPTR_RO'? [-Wimplicit-function-declaration] X-Debbugs-Cc: sanvila@debian.org Message-Id: <E1wIx49-0005WC-0t@paradis.debian.org> Date: Fri, 01 May 2026 23:14:37 +0000 Delivered-To: submit@bugs.debian.org Package: src:r-bioc-hdf5array Version: 1.34.0-3 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-hdf5array, 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-hdf5array/ -O--buildsystem=R I: R Package: HDF5Array Version: 1.34.0 I: Building using R version 4.6.0-2 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Fri, 13 Mar 2026 16:36:46 +0900 mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 16:36:46 +0900'" * installing *source* package ‘HDF5Array’ ... ** this is package ‘HDF5Array’ version ‘1.34.0’ file ‘src/Makevars’ has the wrong MD5 checksum ** using staged installation ** libs using C compiler: ‘x86_64-linux-gnu-gcc (Debian 15.2.0-17) 15.2.0’ make[1]: Entering directory '/<<PKGBUILDDIR>>/src' x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c H5File.c -o H5File.o x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c global_errmsg_buf.c -o global_errmsg_buf.o x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o H5DSetDescriptor.c: In function ‘C_show_H5DSetDescriptor_xp’: H5DSetDescriptor.c:1192:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=] 1192 | Rprintf(" %llu", h5dset->h5dim[h5along]); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | | hsize_t {aka long unsigned int} | long long unsigned int | %lu H5DSetDescriptor.c:1202:38: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=] 1202 | Rprintf(" %llu", | ~~~^ | | | long long unsigned int | %lu 1203 | h5dset->h5chunkdim[h5along]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long unsigned int} x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c h5dimscales.c -o h5dimscales.o x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c uaselection.c -o uaselection.o x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_helpers.c -o h5mread_helpers.o x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_startscounts.c -o h5mread_startscounts.o h5mread_startscounts.c: In function ‘_h5mread_startscounts’: h5mread_startscounts.c:405:29: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 405 | void *mem = DATAPTR(ans); | ^~~~~~~ | DATAPTR_RO h5mread_startscounts.c:405:29: error: initialization of ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] make[1]: *** [/usr/lib/R/etc/Makeconf:190: h5mread_startscounts.o] 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 ‘HDF5Array’ * removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library/HDF5Array’ dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 16:36:46 +0900'" returned exit code 1 make: *** [debian/rules:4: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 -------------------------------------------------------------------------------- ]