Hi,
I tried to upgrade salmon to latest upstream where this problem might
have possibly solved. I'm currently struck by the fact that
https://github.com/COMBINE-lab/RapMap
is needed to build.
I'll stop here and move on to upgrade jellyfish since salmon cmake files
are checking a versioned dependency to the latest jellyfish version. May
be somebody else can take over at this state.
Please have a look at the adapted quilt patches as well. I hope I did
not messed up anything.
Kind regards
Andreas.
On Sun, Aug 28, 2016 at 11:17:35AM +0200, Lucas Nussbaum wrote:
> 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.
>
> _______________________________________________
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
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