>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=seqbias.buildbin-libdir seqbias_1.8.0.tar.gz'
>>>>>>>
* installing *source* package 'seqbias' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c common.c -o common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c miscmath.c -o miscmath.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c pos_table.c -o pos_table.o
In file included from pos_table.c:2:
In file included from ./pos_table.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
pos_table.c:82:33: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
T->A[i].count = U->A[i].pos;
˜ ˜˜˜˜˜˜˜˜^˜˜
pos_table.c:245:76: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
if (bam1_strand(read)) pos = bam_calend(&read->core, bam1_cigar(read)) - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
pos_table.c:264:76: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
if (bam1_strand(read)) pos = bam_calend(&read->core, bam1_cigar(read)) - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
pos_table.c:455:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
uint64_t zeros = (end - start + 1) - nonzeros;
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜ ˜
pos_table.c:461:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
zeros -= MIN(end, xs[0].pos) - start + 1;
˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
pos_table.c:465:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
zeros -= end - MAX(start, xs[m-1].pos) + 1;
˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
pos_table.c:497:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
A[u].tid = j;
˜ ^
pos_table.c:498:35: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
A[u].strand = i;
˜ ^
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools_extra.c -o samtools_extra.o
In file included from samtools_extra.c:3:
In file included from ./samtools_extra.h:11:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from samtools_extra.c:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
samtools_extra.c:62:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
seq0 = seq = (char*)malloc( (p_end_i - p_beg_i + 2) * sizeof(char) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜ ˜
samtools_extra.c:91:73: warning: implicit conversion changes signedness: 'unsigned long long' to 'int64_t' (aka 'long long') [-Wsign-conversion]
razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools_extra.c:91:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools_extra.c:91:83: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools_extra.c:93:30: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
if (isgraph(c)) seq[l++] = tolower(c);
˜ ^˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c kmer_matrix.cpp -o kmer_matrix.o
In file included from kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:145:49: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, long long v) { return emitter.WriteIntegralType(v); }
^
./yaml-cpp/emitter.h:146:58: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, unsigned long long v) { return emitter.WriteIntegralType(v); }
^
kmer_matrix.cpp:196:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32]
kmer L_max = four_pow(h - u - 1);
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
kmer_matrix.cpp:200:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
kmer H_max = four_pow(u);
˜˜˜˜˜˜˜˜ ^
kmer_matrix.cpp:227:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
size_t N = four_pow(h);
˜˜˜˜˜˜˜˜ ^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c logger.cpp -o logger.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c motif.cpp -o motif.o
In file included from motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:145:49: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, long long v) { return emitter.WriteIntegralType(v); }
^
./yaml-cpp/emitter.h:146:58: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, unsigned long long v) { return emitter.WriteIntegralType(v); }
^
motif.cpp:744:25: warning: in-class initializer for static data member of type 'const double' is a GNU extension [-Wgnu]
static const double pseudocount = 1.0;
^ ˜˜˜
motif.cpp:247:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms0, L0, n, m, i_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:248:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms1, L1, n, m, i_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:252:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms0, L0, n, m, i_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:253:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms1, L1, n, m, i_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:260:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms0, L0, n, m, j_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:261:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms1, L1, n, m, j_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:265:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms0, L0, n, m, j_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:266:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms1, L1, n, m, j_best);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
motif.cpp:297:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P0->get_row(j, ps0_j);
˜ ^
motif.cpp:298:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P1->get_row(j, ps1_j);
˜ ^
motif.cpp:300:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P0->get_row(i, ps0_i);
˜ ^
motif.cpp:301:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P1->get_row(i, ps1_i);
˜ ^
motif.cpp:305:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
colcpy(ls0_j, L0, j, n, m);
˜˜˜˜˜˜ ^
motif.cpp:306:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
colcpy(ls1_j, L1, j, n, m);
˜˜˜˜˜˜ ^
motif.cpp:308:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
colcpy(ls0_i, L0, i, n, m);
˜˜˜˜˜˜ ^
motif.cpp:309:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
colcpy(ls1_i, L1, i, n, m);
˜˜˜˜˜˜ ^
motif.cpp:347:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms0, L0, n, m, j);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:349:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms1, L1, n, m, j);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:353:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms0, L0, n, m, i);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:355:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecaddcol(ms1, L1, n, m, i);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:384:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P0->set_row(j, ps0_j);
˜ ^
motif.cpp:385:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P1->set_row(j, ps1_j);
˜ ^
motif.cpp:387:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P0->set_row(i, ps0_i);
˜ ^
motif.cpp:388:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P1->set_row(i, ps1_i);
˜ ^
motif.cpp:392:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms0, L0, n, m, j);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:394:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms1, L1, n, m, j);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:397:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms0, L0, n, m, i);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:399:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vecsubcol(ms1, L1, n, m, i);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:404:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matsetcol(L0, ls0_j, n, m, j);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:405:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matsetcol(L1, ls1_j, n, m, j);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:407:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matsetcol(L0, ls0_i, n, m, i);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:408:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matsetcol(L1, ls1_i, n, m, i);
˜˜˜˜˜˜˜˜˜ ^
motif.cpp:438:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
else i_start = j - max_distance;
^ ˜
motif.cpp:441:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
else i_end = min(m, j + max_distance);
^ ˜
motif.cpp:453:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (M.num_parents(j) >= max_parents) continue;
˜ ^
motif.cpp:459:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (i > j && M.num_parents(j) == 1 && M.num_parents(i) == 1) continue;
˜ ^
motif.cpp:459:69: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (i > j && M.num_parents(j) == 1 && M.num_parents(i) == 1) continue;
˜ ^
motif.cpp:433:20: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
for (j = m - 1; j >= 0; --j) {
˜ ˜˜^˜˜
motif.cpp:438:34: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
else i_start = j - max_distance;
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
motif.cpp:440:50: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
if (max_distance == 0) i_end = m - 1;
˜ ˜˜^˜˜
motif.cpp:441:30: warning: implicit conversion loses integer precision: 'const unsigned long' to 'int' [-Wshorten-64-to-32]
else i_end = min(m, j + max_distance);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
motif.cpp:494:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (i == j && M.num_parents(j) > 1) continue;
˜ ^
motif.cpp:605:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
L0[i * m + j] = 0.0;
˜ ^
motif.cpp:606:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
L1[i * m + j] = 0.0;
˜ ^
motif.cpp:612:53: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if ((*seq)->make_kmer(K, 0, M.parents + j * m, m) > 0) {
^ ˜
motif.cpp:613:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
L0[i * m + j] = (*M.P0)(j, K);
˜ ^
motif.cpp:613:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
L0[i * m + j] = (*M.P0)(j, K);
˜ ^
motif.cpp:614:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
L1[i * m + j] = (*M.P1)(j, K);
˜ ^
motif.cpp:614:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
L1[i * m + j] = (*M.P1)(j, K);
˜ ^
motif.cpp:625:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P0->set_row(j, 0.0);
˜ ^
motif.cpp:626:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P1->set_row(j, 0.0);
˜ ^
motif.cpp:628:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t np = M.num_parents(j);
˜ ^
motif.cpp:637:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
(*M.P0)(j, K) = pseudocount;
˜ ^
motif.cpp:638:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
(*M.P1)(j, K) = pseudocount;
˜ ^
motif.cpp:648:53: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if ((*seq)->make_kmer(K, 0, M.parents + j * m, m) == 0) continue;
^ ˜
motif.cpp:651:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (c < n0) (*M.P0)(j, K) += 1;
˜ ^
motif.cpp:654:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
else (*M.P1)(j, K) += 1;
˜ ^
motif.cpp:666:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P0->make_conditional_distribution(j, np_pred, np);
˜ ^
motif.cpp:667:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P1->make_conditional_distribution(j, np_pred, np);
˜ ^
motif.cpp:669:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P0->dist_log_transform_row(j, np);
˜ ^
motif.cpp:670:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
M.P1->dist_log_transform_row(j, np);
˜ ^
motif.cpp:633:33: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
size_t K_max = four_pow(np);
˜˜˜˜˜˜˜˜ ^˜
motif.cpp:669:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
M.P0->dist_log_transform_row(j, np);
˜ ^˜
motif.cpp:670:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
M.P1->dist_log_transform_row(j, np);
˜ ^˜
motif.cpp:697:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
return reachability[j * m + i];
^ ˜
motif.cpp:697:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
return reachability[j * m + i];
˜ ^
motif.cpp:926:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
parents[j * m + i] = x;
^ ˜
motif.cpp:926:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
parents[j * m + i] = x;
˜ ^
motif.cpp:932:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
return parents[j * m + i];
^ ˜
motif.cpp:932:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
return parents[j * m + i];
˜ ^
motif.cpp:939:42: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
for (i = 0; i < m; ++i) if (has_edge(i, j)) ++N;
˜˜˜˜˜˜˜˜ ^
motif.cpp:939:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
for (i = 0; i < m; ++i) if (has_edge(i, j)) ++N;
˜˜˜˜˜˜˜˜ ^
motif.cpp:949:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
N += four_pow(num_parents(i)) - 1;
˜˜˜˜˜˜˜˜˜˜˜ ^
motif.cpp:949:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
N += four_pow(num_parents(i)) - 1;
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
79 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c seqbias.cpp -o seqbias.o
In file included from seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:145:49: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, long long v) { return emitter.WriteIntegralType(v); }
^
./yaml-cpp/emitter.h:146:58: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, unsigned long long v) { return emitter.WriteIntegralType(v); }
^
In file included from seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:14:
In file included from ./pos_table.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(b->data, src->data, b->data_len);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
seqbias.cpp:131:75: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sequencing_bias* seqbias = new sequencing_bias( c_ref_fn, c_reads_fn, c_n, c_L, c_R );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
seqbias.cpp:169:32: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t n = c_end - c_start + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
seqbias.cpp:366:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
kmer_matrix* c_M = new kmer_matrix( c_n, c_k );
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
seqbias.cpp:366:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
kmer_matrix* c_M = new kmer_matrix( c_n, c_k );
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
seqbias.cpp:419:22: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
(pos_t)i - c_offset + c_M->nrows() <= n &&
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
seqbias.cpp:423:25: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
(*c_M)( j, ks[(pos_t)i - c_offset + j] ) += REAL(count)[i];
˜ ^
seqbias.cpp:451:45: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT( poss = allocVector( REALSXP, n*m ) );
˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
seqbias.cpp:452:45: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT( seqs = allocVector( STRSXP, n*m ) );
˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
seqbias.cpp:453:45: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT( freqs = allocVector( REALSXP, n*m ) );
˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
seqbias.cpp:464:24: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'unsigned long' [-Wsign-conversion]
REAL(poss)[i*m+K] = i - c_offset;
^˜
seqbias.cpp:468:38: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SET_STRING_ELT( seqs, i*m+K, mkChar( Kstr ) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^˜
seqbias.cpp:468:35: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'unsigned long' [-Wsign-conversion]
SET_STRING_ELT( seqs, i*m+K, mkChar( Kstr ) );
^˜
seqbias.cpp:471:25: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'unsigned long' [-Wsign-conversion]
REAL(freqs)[i*m+K] = (*c_M)( i, K );
^˜
seqbias.cpp:471:42: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
REAL(freqs)[i*m+K] = (*c_M)( i, K );
˜ ^
seqbias.cpp:467:33: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
num_to_nuc(Kstr, K, k);
˜˜˜˜˜˜˜˜˜˜ ^
23 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sequencing_bias.cpp -o sequencing_bias.o
In file included from sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:145:49: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, long long v) { return emitter.WriteIntegralType(v); }
^
./yaml-cpp/emitter.h:146:58: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, unsigned long long v) { return emitter.WriteIntegralType(v); }
^
In file included from sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:14:
In file included from ./pos_table.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
memcpy(b->data, src->data, b->data_len);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
sequencing_bias.cpp:227:43: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pos_table_create(&T, reads_f->header->n_targets);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
sequencing_bias.cpp:323:51: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
for (char* c = seq; *c; c++) *c = tolower(*c);
˜ ^˜˜˜˜˜˜˜˜˜˜
sequencing_bias.cpp:335:55: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy(local_seq, seq + S[i].pos - R, (L+1+R)*sizeof(char));
˜˜˜^˜ ˜
sequencing_bias.cpp:340:55: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy(local_seq, seq + (S[i].pos-L), (L+1+R)*sizeof(char));
˜˜˜^˜ ˜
sequencing_bias.cpp:356:57: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy(local_seq, seq + bg_pos - R, (L+1+R)*sizeof(char));
˜˜˜^˜ ˜
sequencing_bias.cpp:361:57: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy(local_seq, seq + (bg_pos-L), (L+1+R)*sizeof(char));
˜˜˜^˜ ˜
sequencing_bias.cpp:381:25: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
L + 1 + R,
˜˜˜˜˜˜^˜˜
sequencing_bias.cpp:336:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
seqrc(local_seq, L+1+R);
˜˜˜˜˜ ˜˜˜^˜
sequencing_bias.cpp:357:37: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
seqrc(local_seq, L+1+R);
˜˜˜˜˜ ˜˜˜^˜
sequencing_bias.cpp:439:30: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
bs[i] = M->eval(seq, i);
˜ ^
sequencing_bias.cpp:425:53: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
start - R, end + L);
˜˜˜˜˜˜^˜˜
sequencing_bias.cpp:425:62: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
start - R, end + L);
˜˜˜˜^˜˜
sequencing_bias.cpp:426:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
if (seqstr) seqrc(seqstr, seqlen + R + L);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
sequencing_bias.cpp:430:53: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
start - L, end + R);
˜˜˜˜˜˜^˜˜
sequencing_bias.cpp:430:62: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
start - L, end + R);
˜˜˜˜^˜˜
sequencing_bias.cpp:492:43: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pos_table_create(&T, reads_f->header->n_targets);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
sequencing_bias.cpp:567:61: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy(local_seq, seq + S[i].pos - R, ((k-1)+L+1+R)*sizeof(char));
˜˜˜˜˜˜˜˜˜^˜ ˜
sequencing_bias.cpp:572:71: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memcpy(local_seq, seq + (S[i].pos - L - (k-1)), ((k-1)+L+1+R)*sizeof(char));
˜˜˜˜˜˜˜˜˜^˜ ˜
sequencing_bias.cpp:584:22: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dest(pos - (k-1), K) += w;
˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
sequencing_bias.cpp:594:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(bg, 0, four_to_k * sizeof(double));
^˜˜˜˜˜˜˜˜ ˜
sequencing_bias.cpp:597:27: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
bg[K] += dest(pos, K);
˜˜˜˜ ^˜˜
sequencing_bias.cpp:610:26: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(kl, 0, (L + 1 + R) * sizeof(double));
˜˜˜˜˜˜^˜˜ ˜
sequencing_bias.cpp:614:27: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (norm_dest(pos, K) > 0.0) {
˜˜˜˜˜˜˜˜˜ ^˜˜
sequencing_bias.cpp:615:38: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
kl[pos] += norm_dest(pos, K) * (log2(norm_dest(pos, K)) - log2(bg[K]));
˜˜˜˜˜˜˜˜˜ ^˜˜
sequencing_bias.cpp:615:64: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
kl[pos] += norm_dest(pos, K) * (log2(norm_dest(pos, K)) - log2(bg[K]));
˜˜˜˜˜˜˜˜˜ ^˜˜
sequencing_bias.cpp:619:66: warning: implicit conversion changes signedness: 'pos_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
kl[pos] += bg[K] * (log2(bg[K]) - log2(norm_dest(pos, K)));
˜˜˜˜˜˜˜˜˜ ^˜˜
sequencing_bias.cpp:568:33: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
seqrc(local_seq, L+1+R);
˜˜˜˜˜ ˜˜˜^˜
35 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c twobitseq.cpp -o twobitseq.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
In file included from yaml-cpp/aliasmanager.cpp:2:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
In file included from yaml-cpp/conversion.cpp:1:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
In file included from yaml-cpp/emitfromevents.cpp:2:
./yaml-cpp/emitter.h:145:49: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, long long v) { return emitter.WriteIntegralType(v); }
^
./yaml-cpp/emitter.h:146:58: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, unsigned long long v) { return emitter.WriteIntegralType(v); }
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitter.cpp:1:
./yaml-cpp/emitter.h:145:49: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, long long v) { return emitter.WriteIntegralType(v); }
^
./yaml-cpp/emitter.h:146:58: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, unsigned long long v) { return emitter.WriteIntegralType(v); }
^
In file included from yaml-cpp/emitter.cpp:2:
yaml-cpp/emitterstate.h:101:37: warning: implicit conversion changes signedness: 'const unsigned int' to 'int' [-Wsign-conversion]
int GetCurIndent() const { return m_curIndent; }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitterstate.h:136:34: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int GetIndent() const { return m_indent.get(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitterstate.h:139:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int GetPreCommentIndent() const { return m_preCommentIndent.get(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitterstate.h:141:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int GetPostCommentIndent() const { return m_postCommentIndent.get(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/emitter.cpp:5:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
yaml-cpp/emitter.cpp:144:30: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
m_pState->SetIndent(indent.value, LOCAL);
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜
yaml-cpp/emitter.cpp:155:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned curIndent = m_pState->GetCurIndent();
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:422:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned curIndent = m_pState->GetCurIndent();
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:492:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned curIndent = m_pState->GetCurIndent();
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:524:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned curIndent = m_pState->GetCurIndent();
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:559:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
m_stream << IndentTo(m_pState->GetCurIndent());
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:610:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned curIndent = m_pState->GetCurIndent();
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:629:57: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
Utils::WriteLiteralString(m_stream, str, curIndent + m_pState->GetIndent());
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:629:59: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
Utils::WriteLiteralString(m_stream, str, curIndent + m_pState->GetIndent());
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitter.cpp:799:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
m_stream << Indentation(m_pState->GetPreCommentIndent());
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
18 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/emitterstate.h:101:37: warning: implicit conversion changes signedness: 'const unsigned int' to 'int' [-Wsign-conversion]
int GetCurIndent() const { return m_curIndent; }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitterstate.h:136:34: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int GetIndent() const { return m_indent.get(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitterstate.h:139:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int GetPreCommentIndent() const { return m_preCommentIndent.get(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitterstate.h:141:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int GetPostCommentIndent() const { return m_postCommentIndent.get(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.cpp:2:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
yaml-cpp/emitterstate.cpp:48:64: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned lastIndent = (m_groups.empty() ? 0 : m_groups.top().indent);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
yaml-cpp/emitterstate.cpp:77:64: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned lastIndent = (m_groups.empty() ? 0 : m_groups.top().indent);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
In file included from yaml-cpp/emitterutils.cpp:2:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/emitterutils.cpp:2:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/emitterutils.cpp:4:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
yaml-cpp/emitterutils.cpp:254:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
out << IndentTo(indent);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
yaml-cpp/emitterutils.cpp:261:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
out << "\n" << IndentTo(indent);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
yaml-cpp/emitterutils.cpp:271:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
out << "#" << Indentation(postCommentIndent);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/emitterutils.cpp:278:63: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
out << "\n" << IndentTo(curIndent) << "#" << Indentation(postCommentIndent);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
In file included from yaml-cpp/exp.cpp:1:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/exp.cpp:1:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/exp.cpp:2:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
yaml-cpp/exp.cpp:24:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
value = (value << 4) + digit;
˜ ^˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
In file included from yaml-cpp/iterator.cpp:1:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
In file included from yaml-cpp/nodebuilder.cpp:3:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/node.cpp -o yaml-cpp/node.o
In file included from yaml-cpp/node.cpp:1:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from yaml-cpp/node.cpp:5:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/node.cpp:10:
./yaml-cpp/emitter.h:145:49: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, long long v) { return emitter.WriteIntegralType(v); }
^
./yaml-cpp/emitter.h:146:58: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
inline Emitter& operator << (Emitter& emitter, unsigned long long v) { return emitter.WriteIntegralType(v); }
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
In file included from yaml-cpp/nodeownership.cpp:2:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/null.cpp -o yaml-cpp/null.o
In file included from yaml-cpp/null.cpp:2:
In file included from ./yaml-cpp/node.h:9:
In file included from ./yaml-cpp/conversion.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
In file included from yaml-cpp/parser.cpp:4:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from yaml-cpp/parser.cpp:7:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
In file included from yaml-cpp/regex.cpp:1:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/regex.cpp:1:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
In file included from yaml-cpp/scanner.cpp:1:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/scanner.cpp:3:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from yaml-cpp/scanner.cpp:4:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/scanner.cpp:4:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
In file included from yaml-cpp/scanscalar.cpp:1:
In file included from yaml-cpp/scanscalar.h:10:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/scanscalar.cpp:1:
In file included from yaml-cpp/scanscalar.h:10:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/scanscalar.cpp:2:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/scanscalar.cpp:4:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
yaml-cpp/scanscalar.cpp:145:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
scalar += std::string(foldedNewlineCount - 1, '\n');
˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
In file included from yaml-cpp/scantag.cpp:1:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/scantag.cpp:2:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/scantag.cpp:2:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/scantag.cpp:4:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
In file included from yaml-cpp/scantoken.cpp:1:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/scantoken.cpp:3:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from yaml-cpp/scantoken.cpp:4:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/scantoken.cpp:4:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
In file included from yaml-cpp/simplekey.cpp:1:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from yaml-cpp/simplekey.cpp:3:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from yaml-cpp/simplekey.cpp:4:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/simplekey.cpp:4:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter 'type' [-Wunused-parameter]
void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
^
In file included from yaml-cpp/singledocparser.cpp:5:
In file included from ./yaml-cpp/exceptions.h:10:
./yaml-cpp/traits.h:26:33: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <long long> { enum { value = true }; };
^
./yaml-cpp/traits.h:27:42: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
template <> struct is_numeric <unsigned long long> { enum { value = true }; };
^
In file included from yaml-cpp/singledocparser.cpp:6:
yaml-cpp/scanner.h:60:37: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int GetFlowLevel() const { return m_flows.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
In file included from yaml-cpp/stream.cpp:3:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:10:
yaml-cpp/stringsource.h:25:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
In file included from yaml-cpp/stream.cpp:3:
In file included from yaml-cpp/exp.h:9:
In file included from yaml-cpp/regex.h:65:
In file included from yaml-cpp/regeximpl.h:11:
yaml-cpp/streamcharsource.h:41:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
source.m_offset += i;
˜˜ ^
yaml-cpp/stream.cpp:140:55: warning: implicit conversion loses integer precision: 'int' to 'const unsigned char' [-Wconversion]
const unsigned char header = ((1 << lead_bits) - 1) << (8 - lead_bits);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/stream.cpp:205:8: warning: implicit conversion changes signedness: 'char_type' (aka 'char') to 'unsigned char' [-Wsign-conversion]
char_traits::to_char_type(intro[nIntroUsed]);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
yaml-cpp/stream.cpp:265:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret.reserve(n);
˜˜˜ ^
yaml-cpp/stream.cpp:316:26: warning: implicit conversion changes signedness: 'unsigned char' to 'const value_type' (aka 'const char') [-Wsign-conversion]
m_readahead.push_back(b);
˜˜˜˜˜˜˜˜˜˜˜ ^
yaml-cpp/stream.cpp:409:29: warning: implicit conversion changes signedness: 'streamsize' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
m_nPrefetchedAvailable = pBuf->sgetn(ReadBuffer(m_pPrefetched),
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -Wall -Wextra -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o seqbias.so common.o miscmath.o pos_table.o samtools_extra.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-2.12-bioc/meat/seqbias.buildbin-libdir/seqbias/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 (seqbias)
>>>>>>>
>>>>>>> FIXING LINKS FOR seqbias.buildbin-libdir/seqbias/libs//seqbias.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" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.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" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"