sagnikbanerjee15 / abridge Goto Github PK

gcc -Ofast -g -Isubmodules/htslib -fvisibility=hidden -fpic -c -Wall   -c -o src/compute_information_for_better_memory_management.o src/compute_information_for_better_memory_management.c
src/compute_information_for_better_memory_management.c: In function 'findMaximumNumberOfReadsMappedToOneNucleotide':
src/compute_information_for_better_memory_management.c:124:13: warning: unused variable 'aln' [-Wunused-variable]
  124 |     bam1_t *aln = bam_init1(); // initialize an alignment
      |             ^~~
src/compute_information_for_better_memory_management.c:123:16: warning: variable 'bamHdr' set but not used [-Wunused-but-set-variable]
  123 |     bam_hdr_t *bamHdr;         // read header
      |                ^~~~~~
src/compute_information_for_better_memory_management.c:113:43: warning: variable 'curr_value' set but not used [-Wunused-but-set-variable]
  113 |     unsigned long long int curr_position, curr_value;
      |                                           ^~~~~~~~~~
src/compute_information_for_better_memory_management.c:108:9: warning: variable 'number_of_fields' set but not used [-Wunused-but-set-variable]
  108 |     int number_of_fields;
      |         ^~~~~~~~~~~~~~~~
src/compute_information_for_better_memory_management.c:107:15: warning: unused variable 'k' [-Wunused-variable]
  107 |     int i, j, k;
      |               ^
src/compute_information_for_better_memory_management.c:107:12: warning: unused variable 'j' [-Wunused-variable]
  107 |     int i, j, k;
      |            ^
In file included from src/compute_information_for_better_memory_management.c:9:
src/function_definitions.h: In function 'convertUnsignedIntegerToString':
src/function_definitions.h:226:1: warning: control reaches end of non-void function [-Wreturn-type]
  226 | }
      | ^
src/compute_information_for_better_memory_management.c: In function 'findMaximumNumberOfReadsMappedToOneNucleotide':
src/compute_information_for_better_memory_management.c:193:24: warning: 'fhr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  193 |     while ((line_len = getline(&line, &len, fhr)) != -1)
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Lsubmodules/htslib -Wl,-rpath=/software/abridge/Abridge/submodules/htslib -lhts  src/compute_information_for_better_memory_management.o   -o src/compute_information_for_better_memory_management
/usr/bin/ld: src/compute_information_for_better_memory_management.o: in function `findMaximumNumberOfReadsMappedToOneNucleotide':
/software/abridge/Abridge/src/compute_information_for_better_memory_management.c:124: undefined reference to `bam_init1'
/usr/bin/ld: /software/abridge/Abridge/src/compute_information_for_better_memory_management.c:150: undefined reference to `hts_open'
/usr/bin/ld: /software/abridge/Abridge/src/compute_information_for_better_memory_management.c:151: undefined reference to `sam_hdr_read'
collect2: error: ld returned 1 exit status
make: *** [<builtin>: src/compute_information_for_better_memory_management] Error 1
rm src/compute_information_for_better_memory_management.o