[Debian-med-packaging] Bug#1054672: megahit: FTBFS: local_assemble.h:31:3: error: ‘uint32_t’ does not name a type

[Lucas Nussbaum]

Source: megahit
Version: 1.2.9-4
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20231027&fusertaguser=lucas@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.