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.