>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rSFFreader.buildbin-libdir rSFFreader_0.8.0.tar.gz'
>>>>>>>
* installing *source* package 'rSFFreader' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_rSFFreader.c -o R_init_rSFFreader.o
R_init_rSFFreader.c:21:2: warning: extra ';' outside of a function [-Wextra-semi]
};
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c SFF-io.c -o SFF-io.o
SFF-io.c:280:5: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
fres - fread( &commonHeader.flowgram_format_code, sizeof(uint8_t),1, file);
^˜˜˜ ˜
SFF-io.c:280:10: warning: expression result unused [-Wunused-value]
fres - fread( &commonHeader.flowgram_format_code, sizeof(uint8_t),1, file);
˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:250:13: warning: unused variable 'uint8' [-Wunused-variable]
uint8_t uint8;
^
SFF-io.c:247:14: warning: unused variable 'padding_size' [-Wunused-variable]
int i, padding_size, fres;
^
SFF-io.c:249:14: warning: unused variable 'uint16' [-Wunused-variable]
uint16_t uint16;
^
SFF-io.c:258:9: warning: unused variable 'size' [-Wunused-variable]
int size = fread( &commonHeader.magic_number, sizeof(uint32_t), 1, file);
^
SFF-io.c:258:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int size = fread( &commonHeader.magic_number, sizeof(uint32_t), 1, file);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:260:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( commonHeader.version, sizeof(char), 4, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:262:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &commonHeader.index_offset, sizeof(uint64_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:265:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &commonHeader.index_length, sizeof(uint32_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:268:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &commonHeader.number_of_reads, sizeof(uint32_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:271:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &commonHeader.commonHeader_length, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:274:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &commonHeader.key_length, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:277:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &commonHeader.number_of_flows_per_read, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:291:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread(&ch, sizeof(char), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:303:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread(&ch, sizeof(char), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:348:65: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
SET_VECTOR_ELT(headerList, 1, Rf_ScalarInteger(commonHeader.magic_number));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:351:65: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
SET_VECTOR_ELT(headerList, 4, Rf_ScalarInteger(commonHeader.index_length));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:352:65: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
SET_VECTOR_ELT(headerList, 5, Rf_ScalarInteger(commonHeader.number_of_reads));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:350:65: warning: implicit conversion loses integer precision: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wshorten-64-to-32]
SET_VECTOR_ELT(headerList, 3, Rf_ScalarInteger(commonHeader.index_offset));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:549:57: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
loader_ext.cached_qual_clip.width = (int *) R_alloc((long) get_XVectorList_length(seq), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:550:57: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
loader_ext.cached_qual_clip.start = (int *) R_alloc((long) get_XVectorList_length(seq), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:552:58: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
loader_ext.cached_adapt_clip.width = (int *) R_alloc((long) get_XVectorList_length(seq), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:553:58: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
loader_ext.cached_adapt_clip.start = (int *) R_alloc((long) get_XVectorList_length(seq), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:670:35: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
data.flows[i] = uint16/100.0;
˜ ˜˜˜˜˜˜^˜˜˜˜˜
SFF-io.c:720:32: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
header.number_of_bases);
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:622:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.read_header_length, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:624:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.name_length, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:626:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.number_of_bases, sizeof(uint32_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:628:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_qual_left, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:630:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_qual_right, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:632:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_adapter_left, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:634:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_adapter_right, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:650:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( data.name, sizeof(char),header.name_length, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:654:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
dataline.length = strlen(data.name);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:668:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &uint16, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:676:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &uint8, sizeof(uint8_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:684:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &ch, sizeof(char), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:692:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
dataline.length = strlen(data.bases);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:701:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &uint8, sizeof(uint8_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:706:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
dataline.length = strlen(data.quality);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:786:74: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
(header.number_of_bases*3))+header.read_header_length-16;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
SFF-io.c:785:59: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
skip = ((commonHeader.number_of_flows_per_read*flowgram_bytes_per_flow) +
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
SFF-io.c:791:36: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
header.number_of_bases);
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:770:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.read_header_length, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:772:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.name_length, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:774:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.number_of_bases, sizeof(uint32_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:776:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_qual_left, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:778:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_qual_right, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:780:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_adapter_left, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:782:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
fres = fread( &header.clip_adapter_right, sizeof(uint16_t), 1, file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SFF-io.c:866:80: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(qclip_start), loader_ext.cached_qual_clip.start, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
SFF-io.c:866:80: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(qclip_start), loader_ext.cached_qual_clip.start, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
SFF-io.c:867:80: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(qclip_width), loader_ext.cached_qual_clip.width, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
SFF-io.c:867:80: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(qclip_width), loader_ext.cached_qual_clip.width, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
SFF-io.c:872:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(aclip_start), loader_ext.cached_adapt_clip.start, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
SFF-io.c:872:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(aclip_start), loader_ext.cached_adapt_clip.start, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
SFF-io.c:873:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(aclip_width), loader_ext.cached_adapt_clip.width, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
SFF-io.c:873:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(aclip_width), loader_ext.cached_adapt_clip.width, sizeof(int) * ans_length);
˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
59 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o SFF-io.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rSFFreader.buildbin-libdir/rSFFreader/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rSFFreader)
>>>>>>>
>>>>>>> FIXING LINKS FOR rSFFreader.buildbin-libdir/rSFFreader/libs//rSFFreader.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs//rSFFreader.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs//rSFFreader.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs//rSFFreader.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs//rSFFreader.so"