SeqArray 1.0.0
Xiuwen Zheng
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/SeqArray | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SeqArray.buildbin-libdir SeqArray_1.0.0.tar.gz'
>>>>>>>
* installing *source* package 'SeqArray' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DCOREARRAY_NO_FORCEINLINE -DCOREARRAY_R_LINK -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c CoreGDSLink.cpp -o CoreGDSLink.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DCOREARRAY_NO_FORCEINLINE -DCOREARRAY_R_LINK -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c main.cpp -o main.o
main.cpp:148:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return string(p, MaxNum) + "...";
˜˜˜˜˜˜ ^˜˜˜˜˜
main.cpp:185:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (s[i] == '/')
˜ ^
main.cpp:187:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
s.insert(i+1, &prefix, 1);
˜ ˜^˜
main.cpp:183:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
for (int i=s.size()-1; i >= 0; i--)
˜ ˜˜˜˜˜˜˜˜^˜
main.cpp:236:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TRUE_ARRAY.resize(Cnt, TRUE);
˜˜˜˜˜˜˜˜˜˜ ^˜˜
main.cpp:367:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
_lines.resize(n);
˜˜˜˜˜˜ ^
main.cpp:369:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
_lines[i] = CHAR(STRING_ELT(val, i));
˜˜˜˜˜˜ ^
main.cpp:558:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CHECK(gds_AppendString(data_obj, (*it)[j].c_str()));
˜ ^
main.cpp:579:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (nMax < (int)I32ss[j].size())
˜˜˜˜˜ ^
main.cpp:580:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
nMax = I32ss[j].size();
˜˜˜˜˜ ^
main.cpp:582:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
I32s.resize(nTotalSample);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:587:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<CoreArray::Int32> &B = I32ss[j];
˜˜˜˜˜ ^
main.cpp:588:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
I32s[j] = (i < (int)B.size()) ? B[i] : NA_INTEGER;
˜˜˜˜ ^
main.cpp:588:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
I32s[j] = (i < (int)B.size()) ? B[i] : NA_INTEGER;
˜ ^
main.cpp:597:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (nMax < (int)F32ss[j].size())
˜˜˜˜˜ ^
main.cpp:598:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
nMax = F32ss[j].size();
˜˜˜˜˜ ^
main.cpp:600:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
F32s.resize(nTotalSample);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:605:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<float> &B = F32ss[j];
˜˜˜˜˜ ^
main.cpp:606:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
F32s[j] = (i < (int)B.size()) ? B[i] : (float)R_NaN;
˜˜˜˜ ^
main.cpp:606:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
F32s[j] = (i < (int)B.size()) ? B[i] : (float)R_NaN;
˜ ^
main.cpp:615:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (nMax < (int)UTF8ss[j].size())
˜˜˜˜˜˜ ^
main.cpp:616:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
nMax = UTF8ss[j].size();
˜˜˜˜˜˜ ^
main.cpp:622:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<string> &B = UTF8ss[j];
˜˜˜˜˜˜ ^
main.cpp:624:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(i < (int)B.size()) ? B[i].c_str() : ""));
˜ ^
main.cpp:580:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
nMax = I32ss[j].size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:598:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
nMax = F32ss[j].size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:616:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
nMax = UTF8ss[j].size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:665:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
out_len.resize(Cnt);
˜˜˜˜˜˜˜ ^˜˜
main.cpp:677:22: warning: implicit conversion changes signedness: 'CoreArray::Int32' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
out_var_sel.resize(out_var_count, TRUE);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:687:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (sel[_start]) break;
˜˜˜ ^˜˜˜˜˜
main.cpp:691:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (sel[_end]) break;
˜˜˜ ^˜˜˜
main.cpp:723:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (sel[pos+i])
˜˜˜ ˜˜˜^˜
main.cpp:661:12: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int Cnt = CHECK(gds_SeqGetCount(Node));
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:689:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int _end = sel.size()-1;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:736:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
out_var_count = out_var_sel.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:894:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Init.GENO_BUFFER.resize(CellCount);
˜˜˜˜ ^˜˜˜˜˜˜˜˜
main.cpp:965:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Init.TRUE_ARRAY.resize(NumCellVariant);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:975:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<string> buffer(CellCount);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
main.cpp:978:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
SET_STRING_ELT(Val, i, mkChar(buffer[i].c_str()));
˜˜˜˜˜˜ ^
main.cpp:1205:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<CBOOL> flag_array(Count);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1215:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (base[i] == TRUE);
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1223:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<int> sample_id(Count);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1229:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
set<int>::iterator it = set_id.find(sample_id[i]);
˜˜˜˜˜˜˜˜˜ ^
main.cpp:1230:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (it != set_id.end());
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1239:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> sample_id(Count);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1245:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
set<double>::iterator it = set_id.find(sample_id[i]);
˜˜˜˜˜˜˜˜˜ ^
main.cpp:1246:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (it != set_id.end());
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1256:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<string> sample_id(Count);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1262:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
set<string>::iterator it = set_id.find(sample_id[i]);
˜˜˜˜˜˜˜˜˜ ^
main.cpp:1263:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (it != set_id.end());
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1310:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<CBOOL> flag_array(Count);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1320:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (base[i] == TRUE);
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1328:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<int> var_id(Count);
˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1334:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
set<int>::iterator it = set_id.find(var_id[i]);
˜˜˜˜˜˜ ^
main.cpp:1335:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (it != set_id.end());
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1344:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> variant_id(Count);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1350:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
set<double>::iterator it = set_id.find(variant_id[i]);
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1351:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (it != set_id.end());
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1361:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<string> variant_id(Count);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
main.cpp:1367:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
set<string>::iterator it = set_id.find(variant_id[i]);
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1368:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
flag_array[i] = (it != set_id.end());
˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:1437:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<int> split(Num_Process);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
main.cpp:1443:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
split[i] = (int)(start + 0.5);
˜˜˜˜˜ ^
main.cpp:1451:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CLEAR_SEL_VALUE(split[i] - st, it);
˜˜˜˜˜ ^
main.cpp:1452:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
st = split[i];
˜˜˜˜˜ ^
main.cpp:1454:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int ans_n = split[Process_Index] - st;
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1456:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
st = split[Process_Index];
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1459:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CLEAR_SEL_VALUE(split[i] - st, it);
˜˜˜˜˜ ^
main.cpp:1460:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
st = split[i];
˜˜˜˜˜ ^
main.cpp:1492:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<int> split(Num_Process);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
main.cpp:1498:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
split[i] = (int)(start + 0.5);
˜˜˜˜˜ ^
main.cpp:1506:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CLEAR_SEL_VALUE(split[i] - st, it);
˜˜˜˜˜ ^
main.cpp:1507:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
st = split[i];
˜˜˜˜˜ ^
main.cpp:1509:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int ans_n = split[Process_Index] - st;
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1511:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
st = split[Process_Index];
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1514:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CLEAR_SEL_VALUE(split[i] - st, it);
˜˜˜˜˜ ^
main.cpp:1515:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
st = split[i];
˜˜˜˜˜ ^
main.cpp:1552:30: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(tmp = NEW_LOGICAL(s.Sample.size()));
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:71:44: note: expanded from macro 'NEW_LOGICAL'
#define NEW_LOGICAL(n) allocVector(LGLSXP,n)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
main.cpp:1555:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
LOGICAL(tmp)[i] = (s.Sample[i] != 0);
˜ ^
main.cpp:1566:30: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(tmp = NEW_LOGICAL(s.Variant.size()));
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:71:44: note: expanded from macro 'NEW_LOGICAL'
#define NEW_LOGICAL(n) allocVector(LGLSXP,n)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
main.cpp:1569:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
LOGICAL(tmp)[i] = (s.Variant[i] != 0);
˜ ^
main.cpp:1547:12: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int L = CHECK(gds_SeqGetCount(varSample));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1561:12: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int L = CHECK(gds_SeqGetCount(varVariant));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1617:23: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
INTEGER(I32)[1] = gds_SeqGetCount(vSample);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1618:23: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
INTEGER(I32)[2] = gds_SeqGetCount(vVariant);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1802:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Variant.resize(DLen[0], TRUE);
˜˜˜ ^˜˜˜˜˜˜
main.cpp:1807:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Sample.resize(DLen[1], TRUE);
˜˜˜ ^˜˜˜˜˜˜
main.cpp:1834:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Sample.resize(Cnt, TRUE);
˜˜˜ ^˜˜
main.cpp:1841:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Variant.resize(Cnt, TRUE);
˜˜˜ ^˜˜
main.cpp:1935:33: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(I32 = NEW_INTEGER(len.size()));
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:72:44: note: expanded from macro 'NEW_INTEGER'
#define NEW_INTEGER(n) allocVector(INTSXP,n)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
main.cpp:1938:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
base[i] = len[i];
˜˜˜ ^
main.cpp:1977:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Sample.resize(DLen[1], TRUE);
˜˜˜ ^˜˜˜˜˜˜
main.cpp:1979:24: warning: implicit conversion changes signedness: 'Int64' (aka 'long long') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Variant.resize(gds_SeqGetCount(N_idx), TRUE);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1995:31: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(I32 = NEW_INTEGER(len.size()));
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:72:44: note: expanded from macro 'NEW_INTEGER'
#define NEW_INTEGER(n) allocVector(INTSXP,n)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
main.cpp:1998:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
base[i] = len[i];
˜˜˜ ^
main.cpp:1832:15: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int Cnt = gds_SeqGetCount(N);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1839:15: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int Cnt = gds_SeqGetCount(N);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1856:29: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
"genotype/data", Root, Sel.Variant.size(),
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:1857:23: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
&Sel.Variant[0], Sel.Sample.size(), &Sel.Sample[0]);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2053:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Sample.resize(Cnt, TRUE);
˜˜˜ ^˜˜
main.cpp:2060:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Sel.Variant.resize(Cnt, TRUE);
˜˜˜ ^˜˜
main.cpp:2079:45: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<TVariable_ApplyByVariant> NodeList(Rf_length(var_name));
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2122:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
NodeList[i].InitObject(VarType, s.c_str(), Root, Sel.Variant.size(),
˜˜˜˜˜˜˜˜ ^
main.cpp:2176:36: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(R_call_param = NEW_LIST(NodeList.size()));
˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:76:41: note: expanded from macro 'NEW_LIST'
#define NEW_LIST(n) allocVector(VECSXP,n)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
main.cpp:2051:14: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int Cnt = gds_SeqGetCount(N);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2058:14: warning: implicit conversion loses integer precision: 'Int64' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int Cnt = gds_SeqGetCount(N);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2122:53: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
NodeList[i].InitObject(VarType, s.c_str(), Root, Sel.Variant.size(),
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2123:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
&Sel.Variant[0], Sel.Sample.size(), &Sel.Sample[0]);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2638:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (n > 0) txt.append(s, n); else txt.push_back('.');
˜˜˜ ^
main.cpp:2679:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int L = _VCF4_INFO_Number[i];
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:2702:52: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
const char *nm = CHAR(STRING_ELT(VarNames, i + 8 + _VCF4_INFO_Number.size()));
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:395:25: note: expanded from macro 'CHAR'
#define CHAR(x) R_CHAR(x)
^
main.cpp:2702:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
const char *nm = CHAR(STRING_ELT(VarNames, i + 8 + _VCF4_INFO_Number.size()));
˜˜^˜˜ ˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:395:25: note: expanded from macro 'CHAR'
#define CHAR(x) R_CHAR(x)
^
main.cpp:2703:32: warning: implicit conversion changes signedness: 'unsigned long' to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP D = VECTOR_ELT(X, i + 8 + _VCF4_INFO_Number.size());
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:2703:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
SEXP D = VECTOR_ELT(X, i + 8 + _VCF4_INFO_Number.size());
˜˜^˜˜ ˜
main.cpp:2764:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int L = _VCF4_FORMAT_Number[it->second];
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
main.cpp:2801:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (p != st) val.erase(0, p - st);
˜˜˜ ˜˜^˜˜˜
main.cpp:2810:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
val.resize(L);
˜˜˜ ^
main.cpp:2803:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int L = val.size();
˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:2840:9: warning: implicit conversion loses integer precision: 'long' to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
return val;
˜˜˜˜˜˜ ^˜˜
main.cpp:2868:17: warning: implicit conversion loses integer precision: 'long' to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
I32.push_back(val);
˜˜˜ ^˜˜
main.cpp:2885:9: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
val = R_NaN;
˜ ^˜˜˜˜
main.cpp:2890:10: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
val = R_NaN;
˜ ^˜˜˜˜
main.cpp:2911:10: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
val = R_NaN;
˜ ^˜˜˜˜
main.cpp:3074:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
format_list.back().I32ss.resize(nTotalSamp);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3077:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
format_list.back().F32ss.resize(nTotalSamp);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3080:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
format_list.back().UTF8ss.resize(nTotalSamp);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3102:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
I32s.reserve(nTotalSamp);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3106:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
F32s.reserve(nTotalSamp);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3110:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
StrList.reserve(nTotalSamp);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3114:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Geno.resize(nTotalSamp);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3116:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
I8s.reserve(nTotalSamp * num_ploidy);
˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3278:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CHECK(gds_AppendString(pInfo->data_obj, StrList[k].c_str()));
˜˜˜˜˜˜˜ ^
main.cpp:3382:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<Int16> &pAllele = Geno[samp_idx];
˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3411:24: warning: implicit conversion loses integer precision: 'CoreArray::Int32' (aka 'int') to 'const value_type' (aka 'const short') [-Wconversion]
pAllele.push_back(val);
˜˜˜˜˜˜˜ ^˜˜
main.cpp:3425:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pAllele.resize(num_ploidy, -1);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
main.cpp:3429:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
I32s.resize(num_ploidy-1, 0);
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3435:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CHECK(gds_AppendData(varPhaseExtra, Len, &(I32s[num_ploidy-1]), svInt32));
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3448:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TVCF_Field_Format *pFmt = fmt_ptr[i];
˜˜˜˜˜˜˜ ^
main.cpp:3460:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
getInt32Array(value, pFmt->I32ss[samp_idx], RaiseError);
˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3461:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pFmt->Check(pFmt->I32ss[samp_idx], name, num_allele, NA_INTEGER);
˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3465:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
getFloatArray(value, pFmt->F32ss[samp_idx], RaiseError);
˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3466:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pFmt->Check(pFmt->F32ss[samp_idx], name, num_allele, (float)R_NaN);
˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3470:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
getStringArray(value, pFmt->UTF8ss[samp_idx]);
˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3471:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pFmt->Check(pFmt->UTF8ss[samp_idx], name, num_allele, BlackString);
˜˜˜˜ ^˜˜˜˜˜˜˜
main.cpp:3497:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<Int16> &pAllele = Geno[i];
˜˜˜˜ ^
main.cpp:3499:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
I8s.push_back((pAllele[j] >> bits) & 0x03);
˜˜˜˜˜˜˜ ^
main.cpp:3507:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<Int16> &pGeno = Geno[i];
˜˜˜˜ ^
main.cpp:3512:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CHECK(gds_AppendData(varGenoExtra, Len, &(pGeno[num_ploidy-1]), svInt32));
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3550:34: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
PROTECT(rv_ans = NEW_CHARACTER(filter_list.size()));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:74:45: note: expanded from macro 'NEW_CHARACTER'
#define NEW_CHARACTER(n) allocVector(STRSXP,n)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
main.cpp:3552:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
SET_STRING_ELT(rv_ans, i, mkChar(filter_list[i].c_str()));
˜˜˜˜˜˜˜˜˜˜˜ ^
main.cpp:3219:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = filter_list.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3221:36: warning: implicit conversion loses integer precision: 'long' to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = p - filter_list.begin() + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
main.cpp:3255:45: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
CHECK(gds_AppendData(pInfo->data_obj, I32s.size(), &(I32s[0]), svInt32));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
main.cpp:3261:45: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
CHECK(gds_AppendData(pInfo->data_obj, F32s.size(), &(F32s[0]), svFloat32));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
main.cpp:3389:29: warning: implicit conversion loses integer precision: 'long' to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
CoreArray::Int32 val = strtol(p, &endptr, 10);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
main.cpp:413:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3254:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Check<int>' requested here
pInfo->Check(I32s, name, num_allele);
^
main.cpp:418:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:428:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:413:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3260:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Check<float>' requested here
pInfo->Check(F32s, name, num_allele);
^
main.cpp:418:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:428:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:413:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:3276:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Check<std::basic_string<char> >' requested here
pInfo->Check(StrList, name, num_allele);
^
main.cpp:418:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:428:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'CoreArray::Int32' (aka 'int') [-Wshorten-64-to-32]
I32 = array.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
main.cpp:457:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(number, val);
˜˜˜˜˜ ^˜˜˜˜˜
main.cpp:3297:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Fill<int>' requested here
pInfo->Fill(I32s, NA_INTEGER);
^
main.cpp:457:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(number, val);
˜˜˜˜˜ ^˜˜˜˜˜
main.cpp:3300:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Fill<float>' requested here
pInfo->Fill(F32s, (float)R_NaN);
^
main.cpp:457:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(number, val);
˜˜˜˜˜ ^˜˜˜˜˜
main.cpp:3307:14: note: in instantiation of function template specialization 'TVCF_Field_Info::Fill<std::basic_string<char> >' requested here
pInfo->Fill(StrList, string());
^
main.cpp:501:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(num_allele-1, missing);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3461:13: note: in instantiation of function template specialization 'TVCF_Field_Format::Check<int>' requested here
pFmt->Check(pFmt->I32ss[samp_idx], name, num_allele, NA_INTEGER);
^
main.cpp:512:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize((num_allele+1)*num_allele/2, missing);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:524:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(number, missing);
˜˜˜˜˜ ^˜˜˜˜˜
main.cpp:501:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(num_allele-1, missing);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3466:13: note: in instantiation of function template specialization 'TVCF_Field_Format::Check<float>' requested here
pFmt->Check(pFmt->F32ss[samp_idx], name, num_allele, (float)R_NaN);
^
main.cpp:512:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize((num_allele+1)*num_allele/2, missing);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:524:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(number, missing);
˜˜˜˜˜ ^˜˜˜˜˜
main.cpp:501:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(num_allele-1, missing);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:3471:13: note: in instantiation of function template specialization 'TVCF_Field_Format::Check<std::basic_string<char> >' requested here
pFmt->Check(pFmt->UTF8ss[samp_idx], name, num_allele, BlackString);
^
main.cpp:512:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize((num_allele+1)*num_allele/2, missing);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
main.cpp:524:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
array.resize(number, missing);
˜˜˜˜˜ ^˜˜˜˜˜
176 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 SeqArray.so CoreGDSLink.o main.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/SeqArray.buildbin-libdir/SeqArray/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 (SeqArray)
>>>>>>>
>>>>>>> FIXING LINKS FOR SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.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" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.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" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"