Bug#835720: marked as done (salmon: FTBFS: BAMQueue.tpp:88:29: error: no matching function for call to 'spdlog::logger::warn()')

Debian Bug Tracking System Sat, 10 Sep 2016 06:36:36 -0700

Your message dated Sat, 10 Sep 2016 13:34:06 +0000
with message-id <e1biiq2-00020q...@franck.debian.org>
and subject line Bug#835720: fixed in salmon 0.7.2+ds1-1
has caused the Debian Bug report #835720,
regarding salmon: FTBFS: BAMQueue.tpp:88:29: error: no matching function for 
call to 'spdlog::logger::warn()'
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
835720: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=835720
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: salmon
Version: 0.4.2+ds1-3
Severity: serious
Tags: stretch sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20160828 qa-ftbfs
Justification: FTBFS on amd64

Hi,

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

Relevant part (hopefully):
> cd /<<BUILDDIR>>/salmon-0.4.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++    
> -I/<<BUILDDIR>>/salmon-0.4.2+ds1/include -I/usr/include/eigen3 
> -I/usr/include/bwa  -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast 
> -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -std=c++11 -Wreturn-type 
> -Werror=return-type -static-libstdc++ -Wno-deprecated-register 
> -Wno-unused-local-typedefs   -o CMakeFiles/salmon.dir/SalmonUtils.cpp.o -c 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:27:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadLibrary.hpp: In copy constructor 
> 'ReadLibrary::ReadLibrary(const ReadLibrary&)':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadLibrary.hpp:35:34: warning: 
> comparison between signed and unsigned integer expressions [-Wsign-compare]
>              for (size_t i = 0; i < mc; ++i) { 
> libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); }
>                                 ~~^~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadLibrary.hpp: In constructor 
> 'ReadLibrary::ReadLibrary(ReadLibrary&&)':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadLibrary.hpp:48:34: warning: 
> comparison between signed and unsigned integer expressions [-Wsign-compare]
>              for (size_t i = 0; i < mc; ++i) { 
> libTypeCounts_[i].store(rl.libTypeCounts_[i].load()); }
>                                 ~~^~~~
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ClusterForest.hpp:7:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:12,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/Transcript.hpp: In constructor 
> 'Transcript::Transcript(size_t, const char*, uint32_t, double)':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/Transcript.hpp:232:12: warning: 
> 'Transcript::logPerBasePrior_' will be initialized after [-Wreorder]
>      double logPerBasePrior_;
>             ^~~~~~~~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/Transcript.hpp:225:12: warning:   
> 'double Transcript::priorMass_' [-Wreorder]
>      double priorMass_;
>             ^~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/Transcript.hpp:16:5: warning:   when 
> initialized here [-Wreorder]
>      Transcript(size_t idIn, const char* name, uint32_t len, double alpha = 
> 0.05) :
>      ^~~~~~~~~~
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp: In member function 'void 
> BAMQueue<FragT>::reset()':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:88:29: error: no matching 
> function for call to 'spdlog::logger::warn()'
>                logger_->warn() << errstr.str();
>                              ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:43:38: note: candidate: template<class ... Args> 
> void spdlog::logger::warn(const char*, const Args& ...)
>      template <typename... Args> void warn(const char* fmt, const Args&... 
> args);
>                                       ^~~~
> /usr/include/spdlog/logger.h:43:38: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:88:29: note:   candidate 
> expects at least 1 argument, 0 provided
>                logger_->warn() << errstr.str();
>                              ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:51:32: note: candidate: template<class T> void 
> spdlog::logger::warn(const T&)
>      template <typename T> void warn(const T&);
>                                 ^~~~
> /usr/include/spdlog/logger.h:51:32: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:88:29: note:   candidate 
> expects 1 argument, 0 provided
>                logger_->warn() << errstr.str();
>                              ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:102:19: error: no 
> matching function for call to 'spdlog::logger::warn()'
>      logger_->warn() << errstr.str();
>                    ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:43:38: note: candidate: template<class ... Args> 
> void spdlog::logger::warn(const char*, const Args& ...)
>      template <typename... Args> void warn(const char* fmt, const Args&... 
> args);
>                                       ^~~~
> /usr/include/spdlog/logger.h:43:38: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:102:19: note:   candidate 
> expects at least 1 argument, 0 provided
>      logger_->warn() << errstr.str();
>                    ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:51:32: note: candidate: template<class T> void 
> spdlog::logger::warn(const T&)
>      template <typename T> void warn(const T&);
>                                 ^~~~
> /usr/include/spdlog/logger.h:51:32: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:102:19: note:   candidate 
> expects 1 argument, 0 provided
>      logger_->warn() << errstr.str();
>                    ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp: In destructor 
> 'BAMQueue<FragT>::~BAMQueue()':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:134:27: error: no 
> matching function for call to 'spdlog::logger::warn()'
>              logger_->warn() << errstr.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:43:38: note: candidate: template<class ... Args> 
> void spdlog::logger::warn(const char*, const Args& ...)
>      template <typename... Args> void warn(const char* fmt, const Args&... 
> args);
>                                       ^~~~
> /usr/include/spdlog/logger.h:43:38: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:134:27: note:   candidate 
> expects at least 1 argument, 0 provided
>              logger_->warn() << errstr.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:51:32: note: candidate: template<class T> void 
> spdlog::logger::warn(const T&)
>      template <typename T> void warn(const T&);
>                                 ^~~~
> /usr/include/spdlog/logger.h:51:32: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:134:27: note:   candidate 
> expects 1 argument, 0 provided
>              logger_->warn() << errstr.str();
>                            ^
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp: In member function 'bool 
> BAMQueue<FragT>::getFrag_(ReadPair&, FilterT)':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:439:27: error: no 
> matching function for call to 'spdlog::logger::warn()'
>              logger_->warn() << errmsg.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:43:38: note: candidate: template<class ... Args> 
> void spdlog::logger::warn(const char*, const Args& ...)
>      template <typename... Args> void warn(const char* fmt, const Args&... 
> args);
>                                       ^~~~
> /usr/include/spdlog/logger.h:43:38: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:439:27: note:   candidate 
> expects at least 1 argument, 0 provided
>              logger_->warn() << errmsg.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:51:32: note: candidate: template<class T> void 
> spdlog::logger::warn(const T&)
>      template <typename T> void warn(const T&);
>                                 ^~~~
> /usr/include/spdlog/logger.h:51:32: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:439:27: note:   candidate 
> expects 1 argument, 0 provided
>              logger_->warn() << errmsg.str();
>                            ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:481:27: error: no 
> matching function for call to 'spdlog::logger::warn()'
>              logger_->warn() << errmsg.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:43:38: note: candidate: template<class ... Args> 
> void spdlog::logger::warn(const char*, const Args& ...)
>      template <typename... Args> void warn(const char* fmt, const Args&... 
> args);
>                                       ^~~~
> /usr/include/spdlog/logger.h:43:38: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:481:27: note:   candidate 
> expects at least 1 argument, 0 provided
>              logger_->warn() << errmsg.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:51:32: note: candidate: template<class T> void 
> spdlog::logger::warn(const T&)
>      template <typename T> void warn(const T&);
>                                 ^~~~
> /usr/include/spdlog/logger.h:51:32: note:   template argument 
> deduction/substitution failed:
> In file included from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.hpp:146:0,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/AlignmentLibrary.hpp:14,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:13:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/BAMQueue.tpp:481:27: note:   candidate 
> expects 1 argument, 0 provided
>              logger_->warn() << errmsg.str();
>                            ^
> In file included from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:18:0:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp: In constructor 
> 'ReadExperiment::ReadExperiment(std::vector<ReadLibrary>&, const 
> boost::filesystem::path&, SalmonOpts&)':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:448:39: warning: 
> 'ReadExperiment::totalAssignedFragments_' will be initialized after 
> [-Wreorder]
>      uint64_t totalAssignedFragments_{0};
>                                        ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:439:52: warning:   
> 'std::vector<FragmentStartPositionDistribution> 
> ReadExperiment::fragStartDists_' [-Wreorder]
>      std::vector<FragmentStartPositionDistribution> fragStartDists_;
>                                                     ^~~~~~~~~~~~~~~
> In file included from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:18:0:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:44:5: warning:   
> when initialized here [-Wreorder]
>      ReadExperiment(std::vector<ReadLibrary>& readLibraries,
>      ^~~~~~~~~~~~~~
> In file included from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:18:0:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:129:42: warning: 
> comparison between signed and unsigned integer expressions [-Wsign-compare]
>                      for (size_t i = 0; i < compLen; ++i) { seq[i] = 
> nucTab[rseq[i]]; }
>                                         ~~^~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp: In member function 
> 'void ReadExperiment::summarizeLibraryTypeCounts(boost::filesystem::path&)':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:345:31: error: no 
> matching function for call to 'spdlog::logger::warn()'
>                      log->warn() << errstr.str();
>                                ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:43:38: note: candidate: template<class ... Args> 
> void spdlog::logger::warn(const char*, const Args& ...)
>      template <typename... Args> void warn(const char* fmt, const Args&... 
> args);
>                                       ^~~~
> /usr/include/spdlog/logger.h:43:38: note:   template argument 
> deduction/substitution failed:
> In file included from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:18:0:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:345:31: note:   
> candidate expects at least 1 argument, 0 provided
>                      log->warn() << errstr.str();
>                                ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:51:32: note: candidate: template<class T> void 
> spdlog::logger::warn(const T&)
>      template <typename T> void warn(const T&);
>                                 ^~~~
> /usr/include/spdlog/logger.h:51:32: note:   template argument 
> deduction/substitution failed:
> In file included from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:18:0:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:345:31: note:   
> candidate expects 1 argument, 0 provided
>                      log->warn() << errstr.str();
>                                ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:392:27: error: no 
> matching function for call to 'spdlog::logger::warn()'
>                  log->warn() << errstr.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:43:38: note: candidate: template<class ... Args> 
> void spdlog::logger::warn(const char*, const Args& ...)
>      template <typename... Args> void warn(const char* fmt, const Args&... 
> args);
>                                       ^~~~
> /usr/include/spdlog/logger.h:43:38: note:   template argument 
> deduction/substitution failed:
> In file included from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:18:0:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:392:27: note:   
> candidate expects at least 1 argument, 0 provided
>                  log->warn() << errstr.str();
>                            ^
> In file included from /usr/include/spdlog/spdlog.h:13:0,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonOpts.hpp:7,
>                  from 
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/SalmonUtils.hpp:23,
>                  from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:12:
> /usr/include/spdlog/logger.h:51:32: note: candidate: template<class T> void 
> spdlog::logger::warn(const T&)
>      template <typename T> void warn(const T&);
>                                 ^~~~
> /usr/include/spdlog/logger.h:51:32: note:   template argument 
> deduction/substitution failed:
> In file included from /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:18:0:
> /<<BUILDDIR>>/salmon-0.4.2+ds1/include/ReadExperiment.hpp:392:27: note:   
> candidate expects 1 argument, 0 provided
>                  log->warn() << errstr.str();
>                            ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp: In function 
> 'TranscriptGeneMap salmon::utils::transcriptGeneMapFromGTF(const string&, 
> std::__cxx11::string)':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:786:12: warning: unused 
> variable 'transcriptCounter' [-Wunused-variable]
>      size_t transcriptCounter = 0;
>             ^~~~~~~~~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp: In instantiation of 'void 
> salmon::utils::normalizeAlphas(const SalmonOpts&, AlnLibT&) [with AlnLibT = 
> ReadExperiment]':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:1159:54:   required from 
> here
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:355:10: warning: unused 
> variable 'v' [-Wunused-variable]
>    double v = transcript.projectedCounts / numMappedReads;
>           ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:297:22: warning: unused 
> variable 'logNumFragments' [-Wunused-variable]
>          const double logNumFragments = 
> std::log(static_cast<double>(numMappedReads));
>                       ^~~~~~~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:353:9: warning: unused 
> variable 'invNFracTotal' [-Wunused-variable]
>   double invNFracTotal = 1.0 / nFracDenom;
>          ^~~~~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp: In instantiation of 'void 
> salmon::utils::normalizeAlphas(const SalmonOpts&, AlnLibT&) [with AlnLibT = 
> AlignmentLibrary<UnpairedRead>]':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:1163:70:   required from 
> here
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:355:10: warning: unused 
> variable 'v' [-Wunused-variable]
>    double v = transcript.projectedCounts / numMappedReads;
>           ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:297:22: warning: unused 
> variable 'logNumFragments' [-Wunused-variable]
>          const double logNumFragments = 
> std::log(static_cast<double>(numMappedReads));
>                       ^~~~~~~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:353:9: warning: unused 
> variable 'invNFracTotal' [-Wunused-variable]
>   double invNFracTotal = 1.0 / nFracDenom;
>          ^~~~~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp: In instantiation of 'void 
> salmon::utils::normalizeAlphas(const SalmonOpts&, AlnLibT&) [with AlnLibT = 
> AlignmentLibrary<ReadPair>]':
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:1166:66:   required from 
> here
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:355:10: warning: unused 
> variable 'v' [-Wunused-variable]
>    double v = transcript.projectedCounts / numMappedReads;
>           ^
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:297:22: warning: unused 
> variable 'logNumFragments' [-Wunused-variable]
>          const double logNumFragments = 
> std::log(static_cast<double>(numMappedReads));
>                       ^~~~~~~~~~~~~~~
> /<<BUILDDIR>>/salmon-0.4.2+ds1/src/SalmonUtils.cpp:353:9: warning: unused 
> variable 'invNFracTotal' [-Wunused-variable]
>   double invNFracTotal = 1.0 / nFracDenom;
>          ^~~~~~~~~~~~~
> At global scope:
> cc1plus: warning: unrecognized command line option '-Wno-deprecated-register'
> src/CMakeFiles/salmon.dir/build.make:137: recipe for target 
> 'src/CMakeFiles/salmon.dir/SalmonUtils.cpp.o' failed
> make[4]: *** [src/CMakeFiles/salmon.dir/SalmonUtils.cpp.o] Error 1

The full build log is available from:
   
http://people.debian.org/~lucas/logs/2016/08/28/salmon_0.4.2+ds1-3_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.

--- End Message ---

--- Begin Message ---

Source: salmon
Source-Version: 0.7.2+ds1-1

We believe that the bug you reported is fixed in the latest version of
salmon, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 835...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated salmon package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Tue, 30 Aug 2016 09:10:48 +0200
Source: salmon
Binary: salmon
Architecture: source amd64
Version: 0.7.2+ds1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
 salmon     - wicked-fast transcript quantification from RNA-seq data
Closes: 835720
Changes:
 salmon (0.7.2+ds1-1) unstable; urgency=medium
 .
   * Team upload
   * New upstream version
   * Make sure build uses Debian's packaged version of dependencies
     (exception: RapMap, see below).
   * d/watch: use xz compression
   * Include necessary parts of RapMap code until upstream sorts out
     code embedding.
   * Adapt spdlog API use to match version of spdlog packaged in Debian.
     Closes: #835720
   * Bump Standards-Version.
   * Drop obsolete override.
   * Enable bindnow flags.
Checksums-Sha1:
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salmon-dbgsym_0.7.2+ds1-1_amd64.deb
 0c9228c8783ad1cd20154569bfd3e87c75760463 1598568 salmon_0.7.2+ds1-1_amd64.deb
Checksums-Sha256:
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salmon_0.7.2+ds1-1.debian.tar.xz
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salmon-dbgsym_0.7.2+ds1-1_amd64.deb
 16145486b649a333bb31b185577dcf9b197f357ada5fca89f81d9f4291a48f9d 1598568 
salmon_0.7.2+ds1-1_amd64.deb
Files:
 e9efb9a13a6875d89173f55b53b739ca 2430 science optional salmon_0.7.2+ds1-1.dsc
 8ccc2502c9209e6e1f06314369f4c68e 946652 science optional 
salmon_0.7.2+ds1.orig.tar.xz
 9a108b7814d689926728b3399f8056c0 75804 science optional 
salmon_0.7.2+ds1-1.debian.tar.xz
 122c2a9700fd6cd6f9d24d63e3b8330c 240584 debug extra 
salmon-dbgsym_0.7.2+ds1-1_amd64.deb
 6784973033233dfce5ce66941b2a7094 1598568 science optional 
salmon_0.7.2+ds1-1_amd64.deb

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--- End Message ---

Bug#835720: marked as done (salmon: FTBFS: BAMQueue.tpp:88:29: error: no matching function for call to 'spdlog::logger::warn()')

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