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May 20, 2016 11:09
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GKNO build failure - cat build_freebayes.*
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| $ cat build_freebayes.* | |
| bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function] | |
| KHASH_MAP_INIT_INT64(cache, cache_t) | |
| ^ | |
| ./khash.h:468:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' | |
| KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) | |
| ^ | |
| ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' | |
| static inline void kh_clear_##name(kh_##name##_t *h) \ | |
| ^ | |
| <scratch space>:33:1: note: expanded from here | |
| kh_clear_cache | |
| ^ | |
| 1 warning generated. | |
| index.c:34:1: warning: unused function 'kh_clear_i' [-Wunused-function] | |
| KHASH_MAP_INIT_INT(i, ti_binlist_t) | |
| ^ | |
| ./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' | |
| KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) | |
| ^ | |
| ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' | |
| static inline void kh_clear_##name(kh_##name##_t *h) \ | |
| ^ | |
| <scratch space>:60:1: note: expanded from here | |
| kh_clear_i | |
| ^ | |
| index.c:34:1: warning: unused function 'kh_del_i' [-Wunused-function] | |
| ./khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' | |
| KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) | |
| ^ | |
| ./khash.h:259:21: note: expanded from macro 'KHASH_INIT' | |
| static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ | |
| ^ | |
| <scratch space>:74:1: note: expanded from here | |
| kh_del_i | |
| ^ | |
| index.c:35:1: warning: unused function 'kh_clear_s' [-Wunused-function] | |
| KHASH_MAP_INIT_STR(s, int) | |
| ^ | |
| ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' | |
| KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) | |
| ^ | |
| ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' | |
| static inline void kh_clear_##name(kh_##name##_t *h) \ | |
| ^ | |
| <scratch space>:89:1: note: expanded from here | |
| kh_clear_s | |
| ^ | |
| index.c:35:1: warning: unused function 'kh_del_s' [-Wunused-function] | |
| ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' | |
| KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) | |
| ^ | |
| ./khash.h:259:21: note: expanded from macro 'KHASH_INIT' | |
| static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ | |
| ^ | |
| <scratch space>:103:1: note: expanded from here | |
| kh_del_s | |
| ^ | |
| Fasta.cpp:90:1: warning: control reaches end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| bedidx.c:20:1: warning: unused function 'kh_clear_reg' [-Wunused-function] | |
| KHASH_MAP_INIT_STR(reg, bed_reglist_t) | |
| ^ | |
| ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' | |
| KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) | |
| ^ | |
| ./khash.h:140:21: note: expanded from macro 'KHASH_INIT' | |
| static inline void kh_clear_##name(kh_##name##_t *h) \ | |
| ^ | |
| <scratch space>:263:1: note: expanded from here | |
| kh_clear_reg | |
| ^ | |
| bedidx.c:20:1: warning: unused function 'kh_del_reg' [-Wunused-function] | |
| ./khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' | |
| KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) | |
| ^ | |
| ./khash.h:259:21: note: expanded from macro 'KHASH_INIT' | |
| static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ | |
| ^ | |
| <scratch space>:9:1: note: expanded from here | |
| kh_del_reg | |
| ^ | |
| Allele.cpp:160:13: warning: enumeration values 'ALLELE_GENOTYPE' and 'ALLELE_NULL' not handled in switch [-Wswitch] | |
| switch (this->type) { | |
| ^ | |
| Allele.cpp:183:1: warning: control may reach end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| Sample.cpp:146:1: warning: control reaches end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| Sample.cpp:158:1: warning: control reaches end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| 2 warnings generated. | |
| 4 warnings generated. | |
| clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated | |
| Genotype.cpp:1306:67: warning: equality comparison result unused [-Wunused-comparison] | |
| allelesWithHomozygousCombos[genotype->front().allele] == true; | |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ | |
| Genotype.cpp:1306:67: note: use '=' to turn this equality comparison into an assignment | |
| allelesWithHomozygousCombos[genotype->front().allele] == true; | |
| ^~ | |
| = | |
| ../vcflib/smithwaterman/LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses] | |
| && (indel.insertion && indel.position == referenceSequence.size() | |
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| ../vcflib/smithwaterman/LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning | |
| && (indel.insertion && indel.position == referenceSequence.size() | |
| ^ | |
| ( ) | |
| LeftAlign.cpp:679:26: warning: '&&' within '||' [-Wlogical-op-parentheses] | |
| && (indel.insertion && indel.position == referenceSequence.size() | |
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| LeftAlign.cpp:679:26: note: place parentheses around the '&&' expression to silence this warning | |
| && (indel.insertion && indel.position == referenceSequence.size() | |
| ^ | |
| ( ) | |
| 1 warning generated. | |
| ../vcflib/src/Variant.cpp:214:5: warning: control may reach end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| 1 warning generated. | |
| ../vcflib/src/Variant.cpp:336:5: warning: control may reach end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| ../vcflib/src/Variant.cpp:370:5: warning: control may reach end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| 1 warning generated. | |
| ../vcflib/src/Variant.cpp:408:5: warning: control may reach end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| ld: warning: option -s is obsolete and being ignored | |
| ld: internal error: atom not found in symbolIndex(__ZNKSt3__16vectorINS_4pairIicEENS_9allocatorIS2_EEE14__annotate_newEm) for architecture x86_64 | |
| clang: error: linker command failed with exit code 1 (use -v to see invocation) | |
| make[2]: *** [smithwaterman] Error 1 | |
| make[2]: *** Waiting for unfinished jobs.... | |
| CMake Warning (dev): | |
| Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake | |
| --help-policy CMP0042" for policy details. Use the cmake_policy command to | |
| set the policy and suppress this warning. | |
| MACOSX_RPATH is not specified for the following targets: | |
| BamTools | |
| This warning is for project developers. Use -Wno-dev to suppress it. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| make[1]: *** [../vcflib/smithwaterman/SmithWatermanGotoh.o] Error 2 | |
| make[1]: *** Waiting for unfinished jobs.... | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.cpp:11: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.cpp:11: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.cpp:15: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] | |
| class SamReadGroup; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here | |
| struct API_EXPORT SamReadGroup { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? | |
| class SamReadGroup; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] | |
| class SamSequence; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here | |
| struct API_EXPORT SamSequence { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? | |
| class SamSequence; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:1: warning: 'SamHeader' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamReader.cpp:11: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:1: warning: 'SamHeader' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamReader.cpp:11: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| 2 warnings generated. | |
| 2 warnings generated. | |
| 1 warning generated. | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.cpp:15: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] | |
| class SamReadGroup; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here | |
| struct API_EXPORT SamReadGroup { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? | |
| class SamReadGroup; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] | |
| class SamSequence; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here | |
| struct API_EXPORT SamSequence { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? | |
| class SamSequence; | |
| ^~~~~ | |
| struct | |
| 3 warnings generated. | |
| 2 warnings generated. | |
| 3 warnings generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:23: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:1: warning: 'BamAlignment' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamWriter_p.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.cpp:14: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:11: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:23: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:1: warning: 'BamAlignment' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamWriter_p.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamWriter_p.h:30:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.cpp:14: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:11: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| 1 warning generated. | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:11: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:11: | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamReader_p.h:28: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/bam/BamRandomAccessController_p.h:28:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| 1 warning generated. | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] | |
| return m_ip4Address < m_ip4Address; | |
| ^ | |
| 2 warnings generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct TcpSocketEngine { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? | |
| class TcpSocketEngine; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/HttpHeader_p.cpp:33:19: warning: unused variable 'TAB_CHAR' [-Wunused-const-variable] | |
| static const char TAB_CHAR = '\t'; | |
| ^ | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp:15: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct TcpSocketEngine { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? | |
| class TcpSocketEngine; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| 1 warning generated. | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct TcpSocketEngine { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? | |
| class TcpSocketEngine; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] | |
| return m_ip4Address < m_ip4Address; | |
| ^ | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct TcpSocketEngine { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? | |
| class TcpSocketEngine; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.cpp:15: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct TcpSocketEngine { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? | |
| class TcpSocketEngine; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_unix_p.cpp:10: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocketEngine_p.h:33:1: warning: 'TcpSocketEngine' defined as a struct here but previously declared as a class [-Wmismatched-tags] | |
| struct TcpSocketEngine { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/TcpSocket_p.h:32:1: note: did you mean struct here? | |
| class TcpSocketEngine; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/io/HttpHeader_p.cpp:33:19: warning: unused variable 'TAB_CHAR' [-Wunused-const-variable] | |
| static const char TAB_CHAR = '\t'; | |
| ^ | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatParser_p.h:28:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] | |
| class SamReadGroup; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here | |
| struct API_EXPORT SamReadGroup { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? | |
| class SamReadGroup; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] | |
| class SamSequence; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here | |
| struct API_EXPORT SamSequence { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? | |
| class SamSequence; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| 1 warning generated. | |
| 1 warning generated. | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamFormatPrinter_p.h:28:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.cpp:12: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:29:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: warning: class 'SamReadGroup' was previously declared as a struct [-Wmismatched-tags] | |
| class SamReadGroup; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamReadGroup.h:18:19: note: previous use is here | |
| struct API_EXPORT SamReadGroup { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:30:1: note: did you mean struct here? | |
| class SamReadGroup; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: warning: class 'SamSequence' was previously declared as a struct [-Wmismatched-tags] | |
| class SamSequence; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamSequence.h:18:19: note: previous use is here | |
| struct API_EXPORT SamSequence { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/internal/sam/SamHeaderValidator_p.h:31:1: note: did you mean struct here? | |
| class SamSequence; | |
| ^~~~~ | |
| struct | |
| 1 warning generated. | |
| 1 warning generated. | |
| 1 warning generated. | |
| 3 warnings generated. | |
| 1 warning generated. | |
| 3 warnings generated. | |
| 1 warning generated. | |
| 1 warning generated. | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/utils/bamtools_fasta.cpp:90:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] | |
| if (seqLength < 0) | |
| ~~~~~~~~~ ^ ~ | |
| 1 warning generated. | |
| 1 warning generated. | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] | |
| if ( (argc == 1) ) return Help(argc, argv); | |
| ~~~~~^~~~ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: note: remove extraneous parentheses around the comparison to silence this warning | |
| if ( (argc == 1) ) return Help(argc, argv); | |
| ~ ^ ~ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools.cpp:149:16: note: use '=' to turn this equality comparison into an assignment | |
| if ( (argc == 1) ) return Help(argc, argv); | |
| ^~ | |
| = | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_sort.cpp:14: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_merge.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_sort.cpp:79:1: warning: 'SortToolPrivate' defined as a class here but previously declared as a struct [-Wmismatched-tags] | |
| class SortTool::SortToolPrivate { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_sort.h:31:9: note: did you mean class here? | |
| struct SortToolPrivate; | |
| ^~~~~~ | |
| class | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_revert.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_random.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_split.cpp:15: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| In file included from /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:13: | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: warning: class 'BamAlignment' was previously declared as a struct [-Wmismatched-tags] | |
| class BamAlignment; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamAlignment.h:32:19: note: previous use is here | |
| struct API_EXPORT BamAlignment { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:19:1: note: did you mean struct here? | |
| class BamAlignment; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: warning: class 'SamHeader' was previously declared as a struct [-Wmismatched-tags] | |
| class SamHeader; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/SamHeader.h:22:19: note: previous use is here | |
| struct API_EXPORT SamHeader { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/api/BamWriter.h:20:1: note: did you mean struct here? | |
| class SamHeader; | |
| ^~~~~ | |
| struct | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_split.cpp:108:1: warning: 'SplitToolPrivate' defined as a class here but previously declared as a struct [-Wmismatched-tags] | |
| class SplitTool::SplitToolPrivate { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_split.h:32:9: note: did you mean class here? | |
| struct SplitToolPrivate; | |
| ^~~~~~ | |
| class | |
| 1 warning generated. | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_filter.cpp:368:1: warning: 'FilterToolPrivate' defined as a class here but previously declared as a struct [-Wmismatched-tags] | |
| class FilterTool::FilterToolPrivate { | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_filter.h:31:9: note: did you mean class here? | |
| struct FilterToolPrivate; | |
| ^~~~~~ | |
| class | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:48:19: warning: unused variable 'OPEN_BRACE_CHAR' [-Wunused-const-variable] | |
| static const char OPEN_BRACE_CHAR = '['; | |
| ^ | |
| /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/src/toolkit/bamtools_resolve.cpp:49:19: warning: unused variable 'CLOSE_BRACE_CHAR' [-Wunused-const-variable] | |
| static const char CLOSE_BRACE_CHAR = ']'; | |
| ^ | |
| 2 warnings generated. | |
| 4 warnings generated. | |
| 2 warnings generated. | |
| 2 warnings generated. | |
| 3 warnings generated. | |
| 3 warnings generated. | |
| 4 warnings generated. | |
| 3 warnings generated. | |
| make: *** [all] Error 2 | |
| cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make autoversion | |
| DETECTED_VERSION = v0.9.21 | |
| CURRENT_VERSION = | |
| Updating version file. | |
| touch src/version_git.h | |
| wget -q http://hypervolu.me/freebayes/build/v0.9.21 & | |
| cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make | |
| cd ../bamtools && mkdir -p build && cd build && cmake .. && /Applications/Xcode.app/Contents/Developer/usr/bin/make | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c BedReader.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c CNV.cpp | |
| gcc -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c fastlz.c | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Fasta.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Parameters.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Allele.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Sample.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Result.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Utility.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Genotype.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c DataLikelihood.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Multinomial.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Ewens.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c ResultData.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Dirichlet.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Marginals.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c split.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c IndelAllele.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c Bias.cpp | |
| g++ -c -o Contamination.o Contamination.cpp | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c SegfaultHandler.cpp | |
| g++ -c -o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/tabix.cpp | |
| DETECTED_VERSION = v0.9.21 | |
| CURRENT_VERSION = v0.9.21 | |
| cd ../vcflib/tabixpp && /Applications/Xcode.app/Contents/Developer/usr/bin/make | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o | |
| cd ../vcflib/smithwaterman && /Applications/Xcode.app/Contents/Developer/usr/bin/make | |
| c++ -c -o smithwaterman.o smithwaterman.cpp | |
| -- The C compiler identification is AppleClang 7.0.2.7000181 | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o | |
| c++ -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp | |
| -- The CXX compiler identification is AppleClang 7.0.2.7000181 | |
| -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o | |
| -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works | |
| -- Detecting C compiler ABI info | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o | |
| c++ -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp | |
| -- Detecting C compiler ABI info - done | |
| -- Detecting C compile features | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o | |
| c++ -c -o Repeats.o Repeats.cpp | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o | |
| g++ -c -o ../vcflib/smithwaterman/LeftAlign.o ../vcflib/smithwaterman/LeftAlign.cpp | |
| gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o | |
| c++ -c -o LeftAlign.o LeftAlign.cpp | |
| g++ -c -o ../vcflib/smithwaterman/Repeats.o ../vcflib/smithwaterman/Repeats.cpp | |
| -- Detecting C compile features - done | |
| -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ | |
| c++ -c -o IndelAllele.o IndelAllele.cpp | |
| gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz | |
| g++ -c -o ../vcflib/smithwaterman/IndelAllele.o ../vcflib/smithwaterman/IndelAllele.cpp | |
| ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o | |
| g++ -c -o disorder.o disorder.c | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c ../vcflib/src/Variant.cpp | |
| ranlib libtabix.a | |
| gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz | |
| -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works | |
| -- Detecting CXX compiler ABI info | |
| g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../bamtools/src -I../ttmath -I../vcflib/src -I../vcflib/ -c bamleftalign.cpp | |
| g++ -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz | |
| -- Detecting CXX compiler ABI info - done | |
| -- Detecting CXX compile features | |
| -- Detecting CXX compile features - done | |
| -- Configuring done | |
| ld -r disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -o sw.o | |
| * linking smithwaterman | |
| -- Generating done | |
| -- Build files have been written to: /Users/Bede/Desktop/gkno/gkno_launcher/tools/freebayes/bamtools/build | |
| Scanning dependencies of target SharedHeaders | |
| Scanning dependencies of target AlgorithmsHeaders | |
| Scanning dependencies of target APIHeaders | |
| Scanning dependencies of target jsoncpp | |
| [ 3%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o | |
| [ 2%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o | |
| [ 3%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o | |
| [ 3%] Built target SharedHeaders | |
| [ 3%] Built target AlgorithmsHeaders | |
| Scanning dependencies of target BamTools-static | |
| Scanning dependencies of target BamTools | |
| [ 4%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o | |
| [ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o | |
| [ 8%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o | |
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| [ 37%] Built target jsoncpp | |
| [ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o | |
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| [100%] Linking CXX executable ../../../bin/bamtools | |
| [100%] Built target bamtools_cmd | |
| $ |
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