sci-biology:mosaik-2.2.30:20220612-233153.log

sci-biology:mosaik-2.2.30:20220612-233153.log (text/plain), 72.50 KB, created by Toralf Förster on 2022-06-13 07:16:06 UTC

 * Package:    sci-biology/mosaik-2.2.30
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * 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 ]
>>> 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 -j4 CC=x86_64-pc-linux-gnu-gcc CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-pipe -march=native -fno-diagnostics-color -O2 -Wall -Wno-char-subscripts' 'CXXFLAGS=-pipe -march=native -fno-diagnostics-color -O2 -Wall -Wno-char-subscripts' 'CPPFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' 
Building MOSAIK for the following platform: linux
=========================================================
- Building in fann-2.1.0
  * compiling floatfann.c
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -Iinclude/ -c -o .././obj/floatfann.o floatfann.c
In file included from floatfann.c:25:
fann.c: In function ‘fann_seed_rand’:
fann.c:1543:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1543 |                 fread(&foo, sizeof(foo), 1, fp);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from floatfann.c:26:
fann_io.c: In function ‘fann_create_from_fd’:
fann_io.c:376:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  376 |         fread(read_version, 1, strlen(FANN_CONF_VERSION "\n"), conf);   /* reads version */
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:463:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  463 |         fscanf(conf, "cascade_activation_functions=");
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:465:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  465 |                 fscanf(conf, "%u ", (unsigned int *)&ann->cascade_activation_functions[i]);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:480:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  480 |         fscanf(conf, "cascade_activation_steepnesses=");
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:482:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  482 |                 fscanf(conf, FANNSCANF" ", &ann->cascade_activation_steepnesses[i]);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:498:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  498 |         fscanf(conf, "layer_sizes=");
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:549:17: note: in expansion of macro ‘SCALE_LOAD’
  549 |                 SCALE_LOAD( scale_mean,                 in )
      |                 ^~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:550:17: note: in expansion of macro ‘SCALE_LOAD’
  550 |                 SCALE_LOAD( scale_deviation,    in )
      |                 ^~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:551:17: note: in expansion of macro ‘SCALE_LOAD’
  551 |                 SCALE_LOAD( scale_new_min,              in )
      |                 ^~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:552:17: note: in expansion of macro ‘SCALE_LOAD’
  552 |                 SCALE_LOAD( scale_factor,               in )
      |                 ^~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:554:17: note: in expansion of macro ‘SCALE_LOAD’
  554 |                 SCALE_LOAD( scale_mean,                 out )
      |                 ^~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:555:17: note: in expansion of macro ‘SCALE_LOAD’
  555 |                 SCALE_LOAD( scale_deviation,    out )
      |                 ^~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:556:17: note: in expansion of macro ‘SCALE_LOAD’
  556 |                 SCALE_LOAD( scale_new_min,              out )
      |                 ^~~~~~~~~~
fann_io.c:535:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  535 |         fscanf( conf, #what "_" #where "=" );                                                                   \
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:557:17: note: in expansion of macro ‘SCALE_LOAD’
  557 |                 SCALE_LOAD( scale_factor,               out )
      |                 ^~~~~~~~~~
fann_io.c:571:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  571 |         fscanf(conf, "neurons (num_inputs, activation_function, activation_steepness)=");
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fann_io.c:598:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  598 |         fscanf(conf, "connections (connected_to_neuron, weight)=");
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- Building in CommonSource
- Building in DataStructures
  * compiling AbstractDnaHash.cpp
  * compiling AlignedReadCache.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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 HashRegionTree.cpp
  * compiling DnaHash.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -I../../CommonSource/DataStructures -I../../CommonSource/Config -I../../CommonSource/Utilities -I../../CommonSource/MosaikReadFormat -I. -c -o ../.././obj/HashRegionTree.o HashRegionTree.cpp
  * compiling JumpDnaHash.cpp
  * compiling MosaikString.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
DnaHash.cpp: In constructor ‘CDnaHash::CDnaHash(unsigned char, unsigned char)’:
DnaHash.cpp:40:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   40 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
DnaHash.cpp: In member function ‘virtual void CDnaHash::Dump()’:
DnaHash.cpp:305:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  305 |         for(unsigned int i = 0; i < mCapacity; i++)
      |         ^~~
DnaHash.cpp:319:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  319 |                 cout << endl;
      |                 ^~~~
DnaHash.cpp: In member function ‘void CDnaHash::GetStatistics(unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, double&, double&)’:
DnaHash.cpp:334:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  334 |         for(unsigned int i = 0; i < mCapacity; i++)
      |         ^~~
DnaHash.cpp:349:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  349 |                 mean = (double)numUsedHashesCount / (double)numUsedHashes;
      |                 ^~~~
DnaHash.cpp:354:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  354 |                 for(unsigned int i = 0; i < mCapacity; i++)
      |                 ^~~
DnaHash.cpp:360:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  360 |                         double variance = diffSumSquare / (numUsedHashes - 1.0);
      |                         ^~~~~~
  * compiling MultiDnaHash.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
  * compiling NaiveAlignmentSet.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
  * compiling UbiqDnaHash.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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: In constructor ‘CJumpDnaHash::CJumpDnaHash(const unsigned char&, const std::string&, const short unsigned int&, const bool&, const bool&, const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const bool&, const bool&, const uint64_t&, const unsigned int&)’:
JumpDnaHash.cpp:95:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   95 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
MultiDnaHash.cpp: In constructor ‘CMultiDnaHash::CMultiDnaHash(unsigned char, unsigned char)’:
MultiDnaHash.cpp:40:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   40 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
MultiDnaHash.cpp: In member function ‘virtual void CMultiDnaHash::Dump()’:
MultiDnaHash.cpp:293:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  293 |         for(unsigned int i = 0; i < mCapacity; i++)
      |         ^~~
MultiDnaHash.cpp:313:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  313 |                 cout << endl;
      |                 ^~~~
JumpDnaHash.cpp: In member function ‘virtual void CJumpDnaHash::Get(const uint64_t&, const unsigned int&, AVLTree::CHashRegionTree&, double&)’:
JumpDnaHash.cpp:237:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  237 |                 fread((char*)&position, KEY_LENGTH, 1, mKeys);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JumpDnaHash.cpp:313:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  313 |                 fread((char*)&numPositions, SIZEOF_INT, 1, mPositions);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JumpDnaHash.cpp:318:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  318 |                 fread(mBuffer, entrySize, 1, mPositions);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JumpDnaHash.cpp: In member function ‘void CJumpDnaHash::LoadBlockPositions(char*, uint64_t&, const unsigned int&)’:
JumpDnaHash.cpp:600:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  600 |                 fread(blockPosition, (size_t)bytesLeft, 1, mPositions);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JumpDnaHash.cpp:604:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  604 |                 fread(blockPosition, (size_t)fillBufferSize, 1, mPositions);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JumpDnaHash.cpp: In member function ‘void CJumpDnaHash::LoadKeys()’:
JumpDnaHash.cpp:582:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  582 |                 fread(pKeys, fillBufferSize, 1, mKeys);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JumpDnaHash.cpp:587:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  587 |         fread(pKeys, (size_t)bytesLeft, 1, mKeys);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
UbiqDnaHash.cpp: In constructor ‘CUbiqDnaHash::CUbiqDnaHash(unsigned char, unsigned char)’:
UbiqDnaHash.cpp:39:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   39 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~

- Building in ExternalReadFormats
  * compiling Fasta.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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 Fastq.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
  * compiling BamWriter.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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: In static member function ‘static bool CSRF::CheckFile(const std::string&, bool)’:
SRF.cpp:53:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   53 |                 fread(signature, CHECK_BYTES, 1, checkStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fasta.cpp: In member function ‘bool CFasta::LoadNextMate(FastaTags&, Mosaik::Mate&)’:
Fasta.cpp:18:114: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   18 |  ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen)   : fgets(mBaseBuffer, mBaseBufferLen, mInStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fasta.cpp:130:9: note: in expansion of macro ‘READ_FILE_GETS’
  130 |         READ_FILE_GETS;
      |         ^~~~~~~~~~~~~~
Fasta.cpp:28:136: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fasta.cpp:145:17: note: in expansion of macro ‘QUALITY_FILE_GETS’
  145 |                 QUALITY_FILE_GETS;
      |                 ^~~~~~~~~~~~~~~~~
Fasta.cpp:18:114: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   18 |  ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen)   : fgets(mBaseBuffer, mBaseBufferLen, mInStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fasta.cpp:173:17: note: in expansion of macro ‘READ_FILE_GETS’
  173 |                 READ_FILE_GETS;
      |                 ^~~~~~~~~~~~~~
Fasta.cpp:28:136: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fasta.cpp:190:25: note: in expansion of macro ‘QUALITY_FILE_GETS’
  190 |                         QUALITY_FILE_GETS;
      |                         ^~~~~~~~~~~~~~~~~
Fasta.cpp: In member function ‘void CFasta::Open(const std::string&)’:
Fasta.cpp:232:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  232 |         fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fasta.cpp:249:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  249 |                 fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fasta.cpp:18:114: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   18 |  ? gzgets(mInZStream, mBaseBuffer, mBaseBufferLen)   : fgets(mBaseBuffer, mBaseBufferLen, mInStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fasta.cpp:290:31: note: in expansion of macro ‘READ_FILE_GETS’
  290 |                 if(ch == '#') READ_FILE_GETS;
      |                               ^~~~~~~~~~~~~~
Fasta.cpp:28:136: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   28 | InQualityZStream, mQualityBuffer, mQualityBufferLen) : fgets(mQualityBuffer, mQualityBufferLen, mInQualityStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fasta.cpp:300:39: note: in expansion of macro ‘QUALITY_FILE_GETS’
  300 |                         if(ch == '#') QUALITY_FILE_GETS;
      |                                       ^~~~~~~~~~~~~~~~~
Fastq.cpp: In member function ‘bool CFastq::LoadNextMate(CMosaikString&, Mosaik::Mate&)’:
Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen)       : fgets(mBuffer, mBufferLen, mInStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fastq.cpp:424:9: note: in expansion of macro ‘READ_FILE_GETS’
  424 |         READ_FILE_GETS;
      |         ^~~~~~~~~~~~~~
Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen)       : fgets(mBuffer, mBufferLen, mInStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fastq.cpp:446:17: note: in expansion of macro ‘READ_FILE_GETS’
  446 |                 READ_FILE_GETS;
      |                 ^~~~~~~~~~~~~~
Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen)       : fgets(mBuffer, mBufferLen, mInStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fastq.cpp:459:9: note: in expansion of macro ‘READ_FILE_GETS’
  459 |         READ_FILE_GETS;
      |         ^~~~~~~~~~~~~~
Fastq.cpp:17:110: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   17 | ssed ? gzgets(mInZStream, mBuffer, mBufferLen)       : fgets(mBuffer, mBufferLen, mInStream))
      |                                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fastq.cpp:470:17: note: in expansion of macro ‘READ_FILE_GETS’
  470 |                 READ_FILE_GETS;
      |                 ^~~~~~~~~~~~~~
Fastq.cpp: In member function ‘void CFastq::Open(const std::string&)’:
Fastq.cpp:532:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  532 |         fread((char*)&magicNumber, SIZEOF_SHORT, 1, checkStream);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- Building in MosaikReadFormat
  * compiling AlignmentWriter.cpp
  * compiling AlignmentReader.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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 ReadReader.cpp
  * compiling ReadWriter.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
ReadWriter.cpp: In constructor ‘MosaikReadFormat::CReadWriter::CReadWriter()’:
ReadWriter.cpp:39:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   39 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
ReadWriter.cpp: In member function ‘void MosaikReadFormat::CReadWriter::AdjustBuffer()’:
ReadWriter.cpp:64:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   64 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
ReadReader.cpp: In member function ‘bool MosaikReadFormat::CReadReader::LoadNextRead(Mosaik::Read&)’:
ReadReader.cpp:167:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  167 |                         fread((char*)&uncompressedSize, SIZEOF_INT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:173:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  173 |                         fread((char*)&compressedSize, SIZEOF_INT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:177:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  177 |                         fread((char*)&mPartitionSize, SIZEOF_SHORT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp: In member function ‘void MosaikReadFormat::CReadReader::Open(const std::string&)’:
ReadReader.cpp:333:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  333 |                 fread((char*)&mNumReads, SIZEOF_UINT64, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:336:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  336 |                 fread((char*)&mNumBases, SIZEOF_UINT64, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:339:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  339 |                 fread((char*)&mReadGroup.MedianFragmentLength, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:349:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  349 |                 fread((char*)&descriptionLen, SIZEOF_SHORT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:362:46: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  362 |                 if(centerNameLen > 0)   fread((void*)mReadGroup.CenterName.data(),   centerNameLen,   1, mInStream);
      |                                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:363:46: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  363 |                 if(descriptionLen > 0)  fread((void*)mReadGroup.Description.data(),  descriptionLen,  1, mInStream);
      |                                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:364:46: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  364 |                 if(libraryNameLen > 0)  fread((void*)mReadGroup.LibraryName.data(),  libraryNameLen,  1, mInStream);
      |                                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:365:46: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  365 |                 if(platformUnitLen > 0) fread((void*)mReadGroup.PlatformUnit.data(), platformUnitLen, 1, mInStream);
      |                                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:367:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  367 |                 fread((void*)mReadGroup.ReadGroupID.data(),  readGroupIDLen,  1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReadReader.cpp:368:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  368 |                 fread((void*)mReadGroup.SampleName.data(),   sampleNameLen,   1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentWriter.cpp: In constructor ‘MosaikReadFormat::CAlignmentWriter::CAlignmentWriter()’:
AlignmentWriter.cpp:48:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   48 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
AlignmentWriter.cpp: In member function ‘void MosaikReadFormat::CAlignmentWriter::AdjustBuffer()’:
AlignmentWriter.cpp:101:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  101 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
  * compiling ReferenceSequenceReader.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
AlignmentReader.cpp: In static member function ‘static bool MosaikReadFormat::CAlignmentReader::CheckFile(const std::string&, SequencingTechnologies&, AlignmentStatus&, bool)’:
AlignmentReader.cpp:134:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  134 |                         fread((char*)&st, SIZEOF_SHORT, 1, checkStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp: In member function ‘void MosaikReadFormat::CAlignmentReader::Jump(unsigned int, unsigned int)’:
AlignmentReader.cpp:277:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  277 |                 fread((char*)&numIndexEntries, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp: In member function ‘void MosaikReadFormat::CAlignmentReader::Open(const std::string&)’:
AlignmentReader.cpp:525:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  525 |                 fread( signature, SIGNATURE_LENGTH, 1, mInStream );
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:560:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  560 |                 fread((char*)&mSeqTech, SIZEOF_SHORT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:566:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  566 |                 fread((char*)&mNumRefSeqs, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:570:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  570 |                 fread((char*)&numReadGroups, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:573:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  573 |                 fread((char*)&mNumReads, SIZEOF_UINT64, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:585:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  585 |                 fread((char*)&mNumBases, SIZEOF_UINT64, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:589:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  589 |                 fread((char*)&referencesOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:592:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  592 |                 fread((char*)&mReferenceGapOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:595:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  595 |                 fread((char*)&mIndexOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:634:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  634 |                         fread((char*)&descriptionLen, SIZEOF_SHORT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:635:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  635 |                         fread((char*)&rgIter->SequencingTechnology, SIZEOF_SHORT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:636:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  636 |                         fread((char*)&rgIter->MedianFragmentLength, SIZEOF_INT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:646:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  646 |                         fread((void*)rgIter->CenterName.data(),   centerNameLen,   1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:647:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  647 |                         fread((void*)rgIter->Description.data(),  descriptionLen,  1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:648:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  648 |                         fread((void*)rgIter->LibraryName.data(),  libraryNameLen,  1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:649:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  649 |                         fread((void*)rgIter->PlatformUnit.data(), platformUnitLen, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:650:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  650 |                         fread((void*)rgIter->ReadGroupID.data(),  readGroupIDLen,  1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:651:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  651 |                         fread((void*)rgIter->SampleName.data(),   sampleNameLen,   1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:721:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  721 |                         fread((char*)&rsIter->NumBases, SIZEOF_INT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:724:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  724 |                         fread((char*)&rsIter->NumAligned, SIZEOF_UINT64, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:729:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  729 |                         fread(pBuffer, 32, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:734:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  734 |                         fread(pBuffer, nameLen, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:747:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  747 |                                 fread(pBuffer, speciesLen, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:754:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  754 |                                 fread(pBuffer, genomeAssemblyIDLen, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:761:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  761 |                                 fread(pBuffer, uriLen, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp: In member function ‘bool MosaikReadFormat::CAlignmentReader::ReadPartition()’:
AlignmentReader.cpp:1031:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1031 |                 fread((char*)&uncompressedSize, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1037:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1037 |                 fread((char*)&compressedSize, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1041:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1041 |                 fread((char*)&mPartitionSize, SIZEOF_SHORT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp: In member function ‘void MosaikReadFormat::CAlignmentReader::ReadTag(Tag&)’:
AlignmentReader.cpp:1086:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1086 |                                 fread((char*)&tag.Double, SIZEOF_DOUBLE, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1089:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1089 |                                 fread((char*)&tag.Float, SIZEOF_FLOAT, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1092:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1092 |                                 fread((char*)&tag.Int16, SIZEOF_SHORT, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1095:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1095 |                                 fread((char*)&tag.Int32, SIZEOF_INT, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1098:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1098 |                                 fread((char*)&tag.Int64, SIZEOF_UINT64, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1101:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1101 |                                 fread((char*)&stringLength, SIZEOF_SHORT, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1102:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1102 |                                 fread(tag.String, stringLength, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1108:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1108 |                                 fread((char*)&tag.UInt16, SIZEOF_SHORT, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1111:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1111 |                                 fread((char*)&tag.UInt32, SIZEOF_INT, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AlignmentReader.cpp:1114:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1114 |                                 fread((char*)&tag.UInt64, SIZEOF_UINT64, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp: In member function ‘void MosaikReadFormat::CReferenceSequenceReader::Load2BitConcatenatedSequence(char*&, char*&, unsigned int&)’:
ReferenceSequenceReader.cpp:310:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  310 |                 fread((char*)&numMaskedPositions, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp: In member function ‘void MosaikReadFormat::CReferenceSequenceReader::Open(const std::string&)’:
ReferenceSequenceReader.cpp:369:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  369 |                 fread((char*)&mNumReferenceSequences, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:372:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  372 |                 fread((char*)&mConcatenatedLen, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:375:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  375 |                 fread((char*)&mConcatenatedOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:378:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  378 |                 fread((char*)&mConcatenated2bLen, SIZEOF_INT, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:381:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  381 |                 fread((char*)&mConcatenated2bOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:384:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  384 |                 fread((char*)&mIndexOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:387:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  387 |                 fread((char*)&mReferenceBasesOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:390:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  390 |                 fread((char*)&mMaskedRegionsOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:437:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  437 |                         fread((char*)&rs.NumBases, SIZEOF_INT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:440:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  440 |                         fread((char*)&rs.Begin, SIZEOF_INT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:443:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  443 |                         fread((char*)&rs.End, SIZEOF_INT, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:446:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  446 |                         fread((char*)&rs.BasesOffset, SIZEOF_OFF_TYPE, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:451:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  451 |                         fread(pBuffer, 32, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:456:30: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  456 |                         fread(pBuffer, nameLen, 1, mInStream);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:462:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  462 |                                 fread(pBuffer, speciesLen, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:469:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  469 |                                 fread(pBuffer, genomeAssemblyIDLen, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ReferenceSequenceReader.cpp:476:38: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  476 |                                 fread(pBuffer, uriLen, 1, mInStream);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- Building in PairwiseAlignment
  * compiling BandedSmithWaterman.cpp
  * compiling SmithWatermanGotoh.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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 ssw_cpp.cpp
  * compiling ConvertSswToAlignment.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
In file included from ../../CommonSource/Config/Mosaik.h:16,
                 from ../../CommonSource/DataStructures/Alignment.h:17,
                 from ConvertSswToAlignment.h:1,
                 from ConvertSswToAlignment.cpp:1:
../../CommonSource/Utilities/SafeFunctions.h: In function ‘errno_t localtime_s(tm*, const time_t*)’:
../../CommonSource/Utilities/SafeFunctions.h:59:21: error: ‘localtime’ was not declared in this scope; did you mean ‘localtime_s’?
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                     ^~~~~~~~~
      |                     localtime_s
../../CommonSource/Utilities/SafeFunctions.h:59:38: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                                      ^~~~~~~~~~~~
../../CommonSource/Utilities/SafeFunctions.h: In function ‘errno_t gmtime_s(tm*, const time_t*)’:
../../CommonSource/Utilities/SafeFunctions.h:64:21: error: ‘gmtime’ was not declared in this scope; did you mean ‘time’?
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                     ^~~~~~
      |                     time
../../CommonSource/Utilities/SafeFunctions.h:64:35: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                                   ^~~~~~~~~~~~
../../CommonSource/Utilities/SafeFunctions.h: In function ‘errno_t asctime_s(char*, size_t, const tm*)’:
../../CommonSource/Utilities/SafeFunctions.h:69:22: error: ‘asctime’ was not declared in this scope; did you mean ‘asctime_s’?
   69 |         char* time = asctime(_tm);
      |                      ^~~~~~~
      |                      asctime_s
make[2]: *** [Makefile:29: ../.././obj/ConvertSswToAlignment.o] Error 1
make[2]: *** Waiting for unfinished jobs....
BandedSmithWaterman.cpp: In constructor ‘CBandedSmithWaterman::CBandedSmithWaterman(float, float, float, float, unsigned int, bool)’:
BandedSmithWaterman.cpp:56:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   56 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
BandedSmithWaterman.cpp: In member function ‘void CBandedSmithWaterman::ReinitializeMatrices(const PositionType&, const unsigned int&, const unsigned int&, const HashRegion&)’:
BandedSmithWaterman.cpp:475:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  475 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
BandedSmithWaterman.cpp:501:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  501 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
SmithWatermanGotoh.cpp: In member function ‘void CSmithWatermanGotoh::Align(Alignment&, const char*, const unsigned int&, const char*, const unsigned int&)’:
SmithWatermanGotoh.cpp:84:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   84 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
SmithWatermanGotoh.cpp:118:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  118 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
SmithWatermanGotoh.cpp:140:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  140 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~

- Building in Utilities
  * compiling ArchiveMerge.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
  * compiling ArchiveSort.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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 Benchmark.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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 BestNSecondBestSelection.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
  * compiling CigarTager.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
In file included from ../../CommonSource/Config/Mosaik.h:16,
                 from ../../CommonSource/DataStructures/Alignment.h:17,
                 from CigarTager.h:7,
                 from CigarTager.cpp:1:
./SafeFunctions.h: In function ‘errno_t localtime_s(tm*, const time_t*)’:
./SafeFunctions.h:59:21: error: ‘localtime’ was not declared in this scope; did you mean ‘localtime_s’?
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                     ^~~~~~~~~
      |                     localtime_s
./SafeFunctions.h:59:38: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                                      ^~~~~~~~~~~~
./SafeFunctions.h: In function ‘errno_t gmtime_s(tm*, const time_t*)’:
./SafeFunctions.h:64:21: error: ‘gmtime’ was not declared in this scope; did you mean ‘time’?
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                     ^~~~~~
      |                     time
./SafeFunctions.h:64:35: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                                   ^~~~~~~~~~~~
./SafeFunctions.h: In function ‘errno_t asctime_s(char*, size_t, const tm*)’:
./SafeFunctions.h:69:22: error: ‘asctime’ was not declared in this scope; did you mean ‘asctime_s’?
   69 |         char* time = asctime(_tm);
      |                      ^~~~~~~
      |                      asctime_s
make[2]: *** [Makefile:51: ../.././obj/CigarTager.o] Error 1
make[2]: *** Waiting for unfinished jobs....


- Building in MosaikBuild
  * compiling BuildMain.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wall -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -I../CommonSource/Config -I../CommonSource/DataStructures -I../CommonSource/ExternalReadFormats -I../CommonSource/MosaikReadFormat -I../CommonSource/Utilities -c -o .././obj/BuildMain.o BuildMain.cpp
  * compiling MosaikBuild.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
make[2]: Nothing to be done for 'all'.
  * compiling CigarTager.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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 CigarTager.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
In file included from ../../CommonSource/Config/Mosaik.h:16,
                 from ../../CommonSource/DataStructures/Alignment.h:17,
                 from CigarTager.h:7,
                 from CigarTager.cpp:1:
./SafeFunctions.h: In function ‘errno_t localtime_s(tm*, const time_t*)’:
./SafeFunctions.h:59:21: error: ‘localtime’ was not declared in this scope; did you mean ‘localtime_s’?
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                     ^~~~~~~~~
      |                     localtime_s
./SafeFunctions.h:59:38: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                                      ^~~~~~~~~~~~
./SafeFunctions.h: In function ‘errno_t gmtime_s(tm*, const time_t*)’:
./SafeFunctions.h:64:21: error: ‘gmtime’ was not declared in this scope; did you mean ‘time’?
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                     ^~~~~~
      |                     time
./SafeFunctions.h:64:35: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                                   ^~~~~~~~~~~~
./SafeFunctions.h: In function ‘errno_t asctime_s(char*, size_t, const tm*)’:
./SafeFunctions.h:69:22: error: ‘asctime’ was not declared in this scope; did you mean ‘asctime_s’?
   69 |         char* time = asctime(_tm);
      |                      ^~~~~~~
      |                      asctime_s
In file included from ../../CommonSource/Config/Mosaik.h:16,
                 from ../../CommonSource/DataStructures/Alignment.h:17,
                 from CigarTager.h:7,
                 from CigarTager.cpp:1:
./SafeFunctions.h: In function ‘errno_t localtime_s(tm*, const time_t*)’:
./SafeFunctions.h:59:21: error: ‘localtime’ was not declared in this scope; did you mean ‘localtime_s’?
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                     ^~~~~~~~~
      |                     localtime_s
./SafeFunctions.h:59:38: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   59 |         memcpy(_tm, localtime(time), sizeof(*_tm));
      |                                      ^~~~~~~~~~~~
./SafeFunctions.h: In function ‘errno_t gmtime_s(tm*, const time_t*)’:
./SafeFunctions.h:64:21: error: ‘gmtime’ was not declared in this scope; did you mean ‘time’?
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                     ^~~~~~
      |                     time
./SafeFunctions.h:64:35: error: invalid application of ‘sizeof’ to incomplete type ‘tm’
   64 |         memcpy(_tm, gmtime(time), sizeof(*_tm));
      |                                   ^~~~~~~~~~~~
./SafeFunctions.h: In function ‘errno_t asctime_s(char*, size_t, const tm*)’:
./SafeFunctions.h:69:22: error: ‘asctime’ was not declared in this scope; did you mean ‘asctime_s’?
   69 |         char* time = asctime(_tm);
      |                      ^~~~~~~
      |                      asctime_s
make[2]: *** [Makefile:51: ../.././obj/CigarTager.o] Error 1
make[1]: *** [Makefile:39: .././obj/ConsoleUtilities.o] Error 2
make[1]: *** Waiting for unfinished jobs....
  * compiling ColorspaceUtilities.cpp
x86_64-pc-linux-gnu-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
make[2]: *** [Makefile:51: ../.././obj/CigarTager.o] Error 1
make[2]: *** Waiting for unfinished jobs....
MosaikBuild.cpp: In constructor ‘CMosaikBuild::CMosaikBuild(const MosaikReadFormat::ReadGroup&)’:
MosaikBuild.cpp:38:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
   38 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
ColorspaceUtilities.cpp: In member function ‘bool CColorspaceUtilities::ConvertAlignmentToBasespace(Alignment&)’:
ColorspaceUtilities.cpp:131:24: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  131 |                 catch( bad_alloc ){
      |                        ^~~~~~~~~
MosaikBuild.cpp: In member function ‘void CMosaikBuild::CreateReferenceArchive(const std::string&, const std::string&)’:
MosaikBuild.cpp:470:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  470 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
MosaikBuild.cpp:527:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  527 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
MosaikBuild.cpp:669:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  669 |                 } catch(bad_alloc) {
      |                         ^~~~~~~~~
In file included from MosaikBuild.h:30,
                 from MosaikBuild.cpp:11:
../CommonSource/Utilities/ProgressBar.h: In instantiation of ‘CProgressBar<K>::CProgressBar(K*, K, K, std::string) [with K = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../CommonSource/Utilities/ProgressBar.h:277:19:   required from ‘static void* CProgressBar<K>::Monitor(void*) [with K = unsigned int]’
../CommonSource/Utilities/ProgressBar.h:209:26:   required from ‘static void CProgressBar<K>::StartThread(K*, K, K, std::string) [with K = unsigned int; std::string = std::__cxx11::basic_string<char>]’
MosaikBuild.cpp:297:42:   required from here
../CommonSource/Utilities/ProgressBar.h:186:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
  186 |         } catch(bad_alloc) {
      |                 ^~~~~~~~~
MosaikBuild.cpp: In member function ‘void CMosaikBuild::ParseBustard(const std::string&, const std::string&, const std::string&, bool)’:
MosaikBuild.cpp:876:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  876 |                         fscanf(seq, "%u\t%u\t%u\t%u\t%s", &lane, &tile, &xcoord, &ycoord, fBuffer);
      |                         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MosaikBuild.cpp:897:39: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  897 |                                 fscanf(prb, "%d %d %d %d", &aBQ, &cBQ, &gBQ, &tBQ);
      |                                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[1]: *** [Makefile:39: .././obj/ColorspaceUtilities.o] Error 2
make: *** [Makefile:32: all] Error 1
 * ERROR: sci-biology/mosaik-2.2.30::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/mosaik-2.2.30::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/mosaik-2.2.30::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:mosaik-2.2.30:20220612-233153.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'