2025-05-06 06:02
ftp://ftp.de.debian.org/debian/pool/main/m/metabat/metabat_2.15.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=boost --library=zlib --library=openmp  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-1022-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: 581f101 (2025-05-05 21:13:30 +0200)
count: 292 297
elapsed-time: 1.1 1.2
head-timing-info:

old-timing-info:

head results:
berkeleylab-metabat-0db17a40717d/src/contigOverlaps.cpp:36:36: error: There is an unknown macro here somewhere. Configuration is required. If VERSION is a macro then please configure it. [unknownMacro]
berkeleylab-metabat-0db17a40717d/src/jgi_summarize_bam_contig_depths.cpp:37:53: error: There is an unknown macro here somewhere. Configuration is required. If VERSION is a macro then please configure it. [unknownMacro]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:403:51: debug: Function::addArguments found argument 'v' with varid 0. [varid0]
berkeleylab-metabat-0db17a40717d/src/ranker.h:16:1: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/ranker.h:23:1: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/ranker.h:31:1: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:28:1: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:26:1: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:142:3: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:45:1: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:523:3: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:590:30: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:596:5: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:604:30: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:619:5: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:634:30: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:995:11: debug: SymbolDatabase couldn't resolve all user defined types. [debug]
berkeleylab-metabat-0db17a40717d/src/igraph.h:224:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/igraph.h:287:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/igraph.h:301:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/igraph.h:354:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:254:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:266:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:274:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:292:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:339:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:582:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:52:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1004:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vertex_index [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1076:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1329:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1407:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1451:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1757:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1789:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1822:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eofbit [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:146:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:152:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:158:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:164:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:170:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:176:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:182:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:188:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:194:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:200:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:206:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:212:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:218:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:224:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:230:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ranker.h:236:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:115:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:207:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:211:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:259:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:323:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:356:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SLOT_PER_BUCKET [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:121:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OFFSET_BITS [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:145:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:152:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:158:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:256:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OFFSET_BITS [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:96:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SLOT_PER_BUCKET [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:102:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOCK_ARRAY_GRANULARITY [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:239:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:248:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:266:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:275:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:403:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable v [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:610:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i1 [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:612:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i2 [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1165:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOCK_T [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1335:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1442:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1800:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1930:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1933:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1951:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1958:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1992:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1998:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2003:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2032:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2045:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buckets_ [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2084:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable status [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:208:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:220:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:270:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:277:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:374:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:34:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1051:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1082:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1114:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eofbit [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1168:134: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1373:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
berkeleylab-metabat-0db17a40717d/src/ProgressTracker.h:10:2: warning: Member variable 'ProgressTracker::msg' is not initialized in the constructor. [uninitMemberVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1233:5: warning:inconclusive: Member variable 'b_slot::depth' is not initialized in the constructor. [uninitMemberVar]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1666:7: warning:inconclusive: Member variable 'const_iterator::buckets_' is not initialized in the constructor. [uninitMemberVar]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:347:36: style:inconclusive: Technically the member function 'libcuckoo_bucket_container::transfer' can be const. [functionConst]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:149:10: performance:inconclusive: Technically the member function 'libcuckoo_lock_array::spinlock::lock' can be static (but you may consider moving to unnamed namespace). [functionStatic]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:155:10: performance:inconclusive: Technically the member function 'libcuckoo_lock_array::spinlock::unlock' can be static (but you may consider moving to unnamed namespace). [functionStatic]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:161:10: performance:inconclusive: Technically the member function 'libcuckoo_lock_array::spinlock::try_lock' can be static (but you may consider moving to unnamed namespace). [functionStatic]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1279:15: performance:inconclusive: Technically the member function 'cuckoohash_map::b_queue::increment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:246:9: style:inconclusive: Technically the member function 'Graph::getNodeCount' can be const. [functionConst]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:250:9: style:inconclusive: Technically the member function 'Graph::getEdgeCount' can be const. [functionConst]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1799:17: warning: The class 'iterator' defines member function with name 'operator*' also defined in its parent class 'const_iterator'. [duplInheritedMember]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1679:17: note: Parent function 'const_iterator::operator*'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1799:17: note: Derived function 'iterator::operator*'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1804:15: warning: The class 'iterator' defines member function with name 'operator->' also defined in its parent class 'const_iterator'. [duplInheritedMember]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1681:15: note: Parent function 'const_iterator::operator->'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1804:15: note: Derived function 'iterator::operator->'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1806:17: warning: The class 'iterator' defines member function with name 'operator++' also defined in its parent class 'const_iterator'. [duplInheritedMember]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1685:23: note: Parent function 'const_iterator::operator++'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1806:17: note: Derived function 'iterator::operator++'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1811:16: warning: The class 'iterator' defines member function with name 'operator++' also defined in its parent class 'const_iterator'. [duplInheritedMember]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1703:22: note: Parent function 'const_iterator::operator++'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1811:16: note: Derived function 'iterator::operator++'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1817:17: warning: The class 'iterator' defines member function with name 'operator--' also defined in its parent class 'const_iterator'. [duplInheritedMember]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1711:23: note: Parent function 'const_iterator::operator--'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1817:17: note: Derived function 'iterator::operator--'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1822:16: warning: The class 'iterator' defines member function with name 'operator--' also defined in its parent class 'const_iterator'. [duplInheritedMember]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1736:22: note: Parent function 'const_iterator::operator--'
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1822:16: note: Derived function 'iterator::operator--'
berkeleylab-metabat-0db17a40717d/src/ProgressTracker.h:10:2: style: Class 'ProgressTracker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/ranker.h:37:2: style: Class 'ranker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_util.hh:88:3: style: Class 'libcuckoo_load_factor_too_low' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_util.hh:119:3: style: Class 'libcuckoo_maximum_hashpower_exceeded' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:48:3: style: Class 'libcuckoo_lock_array' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:118:3: style: Class 'cuckoohash_map' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:636:5: style: Class 'AllBuckets' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2169:5: style: Class 'locked_table' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:237:2: style: Class 'Graph' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: warning: If memory allocation fails, then there is a possible null pointer dereference: ks [nullPointerOutOfMemory]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: note: Assuming allocation function fails
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: note: Assignment 'ks=(struct kstream_t*)calloc(1,sizeof(struct kstream_t))', assigned value is 0
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: note: Null pointer dereference
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: note: Assuming allocation function fails
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: note: Assignment 's=(struct kseq_t*)calloc(1,sizeof(struct kseq_t))', assigned value is 0
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: note: Null pointer dereference
berkeleylab-metabat-0db17a40717d/src/metabat2.h:352:26: warning: If resource allocation fails, then there is a possible null pointer dereference: file [nullPointerOutOfResources]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:348:20: note: Assuming allocation function fails
berkeleylab-metabat-0db17a40717d/src/metabat2.h:348:20: note: Assignment 'file=fopen("/proc/meminfo","r")', assigned value is 0
berkeleylab-metabat-0db17a40717d/src/metabat2.h:352:26: note: Null pointer dereference
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1225:4: warning: If memory allocation fails, then there is a possible null pointer dereference: matrix [nullPointerOutOfMemory]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1220:50: note: Assuming allocation function fails
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1220:30: note: Assignment 'matrix=(Similarity*)malloc(_nobs*nobs*sizeof(Similarity))', assigned value is 0
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1225:4: note: Null pointer dereference
berkeleylab-metabat-0db17a40717d/src/metabat2.h:31:1: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1220:30: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1231:9: style: The scope of the variable 'cov' can be reduced. [variableScope]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1453:12: style: The scope of the variable 'ii' can be reduced. [variableScope]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1739:17: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:679:19: style: Local variable 'i' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:645:16: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:679:19: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1166:28: style: Local variable 'sTNF' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1148:23: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1166:28: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1357:11: style: Local variable 'bases' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:151:19: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1357:11: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:53:40: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:57:34: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:61:35: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:64:38: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:68:41: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:71:35: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:73:33: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:74:34: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:76:29: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:77:30: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:84:56: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:88:50: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:218:32: performance:inconclusive: Function parameter 'i' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:219:38: performance:inconclusive: Function parameter 'i' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:275:25: performance:inconclusive: Function parameter 'new_hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:334:31: performance:inconclusive: Function parameter 'dst_ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:334:50: performance:inconclusive: Function parameter 'dst_slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:335:31: performance:inconclusive: Function parameter 'src_slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:340:31: performance:inconclusive: Function parameter 'dst_ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:340:50: performance:inconclusive: Function parameter 'dst_slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:341:31: performance:inconclusive: Function parameter 'src_slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:48:34: performance:inconclusive: Function parameter 'target' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:106:34: performance:inconclusive: Function parameter 'i' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:111:40: performance:inconclusive: Function parameter 'i' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:196:32: performance:inconclusive: Function parameter 'src' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:256:42: performance:inconclusive: Function parameter 'i' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_lock_array.hh:259:41: performance:inconclusive: Function parameter 'i' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:118:28: performance:inconclusive: Function parameter 'n' should be passed by const reference. However it seems that 'cuckoohash_map' is a callback function. [passedByValueCallback]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2179:18: note: Function pointer used here.
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:118:28: note: Function parameter 'n' should be passed by const reference. However it seems that 'cuckoohash_map' is a callback function.
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:539:52: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:545:52: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:553:48: performance:inconclusive: Function parameter 'hash' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:566:54: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:566:74: performance:inconclusive: Function parameter 'hv' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:575:53: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:575:73: performance:inconclusive: Function parameter 'partial' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:576:53: performance:inconclusive: Function parameter 'index' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:665:47: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:665:67: performance:inconclusive: Function parameter 'lock' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:677:53: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:678:53: performance:inconclusive: Function parameter 'i' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:690:47: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:690:67: performance:inconclusive: Function parameter 'i1' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:691:47: performance:inconclusive: Function parameter 'i2' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:712:30: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:712:50: performance:inconclusive: Function parameter 'i1' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:712:70: performance:inconclusive: Function parameter 'i2' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:713:30: performance:inconclusive: Function parameter 'i3' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:772:52: performance:inconclusive: Function parameter 'bucket_ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:806:60: performance:inconclusive: Function parameter 'partial' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:807:46: performance:inconclusive: Function parameter 'i1' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:807:66: performance:inconclusive: Function parameter 'i2' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:822:61: performance:inconclusive: Function parameter 'partial' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:957:38: performance:inconclusive: Function parameter 'bucket_ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:957:66: performance:inconclusive: Function parameter 'slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:958:38: performance:inconclusive: Function parameter 'partial' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:971:47: performance:inconclusive: Function parameter 'partial' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1078:41: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1079:41: performance:inconclusive: Function parameter 'i1' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1079:61: performance:inconclusive: Function parameter 'i2' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1139:40: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1206:50: performance:inconclusive: Function parameter 'a' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1206:63: performance:inconclusive: Function parameter 'b' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1234:28: performance:inconclusive: Function parameter 'b' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1234:47: performance:inconclusive: Function parameter 'p' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1279:35: performance:inconclusive: Function parameter 'ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1292:38: performance:inconclusive: Function parameter 'hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1292:58: performance:inconclusive: Function parameter 'i1' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1293:38: performance:inconclusive: Function parameter 'i2' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1373:49: performance:inconclusive: Function parameter 'end' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1436:55: performance:inconclusive: Function parameter 'orig_hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1437:55: performance:inconclusive: Function parameter 'new_hp' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1474:76: performance:inconclusive: Function parameter 'end' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1531:40: performance:inconclusive: Function parameter 'bucket_ind' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1531:68: performance:inconclusive: Function parameter 'slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1557:60: performance:inconclusive: Function parameter 'n' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1570:49: performance:inconclusive: Function parameter 'n' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1768:32: performance:inconclusive: Function parameter 'slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1829:46: performance:inconclusive: Function parameter 'index' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1829:63: performance:inconclusive: Function parameter 'slot' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:274:51: performance: Function parameter 'label' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:274:65: performance: Function parameter 'seq' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:901:13: style: Variable 'b1' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:906:13: style: Variable 'b2' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1255:15: style: Variable 'x' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:369:87: style: Parameter 'node_order' can be declared as reference to const [constParameterReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:412:25: style: Variable 'ineis' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:497:11: style: Variable 's' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1361:18: style: Variable 'label' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1365:19: style: Variable 'seq' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1422:19: style: Variable 'label' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1426:20: style: Variable 'seq' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:236:13: style: Variable 's' can be declared as pointer to const [constVariablePointer]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:419:28: performance: Searching before insertion is not necessary. Instead of 'neighbor_scores[k]=0.' consider using 'neighbor_scores.try_emplace(k, 0.);'. [stlFindInsert]
berkeleylab-metabat-0db17a40717d/src/metabat2.h:271:11: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2141:7: style: Consider using std::all_of or std::none_of algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:2154:7: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:708:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:710:16: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:721:7: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:752:18: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:865:16: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:887:16: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1259:50: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: warning: If memory allocation fails, then there is a possible null pointer dereference: ks [nullPointerOutOfMemory]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: note: Assuming allocation function fails
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: note: Assignment 'ks=(struct kstream_t*)calloc(1,sizeof(struct kstream_t))', assigned value is 0
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: note: Null pointer dereference
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: note: Assuming allocation function fails
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: note: Assignment 's=(struct kseq_t*)calloc(1,sizeof(struct kseq_t))', assigned value is 0
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: note: Null pointer dereference
berkeleylab-metabat-0db17a40717d/src/metabat1.h:534:26: warning: If resource allocation fails, then there is a possible null pointer dereference: file [nullPointerOutOfResources]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:530:23: note: Assuming allocation function fails
berkeleylab-metabat-0db17a40717d/src/metabat1.h:530:23: note: Assignment 'file=fopen("/proc/meminfo","r")', assigned value is 0
berkeleylab-metabat-0db17a40717d/src/metabat1.h:534:26: note: Null pointer dereference
berkeleylab-metabat-0db17a40717d/src/igraph.h:31:41: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:55:7: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:67:41: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:68:2: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:77:41: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:224:18: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:239:3: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:301:8: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:354:8: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/igraph.h:430:2: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:30:1: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:728:12: style: C-style pointer casting [cstyleCast]
berkeleylab-metabat-0db17a40717d/src/libcuckoo_bucket_container.hh:364:18: style: Variable 'dst.buckets_' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:236:15: style: Variable 's' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:498:14: style: Variable 'tn' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/igraph.h:369:11: style: The scope of the variable 'k' can be reduced. [variableScope]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1562:12: style: The scope of the variable 'ii' can be reduced. [variableScope]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1231:13: style: Variable 'cov' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1267:9: style: Variable 'cov' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/igraph.h:221:11: style: Checking if unsigned expression 'size' is less than zero. [unsignedLessThanZero]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1303:12: style: Variable 's' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1303:20: style: Variable 's1' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1303:10: style: Variable 's' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1303:17: style: Variable 's1' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1327:10: style: Variable 'kk' is assigned a value that is never used. [unreadVariable]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1200:7: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1416:34: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:609:12: style: Local variable 'fished' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:572:8: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:609:12: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1369:21: style: Local variable 'v' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1336:20: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1369:21: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1627:11: style: Local variable 'p1' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:99:19: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1627:11: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1627:29: style: Local variable 'p2' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:100:19: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1627:29: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1642:12: style: Local variable 'p1' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:99:19: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1642:12: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1642:23: style: Local variable 'p2' shadows outer variable [shadowVariable]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:100:19: note: Shadowed declaration
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1642:23: note: Shadow variable
berkeleylab-metabat-0db17a40717d/src/metabat1.h:278:34: performance: Function parameter 'saveTNFFile' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:316:32: performance: Function parameter 'saveTNFFile' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:328:39: performance: Function parameter 'saveDistanceFile' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:369:37: performance: Function parameter 'saveDistanceFile' should be passed by const reference. [passedByValue]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:384:60: style: Parameter 'boot' can be declared as reference to const [constParameterReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:443:18: style: Variable 's' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:890:18: style: Variable 'label' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:894:19: style: Variable 'seq' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:970:20: style: Variable 'seq' can be declared as reference to const [constVariableReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1207:89: style: Parameter 'good_class_ids' can be declared as reference to const [constParameterReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1277:40: style: Parameter 'medoid_ids' can be declared as reference to const [constParameterReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1277:78: style: Parameter 'leftovers' can be declared as reference to const [constParameterReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1277:102: style: Parameter 'good_class_ids' can be declared as reference to const [constParameterReference]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:629:27: performance: Searching before insertion is not necessary. Instead of 'label_counters[k]=0.' consider using 'label_counters.try_emplace(k, 0.);'. [stlFindInsert]
berkeleylab-metabat-0db17a40717d/src/metabat1.h:275:11: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:585:9: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:843:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:913:14: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
berkeleylab-metabat-0db17a40717d/src/metabat1.cpp:1260:73: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
diff:
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1581:25: performance:inconclusive: Function parameter 'dst_bucket' should be passed by const reference. [passedByValue]
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1581:47: performance:inconclusive: Function parameter 'dst_slot' should be passed by const reference. [passedByValue]
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1581:67: performance:inconclusive: Function parameter 'src_bucket' should be passed by const reference. [passedByValue]
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:1582:25: performance:inconclusive: Function parameter 'src_slot' should be passed by const reference. [passedByValue]
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:682:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOCK_T [valueFlowBailoutIncompleteVar]
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:702:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOCK_T [valueFlowBailoutIncompleteVar]
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:730:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOCK_T [valueFlowBailoutIncompleteVar]
2.17.0 berkeleylab-metabat-0db17a40717d/src/cuckoohash_map.hh:768:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOCK_T [valueFlowBailoutIncompleteVar]
head berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1259:50: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
head berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1303:10: style: Variable 's' is assigned a value that is never used. [unreadVariable]
head berkeleylab-metabat-0db17a40717d/src/metabat2.cpp:1303:17: style: Variable 's1' is assigned a value that is never used. [unreadVariable]


DONE