sci-biology:mosaik-2.2.30:20230903-192226.log

sci-biology:mosaik-2.2.30:20230903-192226.log (text/plain), 68.50 KB, created by Toralf Förster on 2023-09-03 19:48:40 UTC

 * Package:    sci-biology/mosaik-2.2.30:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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<Mosaik::AlignedRead>::operator()' requested here
        if (__comp(*--__e2, *__f1))
            ^
/usr/include/c++/v1/list:2163:5: note: in instantiation of function template
      specialization
      'std::list<Mosaik::AlignedRead>::__sort<std::__less<Mosaik::AlignedRead>>'
      requested here
    __sort(begin(), end(), base::__sz(), __comp);
    ^
/usr/include/c++/v1/list:2154:5: note: in instantiation of function template
      specialization
      'std::list<Mosaik::AlignedRead>::sort<std::__less<Mosaik::AlignedRead>>'
      requested here
    sort(__less<value_type>());
    ^
ArchiveSort.cpp:57:20: note: in instantiation of member function
      'std::list<Mosaik::AlignedRead>::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'