* Package: sci-biology/mosaik-2.2.30:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux * FEATURES: network-sandbox preserve-libs sandbox 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 ] * Applying mosaik-2.2.30-gcc11.patch ... [ ok ] * Applying mosaik-2.2.30-gcc12-time.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 -j5 CC=clang CXX=clang++ 'CFLAGS=-O2 -pipe -march=native -fno-diagnostics-color -Wall -Wno-char-subscripts' 'CXXFLAGS=-O2 -pipe -march=native -fno-diagnostics-color -Wall -Wno-char-subscripts' 'CPPFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -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 clang -O2 -pipe -march=native -fno-diagnostics-color -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:233:36: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...ann->weights[i] = (fann_type) fann_random_weight(); ^~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:143:31: note: expanded from macro 'fann_random_weight' #define fann_random_weight() (fann_rand(-0.1f,0.1f)) ^~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:241:41: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...ann->weights[tmp_con] = (fann_type) fann_random_bias_weight(); ^~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:144:36: note: expanded from macro 'fann_random_bias_weight' #define fann_random_bias_weight() (fann_rand(-0.1f,0.1f)) ^~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:281:54: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...= (fann_type) fann_random_bias_weight(); ^~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:144:36: note: expanded from macro 'fann_random_bias_weight' #define fann_random_bias_weight() (fann_rand(-0.1f,0.1f)) ^~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:293:35: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...random_number = (int) (0.5 + fann_rand(0, num_neurons_out - 1)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:305:37: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...ann->weights[i] = (fann_type) fann_random_weight(); ^~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:143:31: note: expanded from macro 'fann_random_weight' #define fann_random_weight() (fann_rand(-0.1f,0.1f)) ^~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:325:36: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...random_number = (int) (0.5 + fann_rand(0, num_neurons_in - 1)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:344:36: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...ann->weights[i] = (fann_type) fann_random_weight(); ^~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:143:31: note: expanded from macro 'fann_random_weight' #define fann_random_weight() (fann_rand(-0.1f,0.1f)) ^~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:513:36: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...ann->weights[i] = (fann_type) fann_random_weight(); ^~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:143:31: note: expanded from macro 'fann_random_weight' #define fann_random_weight() (fann_rand(-0.1f,0.1f)) ^~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:823:27: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] *weights = (fann_type) (fann_rand(min_weight, max_weight)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:955:46: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...= (fann_type) fann_rand(-scale_factor, scale_factor); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:963:46: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...ann->weights[num_connect] = (fann_type) fann_rand(0, scale_factor); ^~~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:25: ./fann.c:1543:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&foo, sizeof(foo), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ In file included from floatfann.c:26: ./fann_io.c:376:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(read_version, 1, strlen(FANN_CONF_VERSION "\n"), conf); ... ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:463:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(conf, "cascade_activation_functions="); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:465:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fscanf(conf, "%u ", (unsigned int *)&ann->cascade_activation_functions[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:480:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(conf, "cascade_activation_steepnesses="); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:482:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fscanf(conf, FANNSCANF" ", &ann->cascade_activation_steepnesses[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:498:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(conf, "layer_sizes="); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:549:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_mean, in ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:550:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_deviation, in ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:551:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_new_min, in ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:552:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_factor, in ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:554:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_mean, out ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:555:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_deviation, out ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:556:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_new_min, out ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:557:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] SCALE_LOAD( scale_factor, out ) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:535:2: note: expanded from macro 'SCALE_LOAD' fscanf( conf, #what "_" #where "=" )... ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:571:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fscanf(conf, "neurons (num_inputs, activation_function, activation_steepness)="); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:575:76: warning: taking address of packed member 'activation_function' of class or structure 'fann_neuron' may result in an unaligned pointer value [-Waddress-of-packed-member] ...") ", &num_connections, (unsigned int *)&neuron_it->activation_function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:576:5: warning: taking address of packed member 'activation_steepness' of class or structure 'fann_neuron' may result in an unaligned pointer value [-Waddress-of-packed-member] &neuron_it->activation_steepness) != 3) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./fann_io.c:598:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(conf, "connections (connected_to_neuron, weight)="); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from floatfann.c:29: ./fann_error.c:116:15: warning: passing an object that undergoes default argument promotion to 'va_start' has undefined behavior [-Wvarargs] va_start(ap, errno_f); ^ ./fann_error.c:93:71: note: parameter of type 'const enum fann_errno_enum' is declared here void fann_error(struct fann_error *errdat, const enum fann_errno_enum errno_f... ^ In file included from floatfann.c:30: ./fann_cascade.c:345:22: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ...ann->weights[i] = fann_rand(-scale_factor, scale_factor); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ In file included from floatfann.c:30: ./fann_cascade.c:347:22: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] ann->weights[i] = fann_rand(0,scale_factor); ^~~~~~~~~~~~~~~~~~~~~~~~~ include/fann_internal.h:128:114: note: expanded from macro 'fann_rand' ...RAND_MAX+1.0f))) ^~~~~~~~~ /usr/include/stdlib.h:87:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ 33 warnings generated. - Building in CommonSource - Building in DataStructures * compiling AbstractDnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 DnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 * compiling HashRegionTree.cpp * compiling AlignedReadCache.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 JumpDnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 DnaHash.cpp:319:3: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] cout << endl; ^ DnaHash.cpp:305:2: note: previous statement is here for(unsigned int i = 0; i < mCapacity; i++) ^ DnaHash.cpp:349:3: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] mean = (double)numUsedHashesCount / (double)numUsedHashes; ^ DnaHash.cpp:334:2: note: previous statement is here for(unsigned int i = 0; i < mCapacity; i++) ^ DnaHash.cpp:360:4: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] double variance = diffSumSquare / (numUsedHashes - 1.0); ^ DnaHash.cpp:354:3: note: previous statement is here for(unsigned int i = 0; i < mCapacity; i++) ^ * compiling MosaikString.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/MosaikString.o MosaikString.cpp * compiling MultiDnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/MultiDnaHash.o MultiDnaHash.cpp 3 warnings generated. JumpDnaHash.cpp:237:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&position, KEY_LENGTH, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling NaiveAlignmentSet.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/NaiveAlignmentSet.o NaiveAlignmentSet.cpp JumpDnaHash.cpp:313:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:318:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(mBuffer, entrySize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:493:5: error: use of undeclared identifier 'random_shuffle' random_shuffle( positions.begin(), posit... ^ JumpDnaHash.cpp:582:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, fillBufferSize, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:587:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, (size_t)bytesLeft, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:600:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)bytesLeft, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:604:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:769:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin(... ^ JumpDnaHash.cpp:786:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin()... ^ * compiling UbiqDnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/UbiqDnaHash.o UbiqDnaHash.cpp 7 warnings and 3 errors generated. make[2]: *** [Makefile:25: ../.././obj/JumpDnaHash.o] Error 1 make[2]: *** Waiting for unfinished jobs.... MultiDnaHash.cpp:313:3: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] cout << endl; ^ MultiDnaHash.cpp:293:2: note: previous statement is here for(unsigned int i = 0; i < mCapacity; i++) ^ 1 warning generated. UbiqDnaHash.cpp:340:5: error: use of undeclared identifier 'random_shuffle' random_shuffle(pHashPositions->begin(), ... ^ 1 error generated. make[2]: *** [Makefile:24: ../.././obj/UbiqDnaHash.o] Error 1 - Building in ExternalReadFormats * compiling Fastq.cpp * compiling Fasta.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 * compiling SRF.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 * compiling BamWriter.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 SRF.cpp:53:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(signature, CHECK_BYTES, 1, checkStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:232:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp:249:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fastq.cpp:532:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. 1 warning generated. 1 warning generated. - Building in MosaikReadFormat * compiling AlignmentReader.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 * compiling AlignmentWriter.cpp * compiling ReadReader.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 * compiling ReferenceSequenceReader.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/ReadReader.o ReadReader.cpp * compiling ReadWriter.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/ReadWriter.o ReadWriter.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/ReferenceSequenceReader.o ReferenceSequenceReader.cpp ReferenceSequenceReader.cpp:310:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numMaskedPositions, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:369:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mNumReferenceSequences, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:372:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mConcatenatedLen, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:375:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&mConcatenatedOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:378:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mConcatenated2bLen, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:381:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&mConcatenated2bOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:384:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mIndexOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:387:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&mReferenceBasesOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:390:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&mMaskedRegionsOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:437:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&rs.NumBases, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:440:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&rs.Begin, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:443:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&rs.End, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:446:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&rs.BasesOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:451:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, 32, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:456:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, nameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:462:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, speciesLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:469:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread(pBuffer, genomeAssemblyIDLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReferenceSequenceReader.cpp:476:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, uriLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:167:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&uncompressedSize, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:173:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&compressedSize, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:177:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&mPartitionSize, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:333:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mNumReads, SIZEOF_UINT64, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:336:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mNumBases, SIZEOF_UINT64, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:339:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&mReadGroup.MedianFragmentLength, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:349:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&descriptionLen, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:362:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)mReadGroup.CenterName.data(), centerNameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:363:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)mReadGroup.Description.data(), descriptionLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:364:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)mReadGroup.LibraryName.data(), libraryNameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:365:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)mReadGroup.PlatformUnit.data(), platformUnitLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:367:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)mReadGroup.ReadGroupID.data(), readGroupIDLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadReader.cpp:368:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)mReadGroup.SampleName.data(), sampleNameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 13 warnings generated. AlignmentReader.cpp:134:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&st, SIZEOF_SHORT, 1, checkStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:277:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numIndexEntries, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:525:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread( signature, SIGNATURE_LENGTH, 1, mInStream ); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:560:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mSeqTech, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:566:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mNumRefSeqs, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:570:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numReadGroups, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:573:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mNumReads, SIZEOF_UINT64, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:585:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mNumBases, SIZEOF_UINT64, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:589:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&referencesOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:592:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&mReferenceGapOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:595:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mIndexOffset, SIZEOF_OFF_TYPE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:634:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&descriptionLen, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:635:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&rgIter->SequencingTechnology, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:636:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&rgIter->MedianFragmentLength, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:646:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)rgIter->CenterName.data(), centerNameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:647:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)rgIter->Description.data(), descriptionLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:648:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)rgIter->LibraryName.data(), libraryNameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:649:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)rgIter->PlatformUnit.data(), platformUnitLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:650:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)rgIter->ReadGroupID.data(), readGroupIDLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:651:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((void*)rgIter->SampleName.data(), sampleNameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:721:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&rsIter->NumBases, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:724:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&rsIter->NumAligned, SIZEOF_UINT64, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:729:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, 32, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:734:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, nameLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:747:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, speciesLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:754:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread(pBuffer, genomeAssemblyIDLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:761:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pBuffer, uriLen, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1031:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&uncompressedSize, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1037:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&compressedSize, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1041:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&mPartitionSize, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1086:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.Double, SIZEOF_DOUBLE, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1089:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.Float, SIZEOF_FLOAT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1092:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.Int16, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1095:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.Int32, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1098:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.Int64, SIZEOF_UINT64, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1101:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&stringLength, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1102:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(tag.String, stringLength, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1108:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.UInt16, SIZEOF_SHORT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1111:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.UInt32, SIZEOF_INT, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentReader.cpp:1114:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fread((char*)&tag.UInt64, SIZEOF_UINT64, 1, mInStream); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 18 warnings generated. 40 warnings generated. - Building in PairwiseAlignment * compiling BandedSmithWaterman.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 * compiling ConvertSswToAlignment.cpp * compiling SmithWatermanGotoh.cpp * compiling ssw.c * compiling ssw_cpp.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang -O2 -pipe -march=native -fno-diagnostics-color -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 ArchiveSort.cpp * compiling ArchiveMerge.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/ArchiveSort.o ArchiveSort.cpp * compiling BestNSecondBestSelection.cpp * compiling Benchmark.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/Benchmark.o Benchmark.cpp * compiling CigarTager.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/BestNSecondBestSelection.o BestNSecondBestSelection.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/CigarTager.o CigarTager.cpp * compiling ColorspaceUtilities.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/ColorspaceUtilities.o ColorspaceUtilities.cpp * compiling ConsoleUtilities.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/ConsoleUtilities.o ConsoleUtilities.cpp * compiling Entropy.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/Entropy.o Entropy.cpp In file included from ArchiveSort.cpp:19: In file included from ./ArchiveSort.h:21: In file included from /usr/include/c++/v1/vector:281: In file included from /usr/include/c++/v1/__algorithm/copy.h:14: In file included from /usr/include/c++/v1/__algorithm/min.h:12: /usr/include/c++/v1/__algorithm/comp.h:47:71: error: invalid operands to binary expression ('const Mosaik::AlignedRead' and 'const Mosaik::AlignedRead') bool operator()(const _T1& __x, const _T1& __y) const {return __x < __y;} ~~~ ^ ~~~ /usr/include/c++/v1/list:2177:13: note: in instantiation of member function 'std::__less::operator()' requested here if (__comp(*--__e2, *__f1)) ^ /usr/include/c++/v1/list:2163:5: note: in instantiation of function template specialization 'std::list::__sort>' requested here __sort(begin(), end(), base::__sz(), __comp); ^ /usr/include/c++/v1/list:2154:5: note: in instantiation of function template specialization 'std::list::sort>' requested here sort(__less()); ^ ArchiveSort.cpp:57:20: note: in instantiation of member function 'std::list::sort' requested here _alignedReadCache.sort(); ^ /usr/include/c++/v1/__utility/pair.h:465:1: note: candidate template ignored: could not match 'const pair<_T1, _T2>' against 'const Mosaik::AlignedRead' operator< (const pair<_T1,_T2>& __x, const pair<_T1,_T2>& __y) ^ ../../CommonSource/DataStructures/AlignedRead.h:77:22: note: candidate function not viable: 'this' argument has type 'const Mosaik::AlignedRead', but method is not marked const bool operator<( const AlignedRead& x ) { ^ * compiling FastLZIO.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/FastLZIO.o FastLZIO.cpp 1 error generated. make[2]: *** [Makefile:51: ../.././obj/ArchiveSort.o] Error 1 make[2]: *** Waiting for unfinished jobs.... ArchiveMerge.cpp:1033:59: warning: unused variable 'ite' [-Wunused-variable] vector< SortNMergeUtilities::AlignedReadPair >::iterator ite; ^ FastLZIO.cpp:49:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&newBufferLen, SIZEOF_INT, 1, stm); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FastLZIO.cpp:73:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numCompressedBytes, SIZEOF_INT, 1, stm); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FastLZIO.cpp:76:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(mBuffer, numCompressedBytes, 1, stm); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FastLZIO.cpp:92:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&bufferLen, SIZEOF_INT, 1, stm); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FastLZIO.cpp:111:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numCompressedBytes, SIZEOF_INT, 1, stm); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FastLZIO.cpp:112:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(mBuffer, numCompressedBytes, 1, stm); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. 1 warning generated. - Building in MosaikBuild * compiling MosaikBuild.cpp * compiling BuildMain.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 JumpDnaHash.cpp * compiling JumpDnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 * compiling JumpDnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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 JumpDnaHash.cpp:237:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&position, KEY_LENGTH, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:313:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:318:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(mBuffer, entrySize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:237:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&position, KEY_LENGTH, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:313:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:318:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(mBuffer, entrySize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:493:5: error: use of undeclared identifier 'random_shuffle' random_shuffle( positions.begin(), posit... ^ JumpDnaHash.cpp:582:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, fillBufferSize, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:587:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, (size_t)bytesLeft, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:600:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)bytesLeft, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:604:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:493:5: error: use of undeclared identifier 'random_shuffle' random_shuffle( positions.begin(), posit... ^ JumpDnaHash.cpp:769:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin(... ^ JumpDnaHash.cpp:582:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, fillBufferSize, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:587:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, (size_t)bytesLeft, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:600:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)bytesLeft, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:604:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:786:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin()... ^ JumpDnaHash.cpp:769:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin(... ^ JumpDnaHash.cpp:786:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin()... ^ 7 warnings and 3 errors generated. 7 warnings and 3 errors generated. JumpDnaHash.cpp:237:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&position, KEY_LENGTH, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:313:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread((char*)&numPositions, SIZEOF_INT, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:318:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(mBuffer, entrySize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [Makefile:25: ../.././obj/JumpDnaHash.o] Error 1 make[2]: *** [Makefile:25: ../.././obj/JumpDnaHash.o] Error 1 make[1]: *** [Makefile:36: .././obj/MemoryUtilities.o] Error 2 make[1]: *** Waiting for unfinished jobs.... make[1]: *** [Makefile:36: .././obj/FileUtilities.o] Error 2 * compiling UbiqDnaHash.cpp clang++ -O2 -pipe -march=native -fno-diagnostics-color -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/UbiqDnaHash.o UbiqDnaHash.cpp JumpDnaHash.cpp:493:5: error: use of undeclared identifier 'random_shuffle' random_shuffle( positions.begin(), posit... ^ JumpDnaHash.cpp:582:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, fillBufferSize, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:587:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(pKeys, (size_t)bytesLeft, 1, mKeys); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:600:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)bytesLeft, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:604:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(blockPosition, (size_t)fillBufferSize, 1, mPositions); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ JumpDnaHash.cpp:769:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin(... ^ JumpDnaHash.cpp:786:6: error: use of undeclared identifier 'random_shuffle' random_shuffle(positions.begin()... ^ MosaikBuild.cpp:876:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fscanf(seq, "%u\t%u\t%u\t%u\t%s", &lane, &tile, &xcoord, &ycoord, fBuffer); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MosaikBuild.cpp:897:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] ...fscanf(prb, "%d %d %d %d", &aBQ, &cBQ, &gBQ, &tBQ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MosaikBuild.cpp:1088:11: warning: variable 'numMate1Written' set but not used [-Wunused-but-set-variable] uint64_t numMate1Written = 0; ^ MosaikBuild.cpp:1089:11: warning: variable 'numMate2Written' set but not used [-Wunused-but-set-variable] uint64_t numMate2Written = 0; ^ 7 warnings and 3 errors generated. make[2]: *** [Makefile:25: ../.././obj/JumpDnaHash.o] Error 1 make[2]: *** Waiting for unfinished jobs.... UbiqDnaHash.cpp:340:5: error: use of undeclared identifier 'random_shuffle' random_shuffle(pHashPositions->begin(), ... ^ 1 error generated. make[2]: *** [Makefile:25: ../.././obj/UbiqDnaHash.o] Error 1 make[1]: *** [Makefile:36: .././obj/fastlz.o] Error 2 4 warnings generated. 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-2.2.30:20230903-192226.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'