* Package: sci-biology/mosaik-2.2.30 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox >>> Unpacking source... * Unpacking mosaik-2.2.30.tar.gz >>> Source unpacked in /var/tmp/portage/sci-biology/mosaik-2.2.30/work >>> Preparing source in /var/tmp/portage/sci-biology/mosaik-2.2.30/work/mosaik-2.2.30/src ... * Applying mosaik-2.2.30-remove-platform-code.patch ... [ ok ] * Applying mosaik-2.2.30-fix-build-system.patch ... [ ok ] * Applying mosaik-2.2.30-Wformat-security.patch ... [ ok ] * Applying mosaik-2.2.30-gcc7.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/mosaik-2.2.30/work/mosaik-2.2.30/src ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/mosaik-2.2.30/work/mosaik-2.2.30/src ... make -j 1 CC=x86_64-pc-linux-gnu-gcc CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts' 'CXXFLAGS=-pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts' 'CPPFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' Building MOSAIK for the following platform: linux ========================================================= - Building in fann-2.1.0 * compiling floatfann.c x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -Iinclude/ -c -o .././obj/floatfann.o floatfann.c In file included from floatfann.c:25: fann.c: In function ‘fann_seed_rand’: fann.c:1543:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1543 | fread(&foo, sizeof(foo), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from floatfann.c:26: fann_io.c: In function ‘fann_create_from_fd’: fann_io.c:376:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 376 | fread(read_version, 1, strlen(FANN_CONF_VERSION "\n"), conf); /* reads version */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:463:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 463 | fscanf(conf, "cascade_activation_functions="); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:465:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 465 | fscanf(conf, "%u ", (unsigned int *)&ann->cascade_activation_functions[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:480:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 480 | fscanf(conf, "cascade_activation_steepnesses="); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:482:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 482 | fscanf(conf, FANNSCANF" ", &ann->cascade_activation_steepnesses[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:498:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 498 | fscanf(conf, "layer_sizes="); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:549:17: note: in expansion of macro ‘SCALE_LOAD’ 549 | SCALE_LOAD( scale_mean, in ) | ^~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:550:17: note: in expansion of macro ‘SCALE_LOAD’ 550 | SCALE_LOAD( scale_deviation, in ) | ^~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:551:17: note: in expansion of macro ‘SCALE_LOAD’ 551 | SCALE_LOAD( scale_new_min, in ) | ^~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:552:17: note: in expansion of macro ‘SCALE_LOAD’ 552 | SCALE_LOAD( scale_factor, in ) | ^~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:554:17: note: in expansion of macro ‘SCALE_LOAD’ 554 | SCALE_LOAD( scale_mean, out ) | ^~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:555:17: note: in expansion of macro ‘SCALE_LOAD’ 555 | SCALE_LOAD( scale_deviation, out ) | ^~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:556:17: note: in expansion of macro ‘SCALE_LOAD’ 556 | SCALE_LOAD( scale_new_min, out ) | ^~~~~~~~~~ fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fscanf( conf, #what "_" #where "=" ); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:557:17: note: in expansion of macro ‘SCALE_LOAD’ 557 | SCALE_LOAD( scale_factor, out ) | ^~~~~~~~~~ fann_io.c:571:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 571 | fscanf(conf, "neurons (num_inputs, activation_function, activation_steepness)="); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fann_io.c:598:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 598 | fscanf(conf, "connections (connected_to_neuron, weight)="); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Building in CommonSource - Building in DataStructures * compiling AbstractDnaHash.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/AbstractDnaHash.o AbstractDnaHash.cpp * compiling AlignedReadCache.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/AlignedReadCache.o AlignedReadCache.cpp * compiling DnaHash.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/DnaHash.o DnaHash.cpp DnaHash.cpp: In constructor ‘CDnaHash::CDnaHash(unsigned char, unsigned char)’: DnaHash.cpp:40:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 40 | } catch(bad_alloc) { | ^~~~~~~~~ DnaHash.cpp: In member function ‘virtual void CDnaHash::Dump()’: DnaHash.cpp:305:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 305 | for(unsigned int i = 0; i < mCapacity; i++) | ^~~ DnaHash.cpp:319:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 319 | cout << endl; | ^~~~ DnaHash.cpp: In member function ‘void CDnaHash::GetStatistics(unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, double&, double&)’: DnaHash.cpp:334:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 334 | for(unsigned int i = 0; i < mCapacity; i++) | ^~~ DnaHash.cpp:349:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 349 | mean = (double)numUsedHashesCount / (double)numUsedHashes; | ^~~~ DnaHash.cpp:354:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 354 | for(unsigned int i = 0; i < mCapacity; i++) | ^~~ DnaHash.cpp:360:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 360 | double variance = diffSumSquare / (numUsedHashes - 1.0); | ^~~~~~ * compiling HashRegionTree.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/HashRegionTree.o HashRegionTree.cpp * compiling JumpDnaHash.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/JumpDnaHash.o JumpDnaHash.cpp In file included from JumpDnaHash.h:23, from JumpDnaHash.cpp:13: MruCache.h:43:9: error: reference to ‘unordered_map’ is ambiguous 43 | unordered_map*> mMruMap; | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map:42, from UnorderedMap.h:48, from MruCache.h:19, from JumpDnaHash.h:23, from JumpDnaHash.cpp:13: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map.h:180:11: note: candidates are: ‘template class std::tr1::unordered_map’ 180 | class unordered_map | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/unordered_map:47, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/functional:61, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/pstl/glue_algorithm_defs.h:13, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/algorithm:74, from JumpDnaHash.h:18, from JumpDnaHash.cpp:13: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/unordered_map.h:102:11: note: ‘template class std::unordered_map’ 102 | class unordered_map | ^~~~~~~~~~~~~ In file included from JumpDnaHash.h:23, from JumpDnaHash.cpp:13: MruCache.h: In constructor ‘CMruCache::CMruCache(unsigned int)’: MruCache.h:59:3: error: class ‘CMruCache’ does not have any field named ‘mMruMap’ 59 | , mMruMap() | ^~~~~~~ MruCache.h: In member function ‘bool CMruCache::Get(const K&, V&)’: MruCache.h:77:18: error: expected nested-name-specifier before ‘unordered_map’ 77 | typename unordered_map*>::iterator hashIter = mMruMap.find(key); | ^~~~~~~~~~~~~ MruCache.h:77:18: error: expected ‘(’ before ‘unordered_map’ 77 | typename unordered_map*>::iterator hashIter = mMruMap.find(key); | ^~~~~~~~~~~~~ | ( MruCache.h:79:12: error: ‘hashIter’ was not declared in this scope 79 | if(hashIter != mMruMap.end()) { | ^~~~~~~~ MruCache.h:79:24: error: ‘mMruMap’ was not declared in this scope 79 | if(hashIter != mMruMap.end()) { | ^~~~~~~ MruCache.h: In member function ‘void CMruCache::Insert(const K&, const V&)’: MruCache.h:105:18: error: expected nested-name-specifier before ‘unordered_map’ 105 | typename unordered_map*>::iterator hashIter; | ^~~~~~~~~~~~~ MruCache.h:105:18: error: expected ‘(’ before ‘unordered_map’ 105 | typename unordered_map*>::iterator hashIter; | ^~~~~~~~~~~~~ | ( MruCache.h:112:17: error: ‘hashIter’ was not declared in this scope 112 | hashIter = mMruMap.find(tailKey); | ^~~~~~~~ MruCache.h:112:28: error: ‘mMruMap’ was not declared in this scope 112 | hashIter = mMruMap.find(tailKey); | ^~~~~~~ MruCache.h:124:9: error: ‘hashIter’ was not declared in this scope 124 | hashIter = mMruMap.find(key); | ^~~~~~~~ MruCache.h:124:20: error: ‘mMruMap’ was not declared in this scope 124 | hashIter = mMruMap.find(key); | ^~~~~~~ JumpDnaHash.cpp: In constructor ‘CJumpDnaHash::CJumpDnaHash(const unsigned char&, const string&, const short unsigned int&, const bool&, const bool&, const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const bool&, const bool&, const uint64_t&, const unsigned int&)’: JumpDnaHash.cpp:95:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 95 | } catch(bad_alloc) { | ^~~~~~~~~ JumpDnaHash.cpp: In member function ‘virtual void CJumpDnaHash::Get(const uint64_t&, const unsigned int&, AVLTree::CHashRegionTree&, double&)’: JumpDnaHash.cpp:237:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | fread((char*)&position, KEY_LENGTH, 1, mKeys); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:313:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:318:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 318 | fread(mBuffer, entrySize, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp: In member function ‘void CJumpDnaHash::LoadBlockPositions(char*, uint64_t&, const unsigned int&)’: JumpDnaHash.cpp:600:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(blockPosition, (size_t)bytesLeft, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:604:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 604 | fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp: In member function ‘void CJumpDnaHash::LoadKeys()’: JumpDnaHash.cpp:582:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 582 | fread(pKeys, fillBufferSize, 1, mKeys); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:587:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 587 | fread(pKeys, (size_t)bytesLeft, 1, mKeys); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [Makefile:25: ../.././obj/JumpDnaHash.o] Error 1 - Building in ExternalReadFormats * compiling Fasta.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/Fasta.o Fasta.cpp Fasta.cpp: In member function ‘bool CFasta::LoadNextMate(FastaTags&, Mosaik::Mate&)’: Fasta.cpp:18:114: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 18 | ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen) : fgets(mBaseBuffer, mBaseBufferLen, mInStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:130:9: note: in expansion of macro ‘READ_FILE_GETS’ 130 | READ_FILE_GETS; | ^~~~~~~~~~~~~~ Fasta.cpp:28:136: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:145:17: note: in expansion of macro ‘QUALITY_FILE_GETS’ 145 | QUALITY_FILE_GETS; | ^~~~~~~~~~~~~~~~~ Fasta.cpp:18:114: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 18 | ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen) : fgets(mBaseBuffer, mBaseBufferLen, mInStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:173:17: note: in expansion of macro ‘READ_FILE_GETS’ 173 | READ_FILE_GETS; | ^~~~~~~~~~~~~~ Fasta.cpp:28:136: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:190:25: note: in expansion of macro ‘QUALITY_FILE_GETS’ 190 | QUALITY_FILE_GETS; | ^~~~~~~~~~~~~~~~~ Fasta.cpp: In member function ‘void CFasta::Open(const string&)’: Fasta.cpp:232:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 232 | fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:249:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 249 | fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:18:114: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 18 | ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen) : fgets(mBaseBuffer, mBaseBufferLen, mInStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:290:31: note: in expansion of macro ‘READ_FILE_GETS’ 290 | if(ch == '#') READ_FILE_GETS; | ^~~~~~~~~~~~~~ Fasta.cpp:28:136: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:300:39: note: in expansion of macro ‘QUALITY_FILE_GETS’ 300 | if(ch == '#') QUALITY_FILE_GETS; | ^~~~~~~~~~~~~~~~~ * compiling Fastq.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/Fastq.o Fastq.cpp Fastq.cpp: In member function ‘bool CFastq::LoadNextMate(CMosaikString&, Mosaik::Mate&)’: Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fastq.cpp:424:9: note: in expansion of macro ‘READ_FILE_GETS’ 424 | READ_FILE_GETS; | ^~~~~~~~~~~~~~ Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fastq.cpp:446:17: note: in expansion of macro ‘READ_FILE_GETS’ 446 | READ_FILE_GETS; | ^~~~~~~~~~~~~~ Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fastq.cpp:459:9: note: in expansion of macro ‘READ_FILE_GETS’ 459 | READ_FILE_GETS; | ^~~~~~~~~~~~~~ Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fastq.cpp:470:17: note: in expansion of macro ‘READ_FILE_GETS’ 470 | READ_FILE_GETS; | ^~~~~~~~~~~~~~ Fastq.cpp: In member function ‘void CFastq::Open(const string&)’: Fastq.cpp:532:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 532 | fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling SRF.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/SRF.o SRF.cpp SRF.cpp: In static member function ‘static bool CSRF::CheckFile(const string&, bool)’: SRF.cpp:53:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 53 | fread(signature, CHECK_BYTES, 1, checkStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling BamWriter.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/BamWriter.o BamWriter.cpp - Building in MosaikReadFormat * compiling AlignmentReader.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I. -c -o ../.././obj/AlignmentReader.o AlignmentReader.cpp AlignmentReader.cpp: In static member function ‘static bool MosaikReadFormat::CAlignmentReader::CheckFile(const string&, SequencingTechnologies&, AlignmentStatus&, bool)’: AlignmentReader.cpp:134:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 134 | fread((char*)&st, SIZEOF_SHORT, 1, checkStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp: In member function ‘void MosaikReadFormat::CAlignmentReader::Jump(unsigned int, unsigned int)’: AlignmentReader.cpp:277:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 277 | fread((char*)&numIndexEntries, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp: In member function ‘void MosaikReadFormat::CAlignmentReader::Open(const string&)’: AlignmentReader.cpp:525:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread( signature, SIGNATURE_LENGTH, 1, mInStream ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:560:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 560 | fread((char*)&mSeqTech, SIZEOF_SHORT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:566:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 566 | fread((char*)&mNumRefSeqs, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:570:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 570 | fread((char*)&numReadGroups, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:573:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 573 | fread((char*)&mNumReads, SIZEOF_UINT64, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:585:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 585 | fread((char*)&mNumBases, SIZEOF_UINT64, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:589:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread((char*)&referencesOffset, SIZEOF_OFF_TYPE, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:592:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 592 | fread((char*)&mReferenceGapOffset, SIZEOF_OFF_TYPE, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:595:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 595 | fread((char*)&mIndexOffset, SIZEOF_OFF_TYPE, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:634:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 634 | fread((char*)&descriptionLen, SIZEOF_SHORT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:635:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 635 | fread((char*)&rgIter->SequencingTechnology, SIZEOF_SHORT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:636:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 636 | fread((char*)&rgIter->MedianFragmentLength, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:646:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 646 | fread((void*)rgIter->CenterName.data(), centerNameLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:647:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 647 | fread((void*)rgIter->Description.data(), descriptionLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:648:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 648 | fread((void*)rgIter->LibraryName.data(), libraryNameLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:649:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 649 | fread((void*)rgIter->PlatformUnit.data(), platformUnitLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:650:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 650 | fread((void*)rgIter->ReadGroupID.data(), readGroupIDLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:651:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 651 | fread((void*)rgIter->SampleName.data(), sampleNameLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:721:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 721 | fread((char*)&rsIter->NumBases, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:724:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 724 | fread((char*)&rsIter->NumAligned, SIZEOF_UINT64, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:729:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 729 | fread(pBuffer, 32, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:734:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 734 | fread(pBuffer, nameLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:747:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 747 | fread(pBuffer, speciesLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:754:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 754 | fread(pBuffer, genomeAssemblyIDLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:761:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 761 | fread(pBuffer, uriLen, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp: In member function ‘bool MosaikReadFormat::CAlignmentReader::ReadPartition()’: AlignmentReader.cpp:1031:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1031 | fread((char*)&uncompressedSize, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1037:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1037 | fread((char*)&compressedSize, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1041:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1041 | fread((char*)&mPartitionSize, SIZEOF_SHORT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp: In member function ‘void MosaikReadFormat::CAlignmentReader::ReadTag(Tag&)’: AlignmentReader.cpp:1086:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1086 | fread((char*)&tag.Double, SIZEOF_DOUBLE, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1089:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1089 | fread((char*)&tag.Float, SIZEOF_FLOAT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1092:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1092 | fread((char*)&tag.Int16, SIZEOF_SHORT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1095:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1095 | fread((char*)&tag.Int32, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1098:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1098 | fread((char*)&tag.Int64, SIZEOF_UINT64, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1101:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1101 | fread((char*)&stringLength, SIZEOF_SHORT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1102:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1102 | fread(tag.String, stringLength, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1108:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1108 | fread((char*)&tag.UInt16, SIZEOF_SHORT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1111:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1111 | fread((char*)&tag.UInt32, SIZEOF_INT, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1114:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1114 | fread((char*)&tag.UInt64, SIZEOF_UINT64, 1, mInStream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling AlignmentWriter.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I. -c -o ../.././obj/AlignmentWriter.o AlignmentWriter.cpp In file included from AlignmentWriter.cpp:11: AlignmentWriter.h:85:90: error: template argument 1 is invalid 85 | enceGaps(vector >* pRefGapVector); | ^ AlignmentWriter.h:85:90: error: template argument 2 is invalid AlignmentWriter.h:85:90: error: template argument 1 is invalid AlignmentWriter.h:85:90: error: template argument 2 is invalid AlignmentWriter.h:85:90: error: template argument 1 is invalid AlignmentWriter.h:85:90: error: template argument 2 is invalid AlignmentWriter.h:85:39: error: invalid template-id 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~ AlignmentWriter.h:85:46: error: reference to ‘unordered_map’ is ambiguous 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map:42, from ../../CommonSource/DataStructures/UnorderedMap.h:48, from AlignmentWriter.h:35, from AlignmentWriter.cpp:11: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map.h:180:11: note: candidates are: ‘template class std::tr1::unordered_map’ 180 | class unordered_map | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/unordered_map:47, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/functional:61, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/pstl/glue_algorithm_defs.h:13, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/algorithm:74, from AlignmentWriter.h:14, from AlignmentWriter.cpp:11: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/unordered_map.h:102:11: note: ‘template class std::unordered_map’ 102 | class unordered_map | ^~~~~~~~~~~~~ In file included from AlignmentWriter.cpp:11: AlignmentWriter.h:85:60: error: expected primary-expression before ‘unsigned’ 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~~~ AlignmentWriter.h:85:60: error: expected ‘>’ before ‘unsigned’ AlignmentWriter.h:85:39: error: class template placeholder ‘std::vector’ not permitted in this context 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~ AlignmentWriter.h:85:90: error: expected ‘,’ or ‘...’ before ‘>’ token 85 | enceGaps(vector >* pRefGapVector); | ^ AlignmentWriter.h:154:68: error: template argument 1 is invalid 154 | vector >* mpRefGapVector; | ^ AlignmentWriter.h:154:68: error: template argument 2 is invalid AlignmentWriter.cpp: In constructor ‘MosaikReadFormat::CAlignmentWriter::CAlignmentWriter()’: AlignmentWriter.cpp:48:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 48 | } catch(bad_alloc) { | ^~~~~~~~~ AlignmentWriter.cpp: In member function ‘void MosaikReadFormat::CAlignmentWriter::AdjustBuffer()’: AlignmentWriter.cpp:101:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 101 | } catch(bad_alloc) { | ^~~~~~~~~ AlignmentWriter.cpp: In member function ‘void MosaikReadFormat::CAlignmentWriter::Close()’: AlignmentWriter.cpp:212:132: error: request for member ‘at’ in ‘*((MosaikReadFormat::CAlignmentWriter*)this)->MosaikReadFormat::CAlignmentWriter::mpRefGapVector’, which is of non-class type ‘int’ 212 | equestedBytes += SIZEOF_INT + (unsigned int)mpRefGapVector->at(i).size() * (SIZEOF_INT + SIZEOF_SHORT); | ^~ AlignmentWriter.cpp:218:25: error: reference to ‘unordered_map’ is ambiguous 218 | unordered_map::const_iterator refHashMapIter; | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map:42, from ../../CommonSource/DataStructures/UnorderedMap.h:48, from AlignmentWriter.h:35, from AlignmentWriter.cpp:11: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map.h:180:11: note: candidates are: ‘template class std::tr1::unordered_map’ 180 | class unordered_map | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/unordered_map:47, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/functional:61, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/pstl/glue_algorithm_defs.h:13, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/algorithm:74, from AlignmentWriter.h:14, from AlignmentWriter.cpp:11: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/unordered_map.h:102:11: note: ‘template class std::unordered_map’ 102 | class unordered_map | ^~~~~~~~~~~~~ AlignmentWriter.cpp:218:39: error: expected primary-expression before ‘unsigned’ 218 | unordered_map::const_iterator refHashMapIter; | ^~~~~~~~ AlignmentWriter.cpp:222:76: error: template argument 1 is invalid 222 | vector >::const_iterator rgIter; | ^ AlignmentWriter.cpp:222:76: error: template argument 2 is invalid AlignmentWriter.cpp:222:94: error: qualified-id in declaration before ‘rgIter’ 222 | r >::const_iterator rgIter; | ^~~~~~ AlignmentWriter.cpp:223:29: error: ‘rgIter’ was not declared in this scope; did you mean ‘rsIter’? 223 | for(rgIter = mpRefGapVector->begin(); rgIter != mpRefGapVector->end(); rgIter++) { | ^~~~~~ | rsIter AlignmentWriter.cpp:223:54: error: request for member ‘begin’ in ‘*((MosaikReadFormat::CAlignmentWriter*)this)->MosaikReadFormat::CAlignmentWriter::mpRefGapVector’, which is of non-class type ‘int’ 223 | for(rgIter = mpRefGapVector->begin(); rgIter != mpRefGapVector->end(); rgIter++) { | ^~~~~ AlignmentWriter.cpp:223:89: error: request for member ‘end’ in ‘*((MosaikReadFormat::CAlignmentWriter*)this)->MosaikReadFormat::CAlignmentWriter::mpRefGapVector’, which is of non-class type ‘int’ 223 | rgIter = mpRefGapVector->begin(); rgIter != mpRefGapVector->end(); rgIter++) { | ^~~ AlignmentWriter.cpp:237:45: error: ‘refHashMapIter’ was not declared in this scope 237 | for(refHashMapIter = rgIter->begin(); refHashMapIter != rgIter->end(); refHashMapIter++, refGapsIter++) { | ^~~~~~~~~~~~~~ AlignmentWriter.cpp: At global scope: AlignmentWriter.cpp:998:100: error: template argument 1 is invalid 998 | enceGaps(vector >* pRefGapVector) { | ^ AlignmentWriter.cpp:998:100: error: template argument 2 is invalid AlignmentWriter.cpp:998:100: error: template argument 1 is invalid AlignmentWriter.cpp:998:100: error: template argument 2 is invalid AlignmentWriter.cpp:998:100: error: template argument 1 is invalid AlignmentWriter.cpp:998:100: error: template argument 2 is invalid AlignmentWriter.cpp:998:49: error: invalid template-id 998 | void CAlignmentWriter::SetReferenceGaps(vector >* pRefGapVector) { | ^~~~~~ AlignmentWriter.cpp:998:14: error: variable or field ‘SetReferenceGaps’ declared void 998 | void CAlignmentWriter::SetReferenceGaps(vector >* pRefGapVector) { | ^~~~~~~~~~~~~~~~ AlignmentWriter.cpp:998:101: error: missing template arguments before ‘*’ token 998 | nceGaps(vector >* pRefGapVector) { | ^ AlignmentWriter.cpp:998:103: error: ‘pRefGapVector’ was not declared in this scope 998 | eGaps(vector >* pRefGapVector) { | ^~~~~~~~~~~~~ make[2]: *** [Makefile:25: ../.././obj/AlignmentWriter.o] Error 1 - Building in PairwiseAlignment * compiling SmithWatermanGotoh.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I. -c -o ../.././obj/SmithWatermanGotoh.o SmithWatermanGotoh.cpp SmithWatermanGotoh.cpp: In member function ‘void CSmithWatermanGotoh::Align(Alignment&, const char*, const unsigned int&, const char*, const unsigned int&)’: SmithWatermanGotoh.cpp:84:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 84 | } catch(bad_alloc) { | ^~~~~~~~~ SmithWatermanGotoh.cpp:118:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 118 | } catch(bad_alloc) { | ^~~~~~~~~ SmithWatermanGotoh.cpp:140:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 140 | } catch(bad_alloc) { | ^~~~~~~~~ * compiling BandedSmithWaterman.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I. -c -o ../.././obj/BandedSmithWaterman.o BandedSmithWaterman.cpp BandedSmithWaterman.cpp: In constructor ‘CBandedSmithWaterman::CBandedSmithWaterman(float, float, float, float, unsigned int, bool)’: BandedSmithWaterman.cpp:56:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 56 | } catch(bad_alloc) { | ^~~~~~~~~ BandedSmithWaterman.cpp: In member function ‘void CBandedSmithWaterman::ReinitializeMatrices(const PositionType&, const unsigned int&, const unsigned int&, const HashRegion&)’: BandedSmithWaterman.cpp:475:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 475 | } catch(bad_alloc) { | ^~~~~~~~~ BandedSmithWaterman.cpp:501:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 501 | } catch(bad_alloc) { | ^~~~~~~~~ * compiling ssw_cpp.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I. -c -o ../.././obj/ssw_cpp.o ssw_cpp.cpp * compiling ConvertSswToAlignment.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I. -c -o ../.././obj/ConvertSswToAlignment.o ConvertSswToAlignment.cpp * compiling ssw.c x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I. -c -o ../.././obj/ssw.o ssw.c - Building in Utilities * compiling ArchiveMerge.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/Config -I../../CommonSource/DataStructures -I../../CommonSource/MosaikReadFormat -I../../CommonSource/ExternalReadFormats -I../..//fann-2.1.0/include/ -I. -c -o ../.././obj/ArchiveMerge.o ArchiveMerge.cpp In file included from ArchiveMerge.h:28, from ArchiveMerge.cpp:19: ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: template argument 1 is invalid 85 | enceGaps(vector >* pRefGapVector); | ^ ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: template argument 2 is invalid ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: template argument 1 is invalid ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: template argument 2 is invalid ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: template argument 1 is invalid ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: template argument 2 is invalid ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:39: error: invalid template-id 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~ ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:46: error: reference to ‘unordered_map’ is ambiguous 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map:42, from ../../CommonSource/DataStructures/UnorderedMap.h:48, from ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:35, from ArchiveMerge.h:28, from ArchiveMerge.cpp:19: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map.h:180:11: note: candidates are: ‘template class std::tr1::unordered_map’ 180 | class unordered_map | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/unordered_map:47, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/functional:61, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/pstl/glue_algorithm_defs.h:13, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/algorithm:74, from ArchiveMerge.h:22, from ArchiveMerge.cpp:19: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/unordered_map.h:102:11: note: ‘template class std::unordered_map’ 102 | class unordered_map | ^~~~~~~~~~~~~ In file included from ArchiveMerge.h:28, from ArchiveMerge.cpp:19: ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:60: error: expected primary-expression before ‘unsigned’ 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~~~ ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:60: error: expected ‘>’ before ‘unsigned’ ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:39: error: class template placeholder ‘std::vector’ not permitted in this context 85 | void SetReferenceGaps(vector >* pRefGapVector); | ^~~~~~ ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: expected ‘,’ or ‘...’ before ‘>’ token 85 | enceGaps(vector >* pRefGapVector); | ^ ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:154:68: error: template argument 1 is invalid 154 | vector >* mpRefGapVector; | ^ ../../CommonSource/MosaikReadFormat/AlignmentWriter.h:154:68: error: template argument 2 is invalid make[2]: *** [Makefile:51: ../.././obj/ArchiveMerge.o] Error 1 - Building in MosaikBuild * compiling BuildMain.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../CommonSource/Config -I../CommonSource/DataStructures -I../CommonSource/ExternalReadFormats -I../CommonSource/MosaikReadFormat -I../CommonSource/Utilities -c -o .././obj/BuildMain.o BuildMain.cpp * compiling MosaikBuild.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../CommonSource/Config -I../CommonSource/DataStructures -I../CommonSource/ExternalReadFormats -I../CommonSource/MosaikReadFormat -I../CommonSource/Utilities -c -o .././obj/MosaikBuild.o MosaikBuild.cpp MosaikBuild.cpp: In constructor ‘CMosaikBuild::CMosaikBuild(const MosaikReadFormat::ReadGroup&)’: MosaikBuild.cpp:38:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 38 | } catch(bad_alloc) { | ^~~~~~~~~ MosaikBuild.cpp: In member function ‘void CMosaikBuild::CreateReferenceArchive(const string&, const string&)’: MosaikBuild.cpp:470:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 470 | } catch(bad_alloc) { | ^~~~~~~~~ MosaikBuild.cpp:527:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 527 | } catch(bad_alloc) { | ^~~~~~~~~ MosaikBuild.cpp:669:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 669 | } catch(bad_alloc) { | ^~~~~~~~~ In file included from MosaikBuild.h:33, from MosaikBuild.cpp:11: ../CommonSource/Utilities/ProgressBar.h: In instantiation of ‘CProgressBar::CProgressBar(K*, K, K, std::string) [with K = unsigned int; std::string = std::__cxx11::basic_string]’: ../CommonSource/Utilities/ProgressBar.h:277:19: required from ‘static void* CProgressBar::Monitor(void*) [with K = unsigned int]’ ../CommonSource/Utilities/ProgressBar.h:209:57: required from ‘static void CProgressBar::StartThread(K*, K, K, std::string) [with K = unsigned int; std::string = std::__cxx11::basic_string]’ MosaikBuild.cpp:297:31: required from here ../CommonSource/Utilities/ProgressBar.h:186:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 186 | } catch(bad_alloc) { | ^~~~~~~~~ MosaikBuild.cpp: In member function ‘void CMosaikBuild::ParseBustard(const string&, const string&, const string&, bool)’: MosaikBuild.cpp:876:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 876 | fscanf(seq, "%u\t%u\t%u\t%u\t%s", &lane, &tile, &xcoord, &ycoord, fBuffer); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MosaikBuild.cpp:897:39: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 897 | fscanf(prb, "%d %d %d %d", &aBQ, &cBQ, &gBQ, &tBQ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling JumpDnaHash.cpp x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -Og -g -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/JumpDnaHash.o JumpDnaHash.cpp In file included from JumpDnaHash.h:23, from JumpDnaHash.cpp:13: MruCache.h:43:9: error: reference to ‘unordered_map’ is ambiguous 43 | unordered_map*> mMruMap; | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map:42, from UnorderedMap.h:48, from MruCache.h:19, from JumpDnaHash.h:23, from JumpDnaHash.cpp:13: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/tr1/unordered_map.h:180:11: note: candidates are: ‘template class std::tr1::unordered_map’ 180 | class unordered_map | ^~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/unordered_map:47, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/functional:61, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/pstl/glue_algorithm_defs.h:13, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/algorithm:74, from JumpDnaHash.h:18, from JumpDnaHash.cpp:13: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/unordered_map.h:102:11: note: ‘template class std::unordered_map’ 102 | class unordered_map | ^~~~~~~~~~~~~ In file included from JumpDnaHash.h:23, from JumpDnaHash.cpp:13: MruCache.h: In constructor ‘CMruCache::CMruCache(unsigned int)’: MruCache.h:59:3: error: class ‘CMruCache’ does not have any field named ‘mMruMap’ 59 | , mMruMap() | ^~~~~~~ MruCache.h: In member function ‘bool CMruCache::Get(const K&, V&)’: MruCache.h:77:18: error: expected nested-name-specifier before ‘unordered_map’ 77 | typename unordered_map*>::iterator hashIter = mMruMap.find(key); | ^~~~~~~~~~~~~ MruCache.h:77:18: error: expected ‘(’ before ‘unordered_map’ 77 | typename unordered_map*>::iterator hashIter = mMruMap.find(key); | ^~~~~~~~~~~~~ | ( MruCache.h:79:12: error: ‘hashIter’ was not declared in this scope 79 | if(hashIter != mMruMap.end()) { | ^~~~~~~~ MruCache.h:79:24: error: ‘mMruMap’ was not declared in this scope 79 | if(hashIter != mMruMap.end()) { | ^~~~~~~ MruCache.h: In member function ‘void CMruCache::Insert(const K&, const V&)’: MruCache.h:105:18: error: expected nested-name-specifier before ‘unordered_map’ 105 | typename unordered_map*>::iterator hashIter; | ^~~~~~~~~~~~~ MruCache.h:105:18: error: expected ‘(’ before ‘unordered_map’ 105 | typename unordered_map*>::iterator hashIter; | ^~~~~~~~~~~~~ | ( MruCache.h:112:17: error: ‘hashIter’ was not declared in this scope 112 | hashIter = mMruMap.find(tailKey); | ^~~~~~~~ MruCache.h:112:28: error: ‘mMruMap’ was not declared in this scope 112 | hashIter = mMruMap.find(tailKey); | ^~~~~~~ MruCache.h:124:9: error: ‘hashIter’ was not declared in this scope 124 | hashIter = mMruMap.find(key); | ^~~~~~~~ MruCache.h:124:20: error: ‘mMruMap’ was not declared in this scope 124 | hashIter = mMruMap.find(key); | ^~~~~~~ JumpDnaHash.cpp: In constructor ‘CJumpDnaHash::CJumpDnaHash(const unsigned char&, const string&, const short unsigned int&, const bool&, const bool&, const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const bool&, const bool&, const uint64_t&, const unsigned int&)’: JumpDnaHash.cpp:95:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 95 | } catch(bad_alloc) { | ^~~~~~~~~ JumpDnaHash.cpp: In member function ‘virtual void CJumpDnaHash::Get(const uint64_t&, const unsigned int&, AVLTree::CHashRegionTree&, double&)’: JumpDnaHash.cpp:237:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 237 | fread((char*)&position, KEY_LENGTH, 1, mKeys); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:313:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:318:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 318 | fread(mBuffer, entrySize, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp: In member function ‘void CJumpDnaHash::LoadBlockPositions(char*, uint64_t&, const unsigned int&)’: JumpDnaHash.cpp:600:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(blockPosition, (size_t)bytesLeft, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:604:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 604 | fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp: In member function ‘void CJumpDnaHash::LoadKeys()’: JumpDnaHash.cpp:582:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 582 | fread(pKeys, fillBufferSize, 1, mKeys); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:587:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 587 | fread(pKeys, (size_t)bytesLeft, 1, mKeys); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [Makefile:25: ../.././obj/JumpDnaHash.o] Error 1 make[1]: *** [Makefile:36: .././obj/Benchmark.o] Error 2 make: *** [Makefile:32: all] Error 1 * ERROR: sci-biology/mosaik-2.2.30::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/mosaik-2.2.30::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/mosaik-2.2.30::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:mosaik-2.2.30:20210505-111143.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mosaik-2.2.30/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mosaik-2.2.30/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/mosaik-2.2.30/work/mosaik-2.2.30/src' * S: '/var/tmp/portage/sci-biology/mosaik-2.2.30/work/mosaik-2.2.30/src'