[Debian-med-packaging] Bug#963288: mothur: FTBFS: source/datastructures/datavector.hpp:4:10: fatal error: mothurout.h: No such file or directory

[Lucas Nussbaum]

Source: mothur
Version: 1.44.1-1
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200620 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.1\"" -DUSE_READLINE -I.  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/calculators/boneh.o source/calculators/boneh.cpp
> In file included from source/datastructures/sabundvector.hpp:4,
>                  from source/calculators/calculator.h:5,
>                  from source/calculators/ace.h:16,
>                  from source/calculators/ace.cpp:10:
> source/datastructures/datavector.hpp:4:10: fatal error: mothurout.h: No such file or directory
>     4 | #include "mothurout.h"
>       |          ^~~~~~~~~~~~~
> In file included from source/datastructures/sabundvector.hpp:4,
>                  from source/calculators/calculator.h:5,
>                  from source/calculators/accuracy.hpp:12,
>                  from source/calculators/accuracy.cpp:9:
> source/datastructures/datavector.hpp:4:10: fatal error: mothurout.h: No such file or directory
>     4 | #include "mothurout.h"
>       |          ^~~~~~~~~~~~~
> compilation terminated.
> In file included from source/datastructures/sabundvector.hpp:4,
>                  from source/calculators/calculator.h:5,
>                  from source/calculators/bergerparker.h:12,
>                  from source/calculators/bergerparker.cpp:10:
> source/datastructures/datavector.hpp:4:10: fatal error: mothurout.h: No such file or directory
>     4 | #include "mothurout.h"
>       |          ^~~~~~~~~~~~~
> In file included from source/datastructures/sabundvector.hpp:4,
>                  from source/calculators/calculator.h:5,
>                  from source/calculators/boneh.h:13,
>                  from source/calculators/boneh.cpp:10:
> source/datastructures/datavector.hpp:4:10: fatal error: mothurout.h: No such file or directory
>     4 | #include "mothurout.h"
>       |          ^~~~~~~~~~~~~
> compilation terminated.
> compilation terminated.
> compilation terminated.
> make[2]: *** [Makefile:139: source/calculators/accuracy.o] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/06/20/mothur_1.44.1-1_unstable.log

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!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.