Go to:
Gentoo Home
Documentation
Forums
Lists
Bugs
Planet
Store
Wiki
Get Gentoo!
Gentoo's Bugzilla – Attachment 706179 Details for
Bug 788331
sci-biology/mosaik-2.2.30 - MruCache.h: error: reference to unordered_map is ambiguous
Home
|
New
–
[Ex]
|
Browse
|
Search
|
Privacy Policy
|
[?]
|
Reports
|
Requests
|
Help
|
New Account
|
Log In
[x]
|
Forgot Password
Login:
[x]
sci-biology:mosaik-2.2.30:20210505-111143.log
sci-biology:mosaik-2.2.30:20210505-111143.log (text/plain), 71.21 KB, created by
Toralf Förster
on 2021-05-05 12:45:19 UTC
(
hide
)
Description:
sci-biology:mosaik-2.2.30:20210505-111143.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2021-05-05 12:45:19 UTC
Size:
71.21 KB
patch
obsolete
> * 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 âfann_seed_randâ: >fann.c:1543:17: warning: ignoring return value of âfreadâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1543 | fread(&foo, sizeof(foo), 1, fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >In file included from floatfann.c:26: >fann_io.c: In function âfann_create_from_fdâ: >fann_io.c:376:9: warning: ignoring return value of âfreadâ declared with attribute âwarn_unused_resultâ [-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 âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 463 | fscanf(conf, "cascade_activation_functions="); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:465:17: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 465 | fscanf(conf, "%u ", (unsigned int *)&ann->cascade_activation_functions[i]); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:480:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 480 | fscanf(conf, "cascade_activation_steepnesses="); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:482:17: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 482 | fscanf(conf, FANNSCANF" ", &ann->cascade_activation_steepnesses[i]); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:498:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 498 | fscanf(conf, "layer_sizes="); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:549:17: note: in expansion of macro âSCALE_LOADâ > 549 | SCALE_LOAD( scale_mean, in ) > | ^~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:550:17: note: in expansion of macro âSCALE_LOADâ > 550 | SCALE_LOAD( scale_deviation, in ) > | ^~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:551:17: note: in expansion of macro âSCALE_LOADâ > 551 | SCALE_LOAD( scale_new_min, in ) > | ^~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:552:17: note: in expansion of macro âSCALE_LOADâ > 552 | SCALE_LOAD( scale_factor, in ) > | ^~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:554:17: note: in expansion of macro âSCALE_LOADâ > 554 | SCALE_LOAD( scale_mean, out ) > | ^~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:555:17: note: in expansion of macro âSCALE_LOADâ > 555 | SCALE_LOAD( scale_deviation, out ) > | ^~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:556:17: note: in expansion of macro âSCALE_LOADâ > 556 | SCALE_LOAD( scale_new_min, out ) > | ^~~~~~~~~~ >fann_io.c:535:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 535 | fscanf( conf, #what "_" #where "=" ); \ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:557:17: note: in expansion of macro âSCALE_LOADâ > 557 | SCALE_LOAD( scale_factor, out ) > | ^~~~~~~~~~ >fann_io.c:571:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-Wunused-result] > 571 | fscanf(conf, "neurons (num_inputs, activation_function, activation_steepness)="); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >fann_io.c:598:9: warning: ignoring return value of âfscanfâ declared with attribute âwarn_unused_resultâ [-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 âCDnaHash::CDnaHash(unsigned char, unsigned char)â: >DnaHash.cpp:40:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 40 | } catch(bad_alloc) { > | ^~~~~~~~~ >DnaHash.cpp: In member function âvirtual void CDnaHash::Dump()â: >DnaHash.cpp:305:9: warning: this âforâ 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 âforâ > 319 | cout << endl; > | ^~~~ >DnaHash.cpp: In member function âvoid CDnaHash::GetStatistics(unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, double&, double&)â: >DnaHash.cpp:334:9: warning: this âforâ 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 âforâ > 349 | mean = (double)numUsedHashesCount / (double)numUsedHashes; > | ^~~~ >DnaHash.cpp:354:17: warning: this âforâ 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 âforâ > 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 âunordered_mapâ is ambiguous > 43 | unordered_map<K, LinkedListNode<K,V>*> 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::tr1::unordered_mapâ > 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::unordered_mapâ > 102 | class unordered_map > | ^~~~~~~~~~~~~ >In file included from JumpDnaHash.h:23, > from JumpDnaHash.cpp:13: >MruCache.h: In constructor âCMruCache<K, V>::CMruCache(unsigned int)â: >MruCache.h:59:3: error: class âCMruCache<K, V>â does not have any field named âmMruMapâ > 59 | , mMruMap() > | ^~~~~~~ >MruCache.h: In member function âbool CMruCache<K, V>::Get(const K&, V&)â: >MruCache.h:77:18: error: expected nested-name-specifier before âunordered_mapâ > 77 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter = mMruMap.find(key); > | ^~~~~~~~~~~~~ >MruCache.h:77:18: error: expected â(â before âunordered_mapâ > 77 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter = mMruMap.find(key); > | ^~~~~~~~~~~~~ > | ( >MruCache.h:79:12: error: âhashIterâ was not declared in this scope > 79 | if(hashIter != mMruMap.end()) { > | ^~~~~~~~ >MruCache.h:79:24: error: âmMruMapâ was not declared in this scope > 79 | if(hashIter != mMruMap.end()) { > | ^~~~~~~ >MruCache.h: In member function âvoid CMruCache<K, V>::Insert(const K&, const V&)â: >MruCache.h:105:18: error: expected nested-name-specifier before âunordered_mapâ > 105 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter; > | ^~~~~~~~~~~~~ >MruCache.h:105:18: error: expected â(â before âunordered_mapâ > 105 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter; > | ^~~~~~~~~~~~~ > | ( >MruCache.h:112:17: error: âhashIterâ was not declared in this scope > 112 | hashIter = mMruMap.find(tailKey); > | ^~~~~~~~ >MruCache.h:112:28: error: âmMruMapâ was not declared in this scope > 112 | hashIter = mMruMap.find(tailKey); > | ^~~~~~~ >MruCache.h:124:9: error: âhashIterâ was not declared in this scope > 124 | hashIter = mMruMap.find(key); > | ^~~~~~~~ >MruCache.h:124:20: error: âmMruMapâ was not declared in this scope > 124 | hashIter = mMruMap.find(key); > | ^~~~~~~ >JumpDnaHash.cpp: In constructor âCJumpDnaHash::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&)â: >JumpDnaHash.cpp:95:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 95 | } catch(bad_alloc) { > | ^~~~~~~~~ >JumpDnaHash.cpp: In member function âvirtual void CJumpDnaHash::Get(const uint64_t&, const unsigned int&, AVLTree::CHashRegionTree&, double&)â: >JumpDnaHash.cpp:237:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 237 | fread((char*)&position, KEY_LENGTH, 1, mKeys); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:313:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 313 | fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:318:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 318 | fread(mBuffer, entrySize, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp: In member function âvoid CJumpDnaHash::LoadBlockPositions(char*, uint64_t&, const unsigned int&)â: >JumpDnaHash.cpp:600:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 600 | fread(blockPosition, (size_t)bytesLeft, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:604:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 604 | fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp: In member function âvoid CJumpDnaHash::LoadKeys()â: >JumpDnaHash.cpp:582:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 582 | fread(pKeys, fillBufferSize, 1, mKeys); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:587:14: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-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 âbool CFasta::LoadNextMate(FastaTags&, Mosaik::Mate&)â: >Fasta.cpp:18:114: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 18 | ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen) : fgets(mBaseBuffer, mBaseBufferLen, mInStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fasta.cpp:130:9: note: in expansion of macro âREAD_FILE_GETSâ > 130 | READ_FILE_GETS; > | ^~~~~~~~~~~~~~ >Fasta.cpp:28:136: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fasta.cpp:145:17: note: in expansion of macro âQUALITY_FILE_GETSâ > 145 | QUALITY_FILE_GETS; > | ^~~~~~~~~~~~~~~~~ >Fasta.cpp:18:114: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 18 | ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen) : fgets(mBaseBuffer, mBaseBufferLen, mInStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fasta.cpp:173:17: note: in expansion of macro âREAD_FILE_GETSâ > 173 | READ_FILE_GETS; > | ^~~~~~~~~~~~~~ >Fasta.cpp:28:136: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fasta.cpp:190:25: note: in expansion of macro âQUALITY_FILE_GETSâ > 190 | QUALITY_FILE_GETS; > | ^~~~~~~~~~~~~~~~~ >Fasta.cpp: In member function âvoid CFasta::Open(const string&)â: >Fasta.cpp:232:14: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 232 | fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Fasta.cpp:249:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 249 | fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Fasta.cpp:18:114: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 18 | ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen) : fgets(mBaseBuffer, mBaseBufferLen, mInStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fasta.cpp:290:31: note: in expansion of macro âREAD_FILE_GETSâ > 290 | if(ch == '#') READ_FILE_GETS; > | ^~~~~~~~~~~~~~ >Fasta.cpp:28:136: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fasta.cpp:300:39: note: in expansion of macro âQUALITY_FILE_GETSâ > 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 âbool CFastq::LoadNextMate(CMosaikString&, Mosaik::Mate&)â: >Fastq.cpp:17:110: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fastq.cpp:424:9: note: in expansion of macro âREAD_FILE_GETSâ > 424 | READ_FILE_GETS; > | ^~~~~~~~~~~~~~ >Fastq.cpp:17:110: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fastq.cpp:446:17: note: in expansion of macro âREAD_FILE_GETSâ > 446 | READ_FILE_GETS; > | ^~~~~~~~~~~~~~ >Fastq.cpp:17:110: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fastq.cpp:459:9: note: in expansion of macro âREAD_FILE_GETSâ > 459 | READ_FILE_GETS; > | ^~~~~~~~~~~~~~ >Fastq.cpp:17:110: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen) : fgets(mBuffer, mBufferLen, mInStream)) > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Fastq.cpp:470:17: note: in expansion of macro âREAD_FILE_GETSâ > 470 | READ_FILE_GETS; > | ^~~~~~~~~~~~~~ >Fastq.cpp: In member function âvoid CFastq::Open(const string&)â: >Fastq.cpp:532:14: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-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 âstatic bool CSRF::CheckFile(const string&, bool)â: >SRF.cpp:53:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-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 âstatic bool MosaikReadFormat::CAlignmentReader::CheckFile(const string&, SequencingTechnologies&, AlignmentStatus&, bool)â: >AlignmentReader.cpp:134:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 134 | fread((char*)&st, SIZEOF_SHORT, 1, checkStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp: In member function âvoid MosaikReadFormat::CAlignmentReader::Jump(unsigned int, unsigned int)â: >AlignmentReader.cpp:277:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 277 | fread((char*)&numIndexEntries, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp: In member function âvoid MosaikReadFormat::CAlignmentReader::Open(const string&)â: >AlignmentReader.cpp:525:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 525 | fread( signature, SIGNATURE_LENGTH, 1, mInStream ); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:560:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 560 | fread((char*)&mSeqTech, SIZEOF_SHORT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:566:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 566 | fread((char*)&mNumRefSeqs, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:570:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 570 | fread((char*)&numReadGroups, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:573:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 573 | fread((char*)&mNumReads, SIZEOF_UINT64, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:585:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 585 | fread((char*)&mNumBases, SIZEOF_UINT64, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:589:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 589 | fread((char*)&referencesOffset, SIZEOF_OFF_TYPE, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:592:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 592 | fread((char*)&mReferenceGapOffset, SIZEOF_OFF_TYPE, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:595:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 595 | fread((char*)&mIndexOffset, SIZEOF_OFF_TYPE, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:634:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 634 | fread((char*)&descriptionLen, SIZEOF_SHORT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:635:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 635 | fread((char*)&rgIter->SequencingTechnology, SIZEOF_SHORT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:636:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 636 | fread((char*)&rgIter->MedianFragmentLength, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:646:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 646 | fread((void*)rgIter->CenterName.data(), centerNameLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:647:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 647 | fread((void*)rgIter->Description.data(), descriptionLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:648:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 648 | fread((void*)rgIter->LibraryName.data(), libraryNameLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:649:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 649 | fread((void*)rgIter->PlatformUnit.data(), platformUnitLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:650:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 650 | fread((void*)rgIter->ReadGroupID.data(), readGroupIDLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:651:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 651 | fread((void*)rgIter->SampleName.data(), sampleNameLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:721:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 721 | fread((char*)&rsIter->NumBases, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:724:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 724 | fread((char*)&rsIter->NumAligned, SIZEOF_UINT64, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:729:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 729 | fread(pBuffer, 32, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:734:30: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 734 | fread(pBuffer, nameLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:747:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 747 | fread(pBuffer, speciesLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:754:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 754 | fread(pBuffer, genomeAssemblyIDLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:761:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 761 | fread(pBuffer, uriLen, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp: In member function âbool MosaikReadFormat::CAlignmentReader::ReadPartition()â: >AlignmentReader.cpp:1031:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1031 | fread((char*)&uncompressedSize, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1037:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1037 | fread((char*)&compressedSize, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1041:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1041 | fread((char*)&mPartitionSize, SIZEOF_SHORT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp: In member function âvoid MosaikReadFormat::CAlignmentReader::ReadTag(Tag&)â: >AlignmentReader.cpp:1086:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1086 | fread((char*)&tag.Double, SIZEOF_DOUBLE, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1089:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1089 | fread((char*)&tag.Float, SIZEOF_FLOAT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1092:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1092 | fread((char*)&tag.Int16, SIZEOF_SHORT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1095:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1095 | fread((char*)&tag.Int32, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1098:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1098 | fread((char*)&tag.Int64, SIZEOF_UINT64, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1101:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1101 | fread((char*)&stringLength, SIZEOF_SHORT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1102:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1102 | fread(tag.String, stringLength, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1108:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1108 | fread((char*)&tag.UInt16, SIZEOF_SHORT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1111:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1111 | fread((char*)&tag.UInt32, SIZEOF_INT, 1, mInStream); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >AlignmentReader.cpp:1114:38: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-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<unordered_map<unsigned int, unsigned short> >* 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<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^~~~~~ >AlignmentWriter.h:85:46: error: reference to âunordered_mapâ is ambiguous > 85 | void SetReferenceGaps(vector<unordered_map<unsigned int, unsigned short> >* 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::tr1::unordered_mapâ > 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::unordered_mapâ > 102 | class unordered_map > | ^~~~~~~~~~~~~ >In file included from AlignmentWriter.cpp:11: >AlignmentWriter.h:85:60: error: expected primary-expression before âunsignedâ > 85 | void SetReferenceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^~~~~~~~ >AlignmentWriter.h:85:60: error: expected â>â before âunsignedâ >AlignmentWriter.h:85:39: error: class template placeholder âstd::vectorâ not permitted in this context > 85 | void SetReferenceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^~~~~~ >AlignmentWriter.h:85:90: error: expected â,â or â...â before â>â token > 85 | enceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^ > >AlignmentWriter.h:154:68: error: template argument 1 is invalid > 154 | vector<unordered_map<unsigned int, unsigned short> >* mpRefGapVector; > | ^ > >AlignmentWriter.h:154:68: error: template argument 2 is invalid >AlignmentWriter.cpp: In constructor âMosaikReadFormat::CAlignmentWriter::CAlignmentWriter()â: >AlignmentWriter.cpp:48:25: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 48 | } catch(bad_alloc) { > | ^~~~~~~~~ >AlignmentWriter.cpp: In member function âvoid MosaikReadFormat::CAlignmentWriter::AdjustBuffer()â: >AlignmentWriter.cpp:101:25: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 101 | } catch(bad_alloc) { > | ^~~~~~~~~ >AlignmentWriter.cpp: In member function âvoid MosaikReadFormat::CAlignmentWriter::Close()â: >AlignmentWriter.cpp:212:132: error: request for member âatâ in â*((MosaikReadFormat::CAlignmentWriter*)this)->MosaikReadFormat::CAlignmentWriter::mpRefGapVectorâ, which is of non-class type âintâ > 212 | equestedBytes += SIZEOF_INT + (unsigned int)mpRefGapVector->at(i).size() * (SIZEOF_INT + SIZEOF_SHORT); > | ^~ > >AlignmentWriter.cpp:218:25: error: reference to âunordered_mapâ is ambiguous > 218 | unordered_map<unsigned int, unsigned short>::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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::tr1::unordered_mapâ > 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::unordered_mapâ > 102 | class unordered_map > | ^~~~~~~~~~~~~ >AlignmentWriter.cpp:218:39: error: expected primary-expression before âunsignedâ > 218 | unordered_map<unsigned int, unsigned short>::const_iterator refHashMapIter; > | ^~~~~~~~ >AlignmentWriter.cpp:222:76: error: template argument 1 is invalid > 222 | vector<unordered_map<unsigned int, unsigned short> >::const_iterator rgIter; > | ^ > >AlignmentWriter.cpp:222:76: error: template argument 2 is invalid >AlignmentWriter.cpp:222:94: error: qualified-id in declaration before ârgIterâ > 222 | r<unordered_map<unsigned int, unsigned short> >::const_iterator rgIter; > | ^~~~~~ > >AlignmentWriter.cpp:223:29: error: ârgIterâ was not declared in this scope; did you mean ârsIterâ? > 223 | for(rgIter = mpRefGapVector->begin(); rgIter != mpRefGapVector->end(); rgIter++) { > | ^~~~~~ > | rsIter >AlignmentWriter.cpp:223:54: error: request for member âbeginâ in â*((MosaikReadFormat::CAlignmentWriter*)this)->MosaikReadFormat::CAlignmentWriter::mpRefGapVectorâ, which is of non-class type âintâ > 223 | for(rgIter = mpRefGapVector->begin(); rgIter != mpRefGapVector->end(); rgIter++) { > | ^~~~~ >AlignmentWriter.cpp:223:89: error: request for member âendâ in â*((MosaikReadFormat::CAlignmentWriter*)this)->MosaikReadFormat::CAlignmentWriter::mpRefGapVectorâ, which is of non-class type âintâ > 223 | rgIter = mpRefGapVector->begin(); rgIter != mpRefGapVector->end(); rgIter++) { > | ^~~ > >AlignmentWriter.cpp:237:45: error: ârefHashMapIterâ 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<unordered_map<unsigned int, unsigned short> >* 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<unordered_map<unsigned int, unsigned short> >* pRefGapVector) { > | ^~~~~~ >AlignmentWriter.cpp:998:14: error: variable or field âSetReferenceGapsâ declared void > 998 | void CAlignmentWriter::SetReferenceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector) { > | ^~~~~~~~~~~~~~~~ >AlignmentWriter.cpp:998:101: error: missing template arguments before â*â token > 998 | nceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector) { > | ^ > >AlignmentWriter.cpp:998:103: error: âpRefGapVectorâ was not declared in this scope > 998 | eGaps(vector<unordered_map<unsigned int, unsigned short> >* 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 âvoid CSmithWatermanGotoh::Align(Alignment&, const char*, const unsigned int&, const char*, const unsigned int&)â: >SmithWatermanGotoh.cpp:84:25: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 84 | } catch(bad_alloc) { > | ^~~~~~~~~ >SmithWatermanGotoh.cpp:118:25: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 118 | } catch(bad_alloc) { > | ^~~~~~~~~ >SmithWatermanGotoh.cpp:140:25: warning: catching polymorphic type âclass std::bad_allocâ 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 âCBandedSmithWaterman::CBandedSmithWaterman(float, float, float, float, unsigned int, bool)â: >BandedSmithWaterman.cpp:56:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 56 | } catch(bad_alloc) { > | ^~~~~~~~~ >BandedSmithWaterman.cpp: In member function âvoid CBandedSmithWaterman::ReinitializeMatrices(const PositionType&, const unsigned int&, const unsigned int&, const HashRegion&)â: >BandedSmithWaterman.cpp:475:25: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 475 | } catch(bad_alloc) { > | ^~~~~~~~~ >BandedSmithWaterman.cpp:501:25: warning: catching polymorphic type âclass std::bad_allocâ 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<unordered_map<unsigned int, unsigned short> >* 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<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^~~~~~ >../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:46: error: reference to âunordered_mapâ is ambiguous > 85 | void SetReferenceGaps(vector<unordered_map<unsigned int, unsigned short> >* 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::tr1::unordered_mapâ > 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::unordered_mapâ > 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 âunsignedâ > 85 | void SetReferenceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^~~~~~~~ >../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:60: error: expected â>â before âunsignedâ >../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:39: error: class template placeholder âstd::vectorâ not permitted in this context > 85 | void SetReferenceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^~~~~~ >../../CommonSource/MosaikReadFormat/AlignmentWriter.h:85:90: error: expected â,â or â...â before â>â token > 85 | enceGaps(vector<unordered_map<unsigned int, unsigned short> >* pRefGapVector); > | ^ > >../../CommonSource/MosaikReadFormat/AlignmentWriter.h:154:68: error: template argument 1 is invalid > 154 | vector<unordered_map<unsigned int, unsigned short> >* 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 âCMosaikBuild::CMosaikBuild(const MosaikReadFormat::ReadGroup&)â: >MosaikBuild.cpp:38:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 38 | } catch(bad_alloc) { > | ^~~~~~~~~ >MosaikBuild.cpp: In member function âvoid CMosaikBuild::CreateReferenceArchive(const string&, const string&)â: >MosaikBuild.cpp:470:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 470 | } catch(bad_alloc) { > | ^~~~~~~~~ >MosaikBuild.cpp:527:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 527 | } catch(bad_alloc) { > | ^~~~~~~~~ >MosaikBuild.cpp:669:25: warning: catching polymorphic type âclass std::bad_allocâ 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 âCProgressBar<K>::CProgressBar(K*, K, K, std::string) [with K = unsigned int; std::string = std::__cxx11::basic_string<char>]â: >../CommonSource/Utilities/ProgressBar.h:277:19: required from âstatic void* CProgressBar<K>::Monitor(void*) [with K = unsigned int]â >../CommonSource/Utilities/ProgressBar.h:209:57: required from âstatic void CProgressBar<K>::StartThread(K*, K, K, std::string) [with K = unsigned int; std::string = std::__cxx11::basic_string<char>]â >MosaikBuild.cpp:297:31: required from here >../CommonSource/Utilities/ProgressBar.h:186:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 186 | } catch(bad_alloc) { > | ^~~~~~~~~ >MosaikBuild.cpp: In member function âvoid CMosaikBuild::ParseBustard(const string&, const string&, const string&, bool)â: >MosaikBuild.cpp:876:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ [-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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ [-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 âunordered_mapâ is ambiguous > 43 | unordered_map<K, LinkedListNode<K,V>*> 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::tr1::unordered_mapâ > 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: âtemplate<class _Key, class _Tp, class _Hash, class _Pred, class _Alloc> class std::unordered_mapâ > 102 | class unordered_map > | ^~~~~~~~~~~~~ >In file included from JumpDnaHash.h:23, > from JumpDnaHash.cpp:13: >MruCache.h: In constructor âCMruCache<K, V>::CMruCache(unsigned int)â: >MruCache.h:59:3: error: class âCMruCache<K, V>â does not have any field named âmMruMapâ > 59 | , mMruMap() > | ^~~~~~~ >MruCache.h: In member function âbool CMruCache<K, V>::Get(const K&, V&)â: >MruCache.h:77:18: error: expected nested-name-specifier before âunordered_mapâ > 77 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter = mMruMap.find(key); > | ^~~~~~~~~~~~~ >MruCache.h:77:18: error: expected â(â before âunordered_mapâ > 77 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter = mMruMap.find(key); > | ^~~~~~~~~~~~~ > | ( >MruCache.h:79:12: error: âhashIterâ was not declared in this scope > 79 | if(hashIter != mMruMap.end()) { > | ^~~~~~~~ >MruCache.h:79:24: error: âmMruMapâ was not declared in this scope > 79 | if(hashIter != mMruMap.end()) { > | ^~~~~~~ >MruCache.h: In member function âvoid CMruCache<K, V>::Insert(const K&, const V&)â: >MruCache.h:105:18: error: expected nested-name-specifier before âunordered_mapâ > 105 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter; > | ^~~~~~~~~~~~~ >MruCache.h:105:18: error: expected â(â before âunordered_mapâ > 105 | typename unordered_map<K, LinkedListNode<K,V>*>::iterator hashIter; > | ^~~~~~~~~~~~~ > | ( >MruCache.h:112:17: error: âhashIterâ was not declared in this scope > 112 | hashIter = mMruMap.find(tailKey); > | ^~~~~~~~ >MruCache.h:112:28: error: âmMruMapâ was not declared in this scope > 112 | hashIter = mMruMap.find(tailKey); > | ^~~~~~~ >MruCache.h:124:9: error: âhashIterâ was not declared in this scope > 124 | hashIter = mMruMap.find(key); > | ^~~~~~~~ >MruCache.h:124:20: error: âmMruMapâ was not declared in this scope > 124 | hashIter = mMruMap.find(key); > | ^~~~~~~ >JumpDnaHash.cpp: In constructor âCJumpDnaHash::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&)â: >JumpDnaHash.cpp:95:17: warning: catching polymorphic type âclass std::bad_allocâ by value [-Wcatch-value=] > 95 | } catch(bad_alloc) { > | ^~~~~~~~~ >JumpDnaHash.cpp: In member function âvirtual void CJumpDnaHash::Get(const uint64_t&, const unsigned int&, AVLTree::CHashRegionTree&, double&)â: >JumpDnaHash.cpp:237:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 237 | fread((char*)&position, KEY_LENGTH, 1, mKeys); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:313:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 313 | fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:318:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 318 | fread(mBuffer, entrySize, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp: In member function âvoid CJumpDnaHash::LoadBlockPositions(char*, uint64_t&, const unsigned int&)â: >JumpDnaHash.cpp:600:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 600 | fread(blockPosition, (size_t)bytesLeft, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:604:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 604 | fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp: In member function âvoid CJumpDnaHash::LoadKeys()â: >JumpDnaHash.cpp:582:22: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 582 | fread(pKeys, fillBufferSize, 1, mKeys); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >JumpDnaHash.cpp:587:14: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ [-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' >
<b>You cannot view the attachment while viewing its details because your browser does not support IFRAMEs. <a href="attachment.cgi?id=706179">View the attachment on a separate page</a>.</b>
View Attachment As Raw
Actions:
View
Attachments on
bug 788331
:
706167
|
706170
|
706173
|
706176
| 706179
