[Debian-med-packaging] Bug#952102: salmon: FTBFS: SalmonAlevin.cpp:780:6: error: ‘class rapmap::utils::MappingConfig’ has no member named ‘maxSlack’

[Lucas Nussbaum]

Source: salmon
Version: 0.12.0+ds1-1
Severity: serious
Justification: FTBFS on amd64
Tags: buster sid
Usertags: ftbfs-20200222 ftbfs-buster

Hi,

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

Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3 -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -pthread -std=c++14 -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /<<PKGBUILDDIR>>/src/WhiteList.cpp
> In file included from /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp:74:
> /usr/include/tbb/task_scheduler_init.h:21:154: note: #pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.
>    21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
>       |                                                                                                                                                          ^
> In file included from /<<PKGBUILDDIR>>/include/CollapsedCellOptimizer.hpp:9,
>                  from /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp:91:
> /usr/include/tbb/atomic.h:21:141: note: #pragma message: TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.
>    21 | #pragma message("TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
>       |                                                                                                                                             ^
> In file included from /<<PKGBUILDDIR>>/src/WhiteList.cpp:2:
> /usr/include/tbb/task_scheduler_init.h:21:154: note: #pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.
>    21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
>       |                                                                                                                                                          ^
> /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp: In function ‘void processReadsQuasi(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<rapmap::utils::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, RapMapIndexT*, std::vector<Transcript>&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, BiasParams&, SalmonOpts&, std::mutex&, bool, std::atomic<bool>&, volatile bool&, AlevinOpts<ProtocolT>&, SoftMapT&, spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>&)’:
> /<<PKGBUILDDIR>>/src/SalmonAlevin.cpp:780:6: error: ‘class rapmap::utils::MappingConfig’ has no member named ‘maxSlack’
>   780 |   mc.maxSlack = salmonOpts.consensusSlack;
>       |      ^~~~~~~~
> make[4]: *** [src/CMakeFiles/salmon.dir/build.make:274: src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/02/22/salmon_0.12.0+ds1-1_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.