[Debian-med-packaging] Bug#1006776: pbbam: FTBFS: error: ‘optional’ in namespace ‘std’ does not name a template type

[Adrian Bunk]

Control: tags -1 patch

On Fri, Mar 04, 2022 at 09:16:45PM +0100, Sebastian Ramacher wrote:
> Source: pbbam
> Version: 1.7.0+dfsg-2
> Severity: serious
> Tags: ftbfs sid bookworm
> Justification: fails to build from source (but built successfully in the past)
> X-Debbugs-Cc: sramacher at debian.org
> 
> pbbam FTBFS:
> 
> FAILED: src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o 
> c++ -Isrc/libpbbam.so.1.7.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.1.7.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp
> In file included from /usr/include/pbcopper/data/Read.h:11,
>                  from /usr/include/pbcopper/data/MappedRead.h:8,
>                  from ../include/pbbam/BamRecord.h:14,
>                  from ../include/pbbam/AlignmentPrinter.h:11,
>                  from ../src/AlignmentPrinter.cpp:3:
> /usr/include/pbcopper/data/ReadId.h:22:10: error: ‘optional’ in namespace ‘std’ does not name a template type
>    22 |     std::optional<Interval> ZmwInterval;
>       |          ^~~~~~~~
> /usr/include/pbcopper/data/ReadId.h:22:5: note: ‘std::optional’ is only available from C++17 onwards
>...

The upstream fix is
https://github.com/PacificBiosciences/pbbam/commit/0c3da1ac49c42ca443592526a58ae94f2f05493e

The minimal fix would be cpp_std=c++17 in meson.build.

> Cheers

cu
Adrian