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 > -- http://fam-tille.de