[Debian-med-packaging] Bug#939506: unanimity ftbfs in unstable

[Andreas Tille]

Control: tags -1 help

Hi,

On Thu, Sep 05, 2019 at 06:39:33PM +0200, Matthias Klose wrote:
> cd /build/1st/unanimity-3.3.0+dfsg/build/src && /usr/bin/cmake -E
> cmake_link_script CMakeFiles/gcpp.dir/link.txt --verbose=1
> /build/1st/unanimity-3.3.0+dfsg/src/main/ccs.cpp: In function ‘int
> Runner(const PacBio::CLI::Results&)’:
> /build/1st/unanimity-3.3.0+dfsg/src/main/ccs.cpp:570:38: error: ‘move’ was
> not declared in this scope
>   570 |                     read.Sequence(), move(ipd), move(pw),
> read.LocalContextFlags(),
>       |                                      ^~~~

I have pushed the latest upstream version to Git[1].  The whole error message
is now:


...
cd /build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/src && /usr/bin/c++   -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/include -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/generated -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src  -g -O2 -fdebug-prefix-map=/build/unanimity-3.4.1+git20180307.02aa264+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -                   D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs   -fPIC -std=c++14 -o CMakeFiles/ccs.dir/main/ccs.cpp.o -c /build/unanimity-3.4.1+git20180307.02aa264+dfsg/  src/main/ccs.cpp
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:63:12: error: ‘std::setprecision’ has not been declared
   63 | using std::setprecision;
      |            ^~~~~~~~~~~~
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp: In function ‘void WriteResultsReport(std::ostream&, const Results&)’:
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:273:24: error: ‘setprecision’ was not declared in this scope
  273 |     report << fixed << setprecision(2);
      |                        ^~~~~~~~~~~~
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp: In function ‘int Runner(const PacBio::CLI::Results&)’:
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:570:38: error: ‘move’ was not declared in this scope
  570 |                     read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),
      |                                      ^~~~
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:570:38: note: suggested alternatives:
In file included from /usr/include/c++/9/deque:67,
                 from /usr/include/boost/detail/container_fwd.hpp:91,
                 from /usr/include/boost/container_hash/extensions.hpp:22,
                 from /usr/include/boost/container_hash/hash.hpp:760,
                 from /usr/include/boost/type_index/stl_type_index.hpp:43,
                 from /usr/include/boost/type_index.hpp:29,
                 from /usr/include/boost/function/function_base.hpp:21,
                 from /usr/include/boost/function/detail/prologue.hpp:17,
                 from /usr/include/boost/function.hpp:30,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /usr/include/boost/algorithm/string.hpp:23,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:14:
/usr/include/c++/9/bits/stl_deque.h:443:5: note:   ‘std::move’
  443 |     move(_Deque_iterator<_Tp, _Tp&, _Tp*> __first,
      |     ^~~~
In file included from /usr/include/boost/move/algorithm.hpp:29,
                 from /usr/include/boost/move/move.hpp:32,
                 from /usr/include/boost/variant/detail/move.hpp:28,
                 from /usr/include/boost/variant/detail/initializer.hpp:23,
                 from /usr/include/boost/variant/variant.hpp:30,
                 from /usr/include/boost/variant.hpp:17,
                 from /usr/include/pbbam/Tag.h:10,
                 from /usr/include/pbbam/TagCollection.h:13,
                 from /usr/include/pbbam/BamRecordImpl.h:21,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /usr/include/pbbam/BamWriter.h:15,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:22:
/usr/include/boost/move/algo/move.hpp:53:6: note:   ‘boost::move’
   53 |    O move(I f, I l, O result)
      |      ^~~~
In file included from /usr/include/boost/function/function_template.hpp:32,
                 from /usr/include/boost/function/detail/maybe_include.hpp:15,
                 from /usr/include/boost/function/detail/function_iterate.hpp:14,
                 from /usr/include/boost/preprocessor/iteration/detail/iter/forward1.hpp:48,
                 from /usr/include/boost/function.hpp:71,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /usr/include/boost/algorithm/string.hpp:23,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:14:
/usr/include/boost/move/utility_core.hpp:212:93: note:   ‘boost::move’
  212 |          BOOST_MOVE_FORCEINLINE typename ::boost::move_detail::remove_reference<T>::type && move(T&& t) BOOST_NOEXCEPT
      |                                                                                             ^~~~
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:568:20: error: expected primary-expression before ‘{’ token
  568 |             Subread{ReadId(movieNames[movieName], *holeNumber,
      |                    ^
make[3]: *** [src/CMakeFiles/ccs.dir/build.make:66: src/CMakeFiles/ccs.dir/main/ccs.cpp.o] Error 1
...


I'd be really happy if someone could provide a patch.

Kind regards

      Andreas.


[1] https://salsa.debian.org/med-team/unanimity

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