Your message dated Sat, 04 Nov 2023 17:20:15 +0000 with message-id <e1qzkjj-002tsr...@fasolo.debian.org> and subject line Bug#1054672: fixed in megahit 1.2.9-5 has caused the Debian Bug report #1054672, regarding megahit: FTBFS: local_assemble.h:31:3: error: ‘uint32_t’ does not name a type to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1054672: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1054672 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: megahit Version: 1.2.9-4 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20231027 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > /usr/bin/c++ -I/<<PKGBUILDDIR>>/src -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection > -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -DXXH_INLINE_ALL > -ftemplate-depth=3000 -Wall -Wno-unused-function -fprefetch-loop-arrays > -funroll-loops -D__XROOT__='"/<<PKGBUILDDIR>>/src"' -std=gnu++11 -MD -MT > CMakeFiles/megahit_core_no_hw_accel.dir/src/main_assemble.cpp.o -MF > CMakeFiles/megahit_core_no_hw_accel.dir/src/main_assemble.cpp.o.d -o > CMakeFiles/megahit_core_no_hw_accel.dir/src/main_assemble.cpp.o -c > /<<PKGBUILDDIR>>/src/main_assemble.cpp > In file included from /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:27: > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:31:3: error: ‘uint32_t’ does > not name a type > 31 | uint32_t kmin{11}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:1:1: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > +++ |+#include <cstdint> > 1 | /* > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:32:3: error: ‘uint32_t’ does > not name a type > 32 | uint32_t kmax{41}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:32:3: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:33:3: error: ‘uint32_t’ does > not name a type > 33 | uint32_t step{6}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:33:3: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:34:3: error: ‘uint32_t’ does > not name a type > 34 | uint32_t seed_kmer{31}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:34:3: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:36:3: error: ‘uint32_t’ does > not name a type > 36 | uint32_t min_contig_len{200}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:36:3: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:37:3: error: ‘uint32_t’ does > not name a type > 37 | uint32_t sparsity{8}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:37:3: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:39:3: error: ‘uint32_t’ does > not name a type > 39 | uint32_t min_mapping_len{75}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:39:3: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:41:3: error: ‘uint32_t’ does > not name a type > 41 | uint32_t num_threads{0}; > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/localasm/local_assemble.h:41:3: note: ‘uint32_t’ is > defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp: In function ‘LocalAsmOption > {anonymous}::ParseLocalAsmOptions(int, char**)’: > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:40:34: error: ‘struct > LocalAsmOption’ has no member named ‘kmin’ > 40 | desc.AddOption("kmin", "", opt.kmin, ""); > | ^~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:41:34: error: ‘struct > LocalAsmOption’ has no member named ‘kmax’ > 41 | desc.AddOption("kmax", "", opt.kmax, ""); > | ^~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:42:34: error: ‘struct > LocalAsmOption’ has no member named ‘step’ > 42 | desc.AddOption("step", "", opt.step, ""); > | ^~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:43:39: error: ‘struct > LocalAsmOption’ has no member named ‘seed_kmer’ > 43 | desc.AddOption("seed_kmer", "", opt.seed_kmer, > | ^~~~~~~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:45:44: error: ‘struct > LocalAsmOption’ has no member named ‘min_contig_len’ > 45 | desc.AddOption("min_contig_len", "", opt.min_contig_len, ""); > | ^~~~~~~~~~~~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:46:45: error: ‘struct > LocalAsmOption’ has no member named ‘min_mapping_len’ > 46 | desc.AddOption("min_mapping_len", "", opt.min_mapping_len, ""); > | ^~~~~~~~~~~~~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:47:38: error: ‘struct > LocalAsmOption’ has no member named ‘sparsity’ > 47 | desc.AddOption("sparsity", "", opt.sparsity, "sparsity of hash > mapper"); > | ^~~~~~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:50:42: error: ‘struct > LocalAsmOption’ has no member named ‘num_threads’ > 50 | desc.AddOption("num_threads", "t", opt.num_threads, ""); > | ^~~~~~~~~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:64:13: error: ‘struct > LocalAsmOption’ has no member named ‘num_threads’ > 64 | if (opt.num_threads == 0) { > | ^~~~~~~~~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:65:11: error: ‘struct > LocalAsmOption’ has no member named ‘num_threads’ > 65 | opt.num_threads = omp_get_max_threads(); > | ^~~~~~~~~~~ > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp: In function ‘int > main_local(int, char**)’: > /<<PKGBUILDDIR>>/src/main_local_assemble.cpp:83:27: error: ‘struct > LocalAsmOption’ has no member named ‘num_threads’ > 83 | omp_set_num_threads(opt.num_threads); > | ^~~~~~~~~~~ > make[3]: *** [CMakeFiles/megahit_core.dir/build.make:135: > CMakeFiles/megahit_core.dir/src/main_local_assemble.cpp.o] Error 1 The full build log is available from: http://qa-logs.debian.net/2023/10/27/megahit_1.2.9-4_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20231027;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20231027&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
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--- Begin Message ---Source: megahit Source-Version: 1.2.9-5 Done: Nilesh Patra <nil...@debian.org> We believe that the bug you reported is fixed in the latest version of megahit, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1054...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nilesh Patra <nil...@debian.org> (supplier of updated megahit package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 04 Nov 2023 22:39:56 +0530 Source: megahit Architecture: source Version: 1.2.9-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Nilesh Patra <nil...@debian.org> Closes: 1054672 Changes: megahit (1.2.9-5) unstable; urgency=medium . * Team Upload. * Add patch to fix FTBFS with gcc-13 (Closes: #1054672) * Bump Standards-Version to 4.6.2 (no changes needed) Checksums-Sha1: 16293d5b847dc05fe5eb26805b59f66f3d92ad32 1433 megahit_1.2.9-5.dsc 082ecb63cfcac3e84c3af601cb95c6030b7442f6 8556 megahit_1.2.9-5.debian.tar.xz f6feb3b155ed7c2d6353d97076eabc0b316e7556 6764 megahit_1.2.9-5_amd64.buildinfo Checksums-Sha256: 36ba9919d93c765096ac5db6000283dcba094a52c4a1f4a0beda8139eec692d0 1433 megahit_1.2.9-5.dsc 67dde75e73af0d1f8d4c6e0c1e22435a447c9d9aa032e48f1fafe7cf259b64aa 8556 megahit_1.2.9-5.debian.tar.xz 0e4b8fd2aed70abc64f6ad88cc405176ddfaf2a2d8037d0ee0f9f2f440b8d08a 6764 megahit_1.2.9-5_amd64.buildinfo Files: b6e3c7bbdfd70f75d4109171af160544 1433 science optional megahit_1.2.9-5.dsc 7ad6d7debd12fe676dcb20b5781a5809 8556 science optional megahit_1.2.9-5.debian.tar.xz b75b941ce56d68a58989716769d34dd4 6764 science optional megahit_1.2.9-5_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iIgEARYIADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCZUZ8SBIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtqdQQEAlNLPdnqfg/i1IsYxgtrf0WXWA9WgVejy Lz1GU/JonzcBANVuTZ0prVKBhwOFHPN+VRFXiAIspt3brokWu0TX5/UK =YHqJ -----END PGP SIGNATURE-----
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